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https://openalex.org/W2066752448
https://www.biodiversitylibrary.org/partpdf/91880
English
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The Australian land shell, Thersites bipartita, and its allies
Proceedings of the United States National Museum
1,927
public-domain
6,999
2711.—PRocEEDINGS U. S. NATIONAL MUSEUM, VoL. 72, ArT. I5. 1 Manual of Conchology, vol. 6, p. 276, 1892. 2Man. Conch., vol. 2, p. 132, 1894. No. 2711.—PRocEEDINGS U. S. NATIONAL MUSEUM, VoL. 72, ArT. I5. 55223—27 1 By Witu1aM B. MarsHann Assistant Curator, Division of Mollusks, United States National Musewn Recently Mr. C. Walton of Peterhead, Port Adelaide, South Aus- tralia, presented the United States National Museum with a number of land shells of northeastern Australia and islands in Torres Strait. All of the specimens received belong in the group Thersites (Hadra) bipartita Ferussac. They present a great variation in size and form, and the color varies from bipartite (whitish spire, chocolate base) to specimens which are entirely pale straw color, and to others which are entirely dark chestnut, and to others which are chestnut above, darker, sometimes nearly black below. Most of them have a white or pale spiral band at or near the periphery, and a dark band just below the suture. When the mass of material now in the Museum collection is arranged in geographic sequence, many characteristics which hitherto have escaped attention become evident,,. and show plainly that specialization has taken place along certain definite lines, and requires the recognition of additional species and subspecies to properly understand the problem presented. Pilsbry in his first study of Thersttes bipartita* placed it in the genus Camaena, subgenus Hadra, section Hadra s. s., and gavé the following note: The main feature distinguishing Hadra from Chloritis is that the apex in the former is neither concave, notably flattened, nor sculptured. This group seems more justly regarded as a subgenus of Chloritis than as a separate genus. Hedley suggests to me that the microscopic sculpturing of Hadra is a reminis- eence of the hair granules of Chloritis. Later in his analysis of the bipartita group? he places it in the genus Thersiies, subgenus T'hersites, section Hadra and uses the fol- lowing names: bipartita Ferussac+semibadia Albers form unicolor Cox form minor Pilsbry var. semicastanea Pfeiffer funiculata Pfeiffer forsteriana Pfeiffer--hetaera Pfeiffer form major Dohrn darwint Brazier. form major Dohrn darwint Brazier. 1 2 DINGS OF THE NATIONAL MUSEUM 72 Dr. James C. Cox * treated Thersites bipartita and semicastanea as distinct species, but under the latter he says: This species, unquestionably a modified H. bipartita, is so variable that a dozen well-marked varieties might easily be selected from among the hundreds of specimens now before me. I haye taken the preceding description from a Lizard Island specimen. He also treats funiculata as a distinct species, but under sem/- castanea he says: “ H. 3 Monograph of Australian Land Shells, p. 56, 1868. By Witu1aM B. MarsHann funiculata, described elsewhere, I would refer to this head without hesitation. * * *.” The land shells from the Northeastern coast of Australia and ad- jacent islands, the largest of which heretofore have been called Ther- sites bipartita Ferussac and the smaller ones either positively or doubtfully subspecies of that species, have been analyzed in this paper. It should be remembered that the region includes not only the mainland of northeastern Australia but some of the islands off the east coast of Queensland and the islands of Torres Strait. Tor- res Strait is about 80 miles across and crowded with reefs, shoals, and islands. Isolation and environment undoubtedly have been ef- fective causes producing the characteristics of the various subspecies of mollusks living on these islands. Restricting ourselves now to specimens known or believed to come from islands in Torres Strait, we find that so far as known they may be divided inte two great groups, one of which is characterized by being large, pale, angular at the periphery and with the spire but little lighter than the base. This group includes two species, both new, described in this paper under the names Thersites waltoni and. Thersites dalli. The second group, characterized by being smaller, the spire dark reddish in color, the base much darker, sometimes nearly black, and with the periphery rounded, or at least less angu- lar. This group includes three species, namely: 7’. semicastanea Pfeiffer, 7. bartschi Marshall, and 7. funiculata Pfeiffer. The first two are divided into two or more subspecies. Shells from Lizard Island on the east coast of Queensland resemble these dark shells from the islands in Torres Strait, which, however, are easily dis- tinguishable by their very dark colors and unctuous appearance. In the group of Thersites bipartita we now recognize the follow- ing species and subspecies: NEW AUSTRALIAN LAND SHELLS—-MAR ART. lizardensis swma, new. lizardensis rada, new. bartschi barischi, new. bartschi mobiagensis, new. bartschi yamensis, new. bartschi oma, new. baritschi mura, new. barischi nesia, new barischi paulensis, new. barischi murrayensis, new. barischi fama, new. bartschi elfa, new. barischi diva, new. barischit cepa, new. waliom, new. dalli, new. forsteriana forsteriana Pfeiffer. forsteriana major Pfeiffer. forsteriana ada, new. darwin Brazier. lizardensis swma, new. lizardensis rada, new. bartschi barischi, new. bartschi mobiagensis, new. bartschi yamensis, new. bartschi oma, new. baritschi mura, new. barischi nesia, new barischi paulensis, new. barischi murrayensis, new. barischi fama, new. bartschi elfa, new. barischi diva, new. barischit cepa, new. waliom, new. dalli, new. forsteriana forsteriana Pfeiffer. forsteriana major Pfeiffer. forsteriana ada, new. darwin Brazier. lizardensis swma, new. lizardensis rada, new. bartschi barischi, new. bartschi mobiagensis, new. bartschi yamensis, new. bartschi oma, new. baritschi mura, new. barischi nesia, new barischi paulensis, new. barischi murrayensis, new. barischi fama, new. bartschi elfa, new. barischi diva, new. barischit cepa, new. waliom, new. dalli, new. forsteriana forsteriana Pfeiffer. forsteriana major Pfeiffer. forsteriana ada, new. darwin Brazier. lizardensis swma, new. bartschi oma, new. baritschi mura, new. baritschi mura, new. barischi nesia, new barischi paulensis, new. barischi murrayensis, new. barischi murrayensis, new. barischi fama, new. bartschi elfa, new. barischi diva, new. barischit cepa, new. waliom, new. forsteriana forsteriana Pfeiffer. At the present time this arrangement makes possible a satisfac- tory classification of all the material of this group in the collection of the United States National Museum. We believe, however, that when specimens from others of the multitude of islands in Torres Strait are collected, that the list of subspecies will have to be ma- terially enlarged. THERSITES (HADRA) BIPARTITA BIPARTITA Ferussac Plate 1, fig. 3 Plate 1, fig. 3 THDRSITHS (HADRA) bipartita bipartita Kerussae. bipartita minor Pilsbry. bipartiia unicolor Cox. semicastanea semicastanea Pfeiffer. semicastenea alma, new. funiculata Pfeiffer. lizardensis lizardensis, new. 3 NEW AUSTRALIAN LAND SHELLS—-MAR Heliz bipartita Frrussac, Histoire Naturelle des Mollusques, vol. 1, p. 176, pl. 75a, fig. 1. Heliz bipartita Frrussac, Histoire Naturelle des Mollusques, vol. 1, p. 176, pl. 75a, fig. 1. Shell large, globosely turbinate, thick. Whorls slightly more than seven, slightly rounded and convex, each appearing to be a little sunken into the succeeding one, giving a somewhat beehive appear- ance to the spire. Sculpture of many retractive growth riblets which are strongest on the body whorl. Upper whorls with microscopic reticulations, which on the body whorl become minute pittings. Base very convex, widely umbilicated, the face of the umbilicus somewhat flattened. Aperture oblique, whitish but indistinctly showing the bipartite coloring of the exterior. Peristome white, reflected, par- tially concealing the umbilicus. Parietal wall with a rather thick callus which extends as a glaze some distance within the shell. Periphery rounded, showing no sign of an angle. Suture well im- pressed, irregularly crenulated by the upper ends of the growth riblets. Body whorl slowly descending about 7 mm. as it approaches the aperture. Color very conspicuously bipartite, the spire pale straw color, the base chocolate, a white spiral line dividing the colors of the spire and base. DINGS OF THE NATIONAL MUSEUM 4 72 The suture marked by a faint band of chestnut below it. The figured specimen, United States National Museum, Cat. No. 100058 measures: Greater diameter, 64 mm.; lesser diameter, 56 mm.; height, 59 mm. It comes from northeast Australia and was received from R. E. C. Stearns, who obtained it from Dr. J. C. Cox. The collection contains also 15 other specimens, 5 of which are labeled Cape York; 6 Australia; 1 northeast Australia; 1 north Australia; 1 Queensland; and 1 Gulf of Carpentaria. Probably all these speci- mens came from Queensland. Pilsbry cites the following localities: Cape York, Cape Direction, Cape Grenville, Daintree River, and Albany Island, northeast Australia. Albany Island is so close to the mainland that it may be regarded as a part of it. All the localities mentioned are in Queensland. Specimens at hand vary considerably in size and other features. The specimen figured is the largest; the smallest of all is a specimen labeled Australia (Cat. No. 321077) which measures: Greater diam- eter, 50 mm.; lesser diameter, 40 mm.; height, 36.5 mm. Tour other specimens, part of this same lot, are much smaller than the specimen figured. One labeled Gulf of Carpentaria, North Australia (Cat. No. 333790, U.S.N.M.), received from Mr. Heliz bipartita Frrussac, Histoire Naturelle des Mollusques, vol. 1, p. 176, pl. 75a, fig. 1. Walton, measures: Greater diameter, 51 m.; lesser diameter, 43 mm.; height, 41 mm. With more material available and with definite locality data, this subspecies as now considered may have further subdivisions. THERSITES (HADRA) BIPARTITA MINOR Pilsbry 1890. Huhadra (Hadra) bipartita minor PitsBry, Man. Conch., vol. 6, p. 126, pl. 21, f. 44. Like typical bipartita in all respects but size, which Pilsbry gives as diameter, 31 mm.; altitude, 26 mm. No. mention is made of its distribution. THERSITES (HADRA) LIZARDENSIS LIZARDENSIS, new subspecies Plate 2, fig. 7 THERSITES (HADRA) LIZARDENSIS LIZARDENSIS, new subspecies Plate 2, fig. 7 1892. Chloritis (Hadra) bipartita unicolor Cox, in Pilsbry’s Man. Conch., vol. 8, p. 276. 1892. Chloritis (Hadra) bipartita unicolor Cox, in Pilsbry’s Man. Conch., vol. 8, p. 276. Similar to the typical bipartita in size, form, sculpture and thick- ness, but of a nearly uniform yellowish color. All four of the speci- mens in the Museum collection have the white or whitish band which, in typical dbéipartéta, marks the division between the yellowish color of the spire and the chocolate color of the base. The distribution of unicolor is apparently the same as that of typical b¢partita, and it may be only a partially albinistic manifestation instead of a zoogeo- graphic race. THERSITES (HADRA) LIZARDENSIS LIZARDENSIS, new subspecies Plate 2, fig. 7 Shell globosely conical, rather elevated, moderately thick. Whorls 614, slowly increasing in size, a little convex. Base convex; 5 NEW AUSTRALIAN LAND SHELLS—MARS ART. ART. body whorl round, its upper edge descending near the aperture. Sculpture of many retractive fine growth striae and a microscopic reticulation. Sutures moderately impressed, emphasized by a crenu- lated edging to each whorl, and by a narrow white margin below which is a reddish narrow band. Umbilicus wide, partly concealed by the reflected columellar lip. Parietal wall glazed. Aperture broad- ly rounded; peristome white, reflected. Color bipartite, the spire light chestnut and the base much darker, rich, glossy chestnut. A distinct white band at the periphery between the two shades of color. Interior showing the exterior colors softened by a glaze. The type (Cat. No. 317035, U.S.N.M.) measures: Greater diam- eter, 41 mm.; lesser diameter, 36 mm.; height, 32 mm. It and a para- type (Cat. No. 333791, U.S.N.M.) are in the Henderson collection, and came from Lizard Island off east coast of Queensland. This is the species figured by Cox as Helix semicastanea on Plate 5, Figure 10.4 His specimen came from Lizard Island. It seems to stand mid- way between Vhersites bipartita and T. semécastanea, partaking of the characters of each and yet distinct from both. Cat. No. 317032, U.S.N.M. includes two specimens from Lizard Island of much lighter colors. Cat. No. 317034, U.S.N.M. includes two specimens labeled Islands of northeast coast of Australia. These probably come from Lizard Island. Cat. No. 321080, U.S.N.M. includes one specimen labeled “Australia.” This, too, probably came from Lizard Island. Cat. No. 100032, U.S.N.M. labeled “ Northeast Australia,” from Dr. J. C. Cox, in the Stearns collection, also are so like specimens from Lizard Island that it seems likely they came from that island. THERSITES (HADRA) LIZARDENSIS SUMA, new subspecies Plate 1, fig. 2 Similar to 7. lizardensis lizardensis but larger, more elevated, and differently colored, the spire being fawn color, the base light choco- late with a chestnut tinge, the white line dividing the colors of base and spire very prominent. The type (Cat. No. 99944, U.S.N.M.) measures: Greater diameter, 48 mm.; lesser diameter, 41.5 mm.; height, 35 mm. It and a para- type (Cat. No. 333792, U.S.N.M.) form part of the Stearns collec- tion. They are labeled ?Borneo. No similar shells have been found in Borneo, and it seems from their resemblance to Lizard Island specimens that they probably came from some island in its imme- diate vicinity, and probably belong to a subspecies of 7’. lizardensis. 4 Monograph of Australian Land Shells, 1868. Plate 2, fig. 4 Shell similar to Vhersttes lizardensis lizardensis but much smaller, more elevated, with the umbilicus largely concealed by the reflected 6 DINGS OF THE NATIONAL MUSEUM 72 columellar lip, the peristome thicker and less expanded, a heavy callus across the parietal wall joining the two ends of the peristome. Colors much lighter but distinctly bipartite, the spire pale yellowish white, the base faded chestnut. The type (Cat. No. 317033, U.S.N.M.) measures: Greater diameter, 33 mm.; lesser diameter, 28.5 mm.; height, 22.5 mm. Jt and a para- type (Cat. No. 333798, U.S.N.M.) are part of the Henderson collec- tion and come from Lizard Island on the east coast of Queens- land, Australia. While the condition of the interior of these two specimens show that they were “living” shells when collected, the pale colors of the spire and base seem to be due mostly to loss of nearly all the perio- stracum, though a few remaining vestiges of periostracum show that the shell was naturally of very light colors. At first glance this subspecies bears a resemblance to 7’. bipartita, but careful compari- son with that species and with 7’. lizardensis shows that it is more closely related to the latter. THERSITES (HADRA) SEMICASTANEA SEMICASTANEA Pfeiffer Plate 2, fig. 5 Plate 2, fig. 5 1849. Helix semicastanea Pruirrrrn Zeitsch. fur Malak., vol. 6, p. 77; in Chemnitz Conch. Cab. ed. 2, Helix, no. 319, plate 56, figs. 3-5 (title page dated 1846, but the species is quoted from the Zeitschrift for 1849, thus showing that it was described in that year). 1849. Helix semicastanea Pruirrrrn Zeitsch. fur Malak., vol. 6, p. 77; in Chemnitz Conch. Cab. ed. 2, Helix, no. 319, plate 56, figs. 3-5 (title page dated 1846, but the species is quoted from the Zeitschrift for 1849, thus showing that it was described in that year). Shell small, rather thin, depressed conic, whorls from 514 to 6 in number, slowly increasing, slightly convex, body whorl rounded, but just in front of the aperture it -is somewhat angular showing that the concealed periphery of the earlier whorls was angular. Surface with numerous retractive growth striae and surface mi- nutely reticulate, with faint indications here and there of spiral striae. Base convex, umbilicus rather narrow. Aperture rounded, scarcely oblique. Peristome thin, reflected, its columellar portion partially concealing the umbilicus. Parietal wall glazed. Color reddish, the base darker than the spire and glossy, a spiral white or whitish band at the periphery. Interior showing the two shades of the exterior and the white line dividing them. Sutures well im- pressed, irregularly crenulated, marked by a dark lne below and a whitish line above. A very slight descent of the body whorl at the aperture. The figured specimen (Cat. No. 169124, U.S.N.M.) measures: Greater diameter, 34.5 mm.; lesser diameter, 30 mm.; height, 23 mm. Another specimen with the same catalogue number, exactly like the type but smaller, measures: Major diameter, 28 mm.; minor diam- eter, 24 mm.; height, 19.5 mm. They are labeled “ Queensland, Australia,” and were presented by Mr. S. W. Jackson. Cat. No. 100033, U.S.N.M., includes two specimens received from R, E. C. re NEW AUSTRALIAN LAND SHELLS—MARSH ART.15 Stearns, who obtained them from Dr. J. C. Cox. These are labeled “Northeast Australia.” They are dark reddish chestnut, much darker than the type. In one the light peripheral band is quite marked ; in the other it is faint. Apparently the localities “‘ Queens- land” and “Northeast Australia” supplied by Jackson and Cox would lie on the mainiand, but it seems probable that these localities being general would include islands in Torres Strait. Plate 3, fig. 8 Similar to Thersites (Hadra) semicastanea semicastanea, but much smaller, more fragile, slightly less depressed and with the peristome thin and but slightly reflected. The body whorl does not descend near the aperture. It has 514 whorls. The type (Cat. No. 100034, U.S.N.M.) measures: Greater diameter, 25.5 mm.; lesser diameter, 22 mm.; height, 15 mm. It comes from Cape York, Queensland, Australia, and was received from R. E. C. Stearns, who obtained it from Legrand. THERSITES (HADRA) SEMICASTANEA SEMICASTANEA Pfeiffer Plate 2, fig. 5 Pfeiffer’s type locality “Nova Hollandia?” would include both mainland and - islands. Cox and also Pilsbry say “Islands of Torres Strait, Australia, from Lizard Island to Stephens Island.” Doctor Cox in describing and figuring specimens from Lizard Island apparently did not deal with Thersites semicastanea, but with larger and differently colored shells. The specimen figured by Cox on Plate 5, Figure 10,° is not T. semicastanea but rather bipartita minor Pilsbry. The specimen figured on Plate 20, Figure 3,° is 7’. semicastanea semicastenea. 5 Monograph of Australian Land Shells, 1868. THERSITES (HADRA) FUNICULATA Pfeiffer 1854. Helix funiculata Pretrrer, Proc. Zool. Soc., p. 147. Shell umbilicated, depressed, thin, often rudely granulated, some- what shining, reddish; spire obtusely conic; suture subcanaliculate; whorls 6, somewhat convex, slowly increasing; body whorl rounded, a white band above the periphery and with a cord-like carina, de- scending anteriorly; base convex, umbilicus moderate, deep, aperture oblique, subangularly lunate; peristome simple, margins scarcely converging; above straight, a little reflected at the base, upper end of columelia dilated. Greater diameter, 29 mm.; lesser diameter, 24 mm.; height, 14 mm. Plate 1, fig. 1 Similar to Thersttes bartschi bartscht, but thinner, slightly more depressed and less highly colored. The type (Cat. No. 333797, U.S.N.M.) measures: Greater diameter, 44 mm.; lesser diameter, 37.5 mm.; height, 28.5 mm. It comes from Mobiag Island in Torres Strait, and was presented by Mr. C. Walton. (Cat. No. 883798, U.S.N.M.) contains three specimens from the same island sent by Mr. Walton. One of these is young, but when grown apparently will be quite like the adult. The other two specimens are very thin, more elevated, and have a tendency to globoseness. One is nearly adult. Its sutures do not lie accurately along the periphery of the preceding whorls. The other specimen is adult. The suture of its whole body whorl and part of the penultimate whorl fall below the periphery of the preceding whorl. This irregu- larity of growth probably accounts for the departure from usual form. Plate 2, fig. 1 Shell rather thin, depressed, whorls 614, somewhat round, slowly descending, each appearing to be a little immersed in the succeeding whorl. Base convex, about as deep as the spire is high, umbilicus moderate, partly concealed by the reflected columellar lip. Body whorl large, with rounded periphery, its anterior upper edge slightly descending at the aperture. Sculpture of numerous retractive growth lines and microscopic reticulations; sutures deeply impressed, crenu- lated by the ends of the growth striae. Color rich, dark chestnut fumed with darker color, especially along the suture. Base very dark, nearly black, the colors of the spire and base separated by a very distinct white line. Aperture nearly horizontal, widely rounded with the lip moderately reflected. Interior livid purplish. Parietal wall thinly glazed. The type (Cat. No. 333794, U.S.N.M.) measures: Greater diameter, 44 mm.; lesser diameter, 36 mm.; height, 28.5 mm. It and two para- types come from Darnley Island, and were presented by Mr. C. Walton. | OCEEDINGS OF THE NATIONAL MUSEUM V THERSITES (HADRA) BARTSCHI BARTSCHI, new subspecies 8 DINGS OF THE NATIONAL MUSEUM THERSITES (HADRA) BARTSCHI MOBIAGENSIS, new subspecies Plate 1, fig. 1 mm. Habitat.—Torres Strait, Australia. This may be a subspecies of Thersites semicastanea Pfeiffer, but the presence of a cordlike keel at the periphery makes it somewhat doubtful. Unfortunately a definite locality was not cited. Torres Strait includes a multitude of islands. 72 THERSITES (HADRA) BARTSCHI YAMENSIS, new subspecies Plate 1, fig. 4 Shell similar to Thersites bartschd bartscha but larger, more de- pressed, whorls less rounded, growth riblets more marked, body whorl angulated at the periphery (the angle more appreciable to touch than to sight), base slightly less convex; aperture smaller, less 9 NEW AUSTRALIAN LAND SHELLS—-MAR ART. ART. flaring, with the outer lip indistinctly angulated by the angle of the periphery; the whitish line above the nearly black color of the base less distinct but wider. The type (Cat. No. 333799, U.S.N.M.) measures: Greater diameter, 48 mm.; lesser diameter, 44 mm.; height, 32 mm. It and three para- types (one of them juvenile) come from Yam Island in Torres Strait and were presented by Mr. C. Walton. The angulated periphery, the less convex base and the smaller, less flaring aperture distinctly differentiate this subspecies from 7’ hersites bartsche bartschi. One of the paratypes is juvenile, another varies from the type in form, being depressed and each whorl slightly sunken into the suc- ceeding whorl, due to the fact that the suture does not fall along the periphery but is attached a trifle above it. Plate 3, fig. 2 Shell thin, inflated, whorls 614, well-exserted, rounded; body whorl rounded, inflated, its upper edge descending near the aperture. Base very convex, umbilicus rather wide, but little concealed by the expanded columellar tip. Sculpture of rather indistinct lines of growth and microscopic reticulations. Sutures well impressed, irregularly crenulated by the upper ends of the growth lines. Color nearly uniformly rich dark chestnut, the color of the base very little darker than the spire except near the aperture where it is several shades darker. In place of the whitish line dividing the colors of the spire and base this shell has a narrow band of chestnut darker than that of either base or spire. Suture obscurely margined below by dark chestnut. Aperture horizontal, widely rounded, peristome thin, reflected, parietal wall glazed. Interior violaceous; by trans- mitted light distinctly divided by a dark line, into two parts, the upper of which is much lighter in color than the lower. The type (Cat. No. 333801, U.S.N.M.) measures: Greater diameter, 38.5 mm.; lesser diameter, 30 mm.; height, 26 mm. It comes from Yam Island, Torres Strait, and was presented by Mr. C. Walton. THERSITES (HADRA) BARTSCHI NURA, new subspecies Plate 3, fig. 7 Plate 3, fig. 7 Shell small, about one-half the size of Thersites bartschi bartschi similar to it in other respects but with characters less pronounced. The band at the periphery is yellowish-white, the peristome very little reflected, interior violaceous, the upper part lighter than the lower, a clear-white band between them. _ The type (Cat. No. 333802, U.S.N.M.) measures: Major diameter, 31 mm.; minor diameter, ¥8 mm.; height, 21 mm. It comes from Yam Island, Torres Strait, and was presented by Mr. C. Walton. DINGS OF THE NATIONAL MUSEUM 72 10 Another specimen (Cat. No. 333808, U.S.N.M.) of this subspecies is larger but somewhat abnormal in that the whorls at places do not attach themselves accurately to the periphery of the preceding whorl, thus making the shell a little more elevated than it should be for its diameter. It measures: Major diameter, 34 mm.; minor diameter, 33.5 mm.; height, 25.5 mm. This subspecies resembles a typical T'hersttes bartschi bartscha very much reduced in size. It resembles also Thersites bartschi oma but is smaller, the whorls less rounded, the aperture very much less flaring and with a light peripheral band instead of a dark chestnut- colored one. Plate 8, fig. 5 Shell very small, thin; whorls 514, rather flattened. Base very convex, its depth exceeding the height of the spire; umbilicus moder- ate, but little concealed by the reflected columellar tip. Sculpture of many fine retractive growth lines and microscopic reticulations. Body whorl sloping, periphery rounded except in front of the aper- ture where it is sharply angulated. Sutures not deeply impressed, crenulated by the upper ends of growth lines. Aperture very oblique, peristome white, slightly refiected. Color dark chestnut brown, the base somewhat darker than the spire, the sutures margined by an irregular darker band at the top of each whorl, the colors of the base and spire divided by a narrow yellowish band at the perphery. Interior dark brown below, whitish mottled with chestnut above and a clear white band marking the periphery. The type (Cat. No. 333804, U.S.N.M.) measures: Major diameter, 25.5 mm.; minor diameter, 22.5 mm.; height, 20 mm. It comes from Yam Island, Torres Strait, and was presented by Mr. C. Walton. The small size, the deep base, and the oblique aperture distinguish this shell from all others of the group. Its nearest relative is Thersites bartschi nura. Plate 3, fig. 9 This is somewhat smaller than Thersites bartschi murrayensis with the whorls more rounded and more exserted, the sutures more deeply impressed, the colors less pronounced and lighter, the peristome more expanded and the periphery less angulated. The type (Cat. No. 333809, U.S.N.M.) measures: Greater diameter, 43 mm.; lesser diameter, 35.5 mm.; height, 31 mm. It and a para- type (Cat. No. 333810, U.S.N.M.) come from Murray Islands, ‘Torres Strait, and were presented by Mr. C. Walton. THERSITES (HADRA) BARTSCHI PAULENSIS, new subspecies Plate 3. fig. 10 Sunilar to Thersites bartscht bartscht, but smaller, whorls a trifle more rounded, base slightly more convex, aperture less flaring. Color nearly uniform dark rich chestnut, a little darker on the base, darkest just behind the aperture. The peripheral band is not whitish but light chestnut. Interior sharply divided into upper lighter and lower darker portions by a very distinct white band. | The type (Cat. No. 333805, U.S.N.M.) measures: Greater di- ameter, 41 mm.; lesser diameter, 35 mm.; height, 28.5 mm. It and 11 NEW AUSTRALIAN LAND SHELLS—MABS ART. three paratypes (Cat. No. 333806, U.S.N.M.) come from St. Paul’s Island, Torres Strait, and were presented by Mr. C. Walton. Material at hand from Murray Islands is divisible into two species, namely, the large whitish form described herein as Thersites waltont; and the smaller, dark forms. The latter are divided in this paper into the five subspecies of Thersites bartschi which are described below. As Murray Islands are a group of islands, it is probable that these five subspecies come from separate islands, or perhaps in some cases from the same island but from different locations. three paratypes (Cat. No. 333806, U.S.N.M.) come from St. Paul’s Island, Torres Strait, and were presented by Mr. C. Walton. Material at hand from Murray Islands is divisible into two species, namely, the large whitish form described herein as Thersites waltont; and the smaller, dark forms. The latter are divided in this paper into the five subspecies of Thersites bartschi which are described below. As Murray Islands are a group of islands, it is probable that these five subspecies come from separate islands, or perhaps in some cases from the same island but from different locations. Plate 1, fig. 5 Shell large, rather thick, conic. Whorls 614 but little rounded. Base moderately convex, umbilicus large, partly concealed by the refiected columellar lip. Body whorl angled at the periphery, the angle more appreciable to touch than to sight, abruptly descending at the aperture. Sculpture rather crude, of many prominent, retrac- tive growth riblets, and with microscopic reticulations, which have a tendency to spiral arrangement, especially on the body-whorl. Aper- ture moderate, slightly oblique, peristome white simple at its upper part, reflected from the periphery around to the umbilicus. Parietal wall with a transparent glaze. Sutures crenulated by the upper ends of the growth riblets, not deeply impressed, but emphasized by a faint dark line below. Color of spire light chestnut, deepening to dark chestnut on the last two whorls. Base very dark, nearly black, an irregular whitish line suffusing the periphery and dividing the colors of the spire and base. Interior bipartite in color, the upper part nearly white, the lower part light violaceous. The type (Cat. No. 333807, U.S.N.M.) measures: Greater diameter, 46 mm.; lesser diameter, 41 mm.; height, 28.5 mm. It comes from Murray Islands, Torres Strait, and was presented by Mr. C. Walton. Plate 3, fig. 3 This is a dwarfed form very like Thersites bartschi fama, which it approaches in all features but size. 12 EDINGS OF THE NATIONAL MUSEUM 72 The type (Cat. No. 333811, U.S.N.M.) measures: Greater diameter, 30 mm.; lesser diameter, 25 mm.; height, 21 mm. It and a paratype (Cat. No. 833812, U.S.N.M.) come from Murray Islands, Torres Strait, and were presented by Mr. C. Walton. Plate 3, fig. 1 Plate 3, fig. 1 Resembles Vhersites bartschi diva, but smaller, whorls not quite so rounded, colors still less pronounced, the body whorl very faintly angulated at the periphery, the angle more appreciable by touch than by sight. The type (Cat. No. 333814, U.S.N.M.) measures: Greater diam- eter, 388 mm.; lesser diameter, 32 mm.; height, 29 mm. It and a paratype (Cat. No. 333815, U.S.N.M.) come from Murray Islands, Torres Strait, and were presented by Mr. C. Walton. Plate 2, fig. 2 More elevated than Vhersites bartschi fama, the whorls still more rounded and more exserted, the base more convex, and the colors lighter and less pronounced, the body whorl rounded, with no angle at the periphery except just in front of the aperture. | The type (Cat. No. 333813, U.S.N.M.) measures: Major diameter, 41.5 mm.; minor diameter, 35.5 mm.; height, 31.5 mm. It comes from Murray Islands, Torres Strait, and was presented by Mr. C. Walton. THERSITES (HADRA) WALTONI, new species THERSITES (HADRA) WALTONI, new species Plate 2, fig. 3 Plate 2, fig. 3 Shell rather large, thin, much depressed, whorls 614, flattened, slowly increasing. Body whorl abruptly descending near the aper- ture, periphery rather sharply angulated. Sculpture of many slightly retractive, nearly obsolete lines of growth, and a microscopic reticulation which has a tendency to spiral arrangement. Sutures not deeply impressed, crudely crenulated by the upper ends of the growth lines. Base convex, its depth nearly equal to the height of the spire. Umbilicus wide, but largely concealed by the reflected columella. Peristome simple at its upper portion and not reflected there. At the peripheral angle the peristome begins to expand and is broadly reflected, especially at its junction with the parietal wall which is covered with a thin glaze. Color of spire pale tawny, base slightly darker, the darker shade more pronounced just behind the aperture; periphery marked by a fairly broad white spiral band. The type (Cat. No. 333816, U.S.N.M.) measures: Major diameter, 62 mm.; minor diameter, 46 mm.; height, 35 mm. It comes from 15 NEW AUSTRAL 13 NEW AUSTRALIAN LAND SHELLS—MARS ART. Murray Islands, Torres Strait, and was presented by Mr. C. Walton, in whose honor the species is named. Mr. Walton presented seven other specimens of this species from the same locality (Cat. No. 333817 and 333820, U.S.N.M.). Three of these are immature; one is abnormal in that it has the whorls rounded, and each slightly sunken into the succeeding whorl, has the periphery rounded instead of angular, and is distinctly spirally striate on the body whorl near the suture; the other two specimens are similar to the type but smaller. The pale colors, flattened whorls, angular periphery and peculiar peristome, sharp at its upper portion and widely reflected from the peripheral angle to the umbilicus, make this one of most distinct species of the fauna of Torres Strait. °Monographia Heliceorum Viventium, vol. 5, p. 377, 1868. Plate 2, fig. 8 Shell turbinate-conical, thin, rather elevated; whorls 614, slightly convex, each appearing to be a little sunken into the succeeding whorl. Body whorl suddenly bent down near the aperture; pe- riphery moderately angulated on the back of the body whorl, strongly angulated in front of the aperture, the outer lip showing scarcely any sign of being affected by the angle of the periphery. Sculpture of many slightly retractive growth riblets and a micro- scopic reticulation of fine lines. Sutures well impressed, somewhat crenulated by the upper ends of the growth riblets. Base convex, its depth slightly less than the height of the spire. Umbilicus wide, largely concealed by the reflected columellar ip. Aperture rounded, upper portion of the peristome simple, scarcely reflected; beginning to expand at the periphery until at the columella it is very broadly reflected and conceals a large part of the umbilicus. Parietal wall with a moderately thick glaze. Color of entire shell tawny, the base very slightly darker than the spire; an indistinct whitish band mark- ing the periphery. The type (Cat. No. 100176, U.S.N.M.) measures: Greater diameter, 44 mm.; lesser diameter, 88 mm.; height, 30.5 mm. It and a para- type (Cat. No. 333818, U.S.N.M.) were received from R. E. C. Stearns to whom they were sent by Dr. J. C. Cox, with the label “Helix (Camaena) semicastanea Pfeiffer; northeast Australia.” ‘These specimens show the wide range of variation allowed by Doctor Cox in his identifications of Thersites semicastanea. They bear but little resemblance to that species. They are closely related to Thersites waltont Marshall in color, texture, and general form, but differ from it in being smaller, less angular at the periphery, more elevated, with the whorls slightly more rounded, and in having the 14 EDINGS OF THE NATIONAL MUSEUM 72 aperture rounded with no sign of an angle in the outer lip to mark the angle of the periphery. Doctor Cox’s locality “ northeast Australia ” seems to indicate that these specimens came from the mainland. More likely it is simply a general locality and as such would include the islands in Torres Strait. Because of their close relationship to Thersites waltona of Murray Islands which are quite distant from the coast it seems almost certain that they came from an island and not from the mainland. Plate 3, fig. 6 Plate 3, fig. 6 1859. Helix forsteriana major Prrirrer, Monographia Heliceorum Viven- tium, vol. 4, p. 174. (Not Helix forsteriana major Pfeiffer, Monographia Heliceorum Viventium, vol. 5, p. 377, 1866.) 1859. Helix forsteriana major Prrirrer, Monographia Heliceorum Viven- tium, vol. 4, p. 174. (Not Helix forsteriana major Pfeiffer, Monographia Heliceorum Viventium, vol. 5, p. 377, 1866.) Similar to Thersites forsteriana forsteriana but somewhat larger, with lines of growth more prominent and with the periphery ob- scurely angulate, and with colors less delicate. The figured specimen is one belonging with four others under Cat. No. 100188, U.S.N.M. It measures: Major diameter, 24.5 mm.; minor diameter, 21 mm.; height, 17 mm. They belong to the Stearns collection and came from Dr. J. C. Cox, who labeled them “ Helix (Camaena) forsteriana Pfeiffer ” and quoted the locality as northeast Australia. Tt seems almost certain that Pfeiffer described specimens like these as var. major. Later he gave another description of major’ which was for a much larger shell and which Dohrn figured.* These are not subspecies major, but belong to the new subspecies described below. THERSITE (HADRA) FORSTERIANA FORSTERIANA Pfeiffer Plate 2, fig. 6 Plate 2, fig. 6 Plate 2, fig. 6 1854. Helix forsteriana Preirrer, Proc. Zool. Soc., p. 254. 1846-53. Helix forsieriana PreirreR, Conch. Cab., p. 373, pl. 140, figs. 9-10. 1860. Helix hetaera PrEirrER Proc. Zool. Soc., p. 134. 1854. Helix forsteriana Preirrer, Proc. Zool. Soc., p. 254. 1846-53. Helix forsieriana PreirreR, Conch. Cab., p. 373, pl. 140, figs. 9-10. 1860. Helix hetaera PrEirrER Proc. Zool. Soc., p. 134. Shell small, depressed-conic, moderately thick; whorls 6, slightly convex, body whorl narrowly rounded, scarcely descending in front; base moderately convex, umbilicus rather small, partly concealed by the reflected columella. Sutures well impressed, crenulated. Sculp- ture of fine, slightly retractive growth lines and microsopic reticula- tions or granulations finer and more plentiful than in other species of the group. Aperture sublunate, peristome thin, reflected at its lower part and broadly reflected at the columella. Color of spire pale yellowish with three spiral bands of light chestnut, one below and one above the periphery and one at the suture. A whitish periph- eral band. Base very pale straw color much lighter than the spire. Columella with a tint of chestnut at its upper end. Interior whitish with the three exterior bands showing as tints of lavendar, the periph- eral white band very distinct, peristome margined inside with pale lavendar. The specimen figured (Cat. No. 317037 U.S.N.M.) measures: Greater diameter, 21.5 mm.; lesser diameter, 18.5 mm.; height, 15 mm. It forms part of the Henderson collection and is labeled “Lizard Island, Northeast Australia.” The same lot contains two other specimens in the same collection and from the same place. They are almost exactly like the figured specimen. This species, although belonging in the group of Thersites bi- panrtita, has a different color pattern and has a spire lighter than the base. The granulation or reticulations of the spire while finer and more plentiful than in other species is essentially of the same kind. Pfeiffer himself ® says that his Helix hetaera is the same as his Helix forsteriana. 15 NEW AUSTRALIAN LAND SHELLS—MARS ART. ART. ®§ Conch, Cab., pl. 171, figs. 8, 9, 10, 1879. 7Monographia Heliceorum Viventium, vol. 5, p. 377, 1868. , , p , g , , , 9 Mon. Hel. Viv., vol. 5, p. 377, 1868. 1871. Helix (Hadra) darwint Brazizr, Proce. Zool. Soc., p. 639. Having no specimens and no illustrations to which to refer, the best that can be done for this species is to reproduce Brazier’s origi- nal description and remarks. Shell umbilicated, depressedly globose, very thin, finely granulated and radiately striated; spire moderately elevated, obtuse; whorls 5, slowly inereas- ing, convex, last roundly convex, slightly descending in front, dirty yellow; base convex, sculptured the same as the upper surface; umbilicus rather small, deep; aperture diagonal, ovately lunate; peristome very little reflected, white; margins approximating and joined by a thin callus, columellar mar- gin reflected and half covering the umbilicus. Diam. maj. 7, min. 5%, alt. 4 lines. Habitat: North coast of Australia (coll. Brazier). I received two specimens of this species from a friend who collected them in the far north of Australia, but the precise locality was not sent with them. It is allied to Helix forsteri- ana Pfr., from Northeast Australia. PLATE 1 Fie. 1. Thersites (Hadra) barischi mebiagensis, new subspecies. 2. Thersites (Hadra) lizgardensis suma, new subspecies. . Thersites (Hadra) bipartita bivartita Ferussac. . Thersites (Hadra) bartschi yamensis, new subspecies. . Thersites (Hadra) bartschi murrayensis, new subspecies. OU we CO THERSITES (HADRA) FORSTERIANA ADA, new subspecies Plate 3, fig. 4 1866. Helix forsteriana major Prrrrrer, Monographia Heliceorum Viven- tium, vol. 5, p. 377. (Not Helix forsteriana major Pfeiffer, Mono- graphia Heliceorum Viventium, vol. 4, p. 174, 1859.) 1879. Helix forsteriana major DoHREN, Conch, Cab., pl. 171, figs. 8-10. Shell similar to Thersites forsteriana forstertana, but very much larger, more depressed and the body whori more descending in front. The type (Cat. No. 317036, U.S.N.M.) comes from Lizard Island, off » the east coast of Queensland, and belongs in the Henderson collection. it measures: Greater diameter, 31 mm.; lesser diameter, 27 mm.; height, 18 mm. A paratype (Cat. No. 333819, U.S.N.M.) agrees in all respects with the type. Probably the specimens used by Pfeiffer in his second description of “var major”® were from the same locality as the specimens used here. He cites Cape Flattery, Aus- tralia. Lizard Island les just off Cape Flattery on the east coast of Queensland. The specimens figured by Dohrn as Helix forsteriana mujor were from the same lot as those used by Pfeiffer in his second description of major, though he gives no definite locality. Dohrn’s figures agree exactly with our specimens of Thersites forsteriana ada. 16 EDINGS OF THE NATIONAL MUSEUM 72 PLATE 2 Fie. 1. Thersites (Hadra) barischi bartschi, new subspecies. . Thersites (Hadra) bartschi diva, new subspecies. . Thersites (Hadra) wationi, new species. Thersites (Hadra) lizardensis rada, new subspecies. Thersites (Hadra) semicastanea semicastanea Pfeiffer. . Thersites (Hadra) forsteriana forsteriana Pfeiffer. . Thersites (Hadra) lizardensis ligardensis, new subspecies. . Thersites (Hadra) dalli, new species. MAD NR wD pe Fie. 1. Thersites (Hadra) barischi bartschi, new subspecies. . Thersites (Hadra) bartschi diva, new subspecies. . Thersites (Hadra) wationi, new species. Thersites (Hadra) lizardensis rada, new subspecies. Thersites (Hadra) semicastanea semicastanea Pfeiffer. . Thersites (Hadra) forsteriana forsteriana Pfeiffer. . Thersites (Hadra) lizardensis ligardensis, new subspecies. . Thersites (Hadra) dalli, new species. MAD NR wD pe THERSITES (HADRA) DARWINI Brazier 1871. Helix (Hadra) darwint Brazizr, Proce. Zool. Soc., p. 639. Marshall, William B. 1927. "The Australian land shell Thersites bipartita and its allies." Proceedings of the United States National Museum 72, 1–16. View This Item Online: https://www.biodiversitylibrary.org/item/100797 Permalink: https://www.biodiversitylibrary.org/partpdf/91880 Sponsored by Sponsored by Biodiversity Heritage Library Biodiversity Heritage Library Smithsonian Libraries and Archives Smithsonian Libraries and Archives PLATE 3 Fic. Thersites (Hadra) bartschi cepa, new subspecies. . Thersites (Hadra) bartschi oma, new subspecies. . Thersites (Hadra) bartschi elfa, new subspecies. . Thersites (Hadra) forsteriana ada, new subspecies. . Thersites (Hadra) bartschi nesia, new subspecies. Thersites (Hadra) forsteriana major Pfeiffer. . Thersites (Hadra) bartschi nura, new subspecies. . Thersites (Hadra) semicasianea alma, new subspecies. . Thersites (Hadra) bartschi fama, new subspecies. . Thersites (Hadra) baritschi poulensis, new subspecies. SOMARDMA WDE = . Thersites (Hadra) bartschi fama, new subspecies. . Thersites (Hadra) baritschi poulensis, new subspecies. = O O This file was generated 1 April 2024 at 13:25 UTC Copyright & Reuse Copyright Status: Public domain. The BHL considers that this work is no longer under copyright protection. This document was created from content at the Biodiversity Heritage Library, the world's largest open access digital library for biodiversity literature and archives. 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Spanish; Castilian
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Revista internacional de sociología
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Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ Metodología de la investigación social Técnicas innovadoras y sus aplicaciones Madrid, Ediciones Síntesis, 2012 No leer esta obra sería perder la opor­ tunidad de explorar y (re)conocer un “manual de última generación o de nuevo cuño” en el área de Metodología e Investigación Social. Varios son los criterios o puntos fuertes que otorgan a esta compilación, desde mi punto de vista, los adjetivos o título de “manual o handbook” en mayúsculas y en la mejor de las acepciones. Cumple todos los requisitos para ser etiquetado como manual pero incluso camina unos pasos más allá. Estamos ante un trabajo per­ tinente, minucioso, excelente y nece­ sario. Por tanto, varios son los avales que permiten calificarlo como altamente “recomendable” y darle toda legitimidad y credibilidad. Véanse: antigüedad con profesionalidad y contri­ buciones clave. Dinámico y didáctico. Las 350 pági­ nas parecen acortarse debido al estilo pedagógico y ameno que desprende. El libro puede leerse tanto capítulo a capí­ tulo, de manera independiente, como de una vez; ofrece una linealidad y coheren­ cia argumental en la que el lector/a no se pierde. Además, los capítulos están vinculados y articulados. Por ejemplo, el capítulo 5 (página 111) hace referencia al capítulo 9, el capítulo 10 (pág. 227) se refiere al capítulo 11. El capítulo 9 alude al capítulo 4 y al 10, y así en diversas ocasiones. La adecuada coordinación de Arroyo y Sádaba, ese hombro a hombro de los autores y textos, es indicador del nexo que les une y que ayuda a sumer­ girse en todos sus contenidos. Se reco­ mienda hacer una lectura entre líneas de cada uno de los capítulos, de manera pormenorizada y que aquí no ha lugar. Sin embargo, se invita a realizar esta grata inmersión en Metodología. Autoría. Es una garantía indudable. El equipo de 23 autores/as constituye un punto de partida que explica el buen resultado final.Se observa que todos son especialistas en su campo y parecen aportar lo mejor de sus investigaciones y enseñanzas. Nueve de ellos son profe­ sores e investigadores del Departamento de Sociología IV de la UCM. Los otros catorce, vinculados al mismo departa­ mento y colaboradores (de centros públi­ cos o privados, españoles o de otros países), ratifican que la obrapuede servir para consolidar los más recientes apor­ tes metodológicos. El texto reúne tanto a veteranos y prestigiosos autores, como a “jóvenes” académicos que suplen su corta g Todo ello permite la consulta en un tiempo prudencial. 482 • LIBROS / BOOK REVIEWS 482 • LIBROS / BOOK REVIEWS RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ Metodología de la investigación social Técnicas innovadoras y sus aplicaciones Madrid, Ediciones Síntesis, 2012 Se denota que este grupo de docentes e investigadores cuen­ tan con una sólida formación en metodolo­ gía adquirida, a juzgar por las referencias, del buen hacer de profesionales que les precedieron y de otros manuales tanto españoles como extranjeros. Se suma el hecho de que nos desvelan la tramoya o trastienda de investigaciones propias RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 LIBROS / BOOK REVIEWS • 483 actuales para ejemplificar sus técnicas expuestas. actuales para ejemplificar sus técnicas expuestas. estudiantes de Ciencias Sociales y profe­ sionales de la investigación social). Sin embargo, también sacia la necesidad de lectores/as ávidos de otras perspectivas o de actualizarse en las herramientas clásicas de abordaje de la sociedad de la información o sociedad web 2.0. El carác­ ter “avezado” del mismo podría ser una rémora; por contra, desmenuzan cada técnica o tendencia, ofrecen una inmer­ sión práctica a dichos instrumentos. Tal como mencionan Arroyo y Sádaba en la introducción, “se ha procurado evitar (…) un enfoque excesivamente teórico, por lo que se pretende una enseñanza aplicada” (pág. 13). Y, desde mi punto de mira, lo consiguen. Pretenden colmar las necesi­ dades que plantean el EEES, la exigencia de complementar y ampliar la bibliografía, de mayor especialización metodológica. Y también lo consiguen. Presentacióny formato. Al hilo del punto anterior, la obra incluye cuadros, esquemas, imágenes-fotos, que ilustran la consulta. La distribución de los 14 capí­ tulos en 4 partes o bloques es adecuada y congruente: la primera focaliza el análi­ sis discursivo desde perspectivas plura­ les (caps. 1 al 3). La segunda abarca el análisis cuantitativo de datos obtenidos mediante encuesta virtual (cap. 4), análisis de imágenes (cap.5) y de textos (cap. 6). La tercera se centra en metodologías parti­ cipativas (cap. 7) y evaluativas (cap. 8). En la cuarta y última, no en importancia sino porque trata metodologías emergentes, abordan la investigación online (cap. 9), de materiales visuales y espaciales (caps. 10 al 12), redes sociales (cap. 13) y simulación social (cap. 14).Nos encontramos ante una brillante visión y (re)visión de estos temas. Además, los autores huyen de un estilo recargado y distante y se expresan en un lenguaje cercano a la par queriguroso. Cubre carencias y es equilibrado. Completa el hueco existente en la biblio­ grafía metodológica en castellano y en las lenguas co-oficiales españolas. Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ Metodología de la investigación social Técnicas innovadoras y sus aplicaciones Madrid, Ediciones Síntesis, 2012 Se dispo­ nede diversos manuales básicos y centra­ dos en algunas técnicas pero no abundan los dedicados a otras perspectivas. Los textos previos, imprescindibles, están más orientados a herramientas clásicas de investigación. Metodología, sin embargo, se ubica en esta sociedad global y cam­ biante y nace en un momento idóneo de revitalización. Estas características de la Investigación Social son bien explicadas porque se abordan temáticas fundamen­ tales para el análisis sociológico del siglo XXI y con las vías que abre la tecnología: tratamiento de materiales audiovisuales y geoespaciales; crecientes análisis de con­ tenido de tipo diverso; adaptación de la Planteamiento general y destina­ tarios. Se trata de un manual avanzado sobre metodología y aplicaciones selec­ cionadas por su carácter original o por la frecuencia de utilización (v. gr. encuesta) en la investigación. La obra tiene espe­ cialmente en cuenta las nuevas estrate­ gias de recogida y análisis de información sociológica, las mediciones desde la apa­ ratologíadigital, la gestión integral y rápida de información (como los datos geo- espaciales), y los medios de registro e interpretación de materialesvirtuales (que incluyen imagen, audio y vídeo). Metodología se destina a un público iniciado en los fundamentos básicos (para RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 484 • LIBROS / BOOK REVIEWS siempreurge la reflexión y actualización, que es lo que viene a cubrir Metodología. Arroyo y Sádaba coordinan un manual actual sin olvidar los orígenes, lo cual sería inexcusable. El enfoque histórico se desarrolla de manera transversal y se observa en muchos capítulos. Los autores se curan en salud y cuando van a obviar algo lo advierten y nos (re-)conducen a los clásicos para justificar las ausencias y no exceden el espacio recomendable en un texto de este perfil. investigación demoscópica clásica a apli­ caciones recientes (sistemas CATI/CAWI, etc.); nuevas tendencias de estudios on line y otras opciones cualitativas (etnogra­ fía virtual, entrevistas en línea, p.e.); resur­ gimiento del interés por el análisis de redes sociales, aproximaciones de simulación social como resultado de la inteligencia artificial, etc. No da preminencia a unas perspecti­ vas sobre otras, las trata en condiciones de igualdad. Eso sí, dedica 6 capítulos de 14 a los “Paradigmas y metodologías emergentes en Investigación Social” (parte IV), cuando el resto de las partes transitan por las más clásicas pero con aire renovado, tanto cualitativas (parte I, caps. 1 al 3) como cuantitativas (parte II, caps. Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ Metodología de la investigación social Técnicas innovadoras y sus aplicaciones Madrid, Ediciones Síntesis, 2012 Todo ello deviene más importante que lo aplicado: p.e., el SPSS, el OpenGeoDA o Atlas.ti nos ofrecen cruces pero no seleccionanlos códigos, nodos o variables a analizar. Estamos de acuerdo en que este prisma “nos acerca a una nueva forma de “artesanía digital” [entrecomillado de los autores] que ve en el software libre su máxima expresión” (pág. 279). Las técnicas ayudan pero, de momento, no suplen al cerebro y la crea­ tividad. Ello me sugiere las palabras de Wright Mills: “Sed buenos artesanos. Huid de todo procedimiento rígido. Sobre todo, desarrollad y usad la imaginación socioló­ gica”, o “Evitad el fetichismo del método y de la técnica”. siempre… Es de “nueva generación” en cuanto que contempla tecnologías y ten­ dencias novedosas. En la última década, se están fraguando importantes cambios que se han reflejado poco y de forma frag­ mentada en la bibliografía metodológica española. Arroyo y Sádaba mencionan que nuestro contexto hipertecnológico “nos alejará del protagonismo casi hege­ mónico de la investigación demoscópica cuantitativa y cualitativa del siglo XX”; y también suscribo cuando matizan: “dicha evolución, sin renunciar a la aproximación clásica, nos aproximará paulatinamente a una mayor diversificación, pluralidad y a los enfoques multimétodo” (pág. 14). ( g ) Alguna muestra de ello. Por ejemplo, los autores presentan la “minería de textos y de opiniones” (págs. 146-150) como herramientas aún infrautilizadas y que, junto a un componente teórico necesa­ rio para respaldarlas, podría pasar de un niveldescriptivo a otro escalafón más expli­ cativo y profundo. También se propone un “modelo interpretativo estructural” que da lugar a cuatro posibles tipos de IAP (pág. 173). Entre varias convergencias, coincido con los autores en que “nuestras técnicas de investigación poseen grosso modo la misma filosofía que usaban los incipientes sociólogos de antaño. Por decirlo un poco provocativamente, los métodos de investi­ gación social han ido sumando recursos y herramientas (…), pero han mantenido el núcleo epistemológico relativamente inal­ terado” (pág. 199). Además, parece que “Está servido el debate sobre si estamos ante antiguas técnicas de investigación bajo el disfraz de la mediación digital o si realmente asistimos al nacimiento de nuevas técnicas stricto sensu” (pág. 202). Metodología no se queda anclada en el pasado, ni en el presente. Tampoco se deja llevar por la euforia de las TIC. Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ Metodología de la investigación social Técnicas innovadoras y sus aplicaciones Madrid, Ediciones Síntesis, 2012 4 al 6). La parte III, más breve, y eso podría ser un punto “crítico”, sólocuenta con dos capítulos (el 7 y 8) dedicados a metodolo­ gías participativas y evaluativas respecti­ vamente. En cualquier caso, el texto invita a recuperar, aunque no lo mencionen, la estela de Lewin al abogar por esa unión teoría-praxis que puede lograrse “si el teó­ rico no mira los problemas aplicados con aversión erudita o con temor a los proble­ mas sociales, y si el aplicado comprende que no hay nada tan práctico como una buena teoría” (1951/1984:161). Los artefactos tecnológicos no suelen ser sólo eso, meros adelantos técnicos, sino que han permitido reorientar algunas estrategias metodológicas e incluso desa­ rrollar formas originales de investigar. Nos situamos, pues, ante una obra de incues­ tionable pertinencia en este contexto supratecnológico e idónea para observarla crisis como reto y oportunidad. Por añadi­ dura, siguiendo a los autores, para ofrecer una perspectiva integral y reformada, han decidido acertadamente al abordar aspec­ tos no tan innovadores pero que siguen y seguirán, comparto con ellos, presentes en la praxis investigadora: metodologías participativas; encuesta; planificación y evaluación de programas sociales; y dis­ tintos enfoques de análisis discursivo. Tienen razón los coordinadores cuando afirman que los manuales de metodología apenas cubren otras alternativas o, si es así, se perfila sólo de manera monográ­ fica los aspectos señalados. Esta obra sí integra todo ello y lo realiza de manera convincente. Tradicional y “artesano” y… Como si de un producto de alta gama o de cali­ dad certificada se tratara, que conserva el mejor sabor y aroma que indica la marca, han amasado un manual siguiendo las recetas de sus progenitores y prede­ cesores, pero ahora aportando nuevos ingredientes y especias. Las bibliotecas (bibliografía y webgrafía) sobre metodolo­ gía sonvastas y exhaustivas. Sin embargo, Mucho más relevante que el procedi­ miento de técnicas o software sofisticados, procede diseñar y analizar correctamente, organizar adecuadamente la informa­ RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 LIBROS / BOOK REVIEWS • 485 ción, seleccionar lo esencial. Entre varias sinergias, coincido con los autores en que “Cabe reservar un papel estelar a los métodos demoscópicos conversacio­ nales tradicionales, a la investigación por encuesta y a la investigación cualitativa, herramientas que han sido, son y seguirán siendo fundamentales para la aprehen­ sión de las representaciones mentales” (págs. 110-111). Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ Metodología de la investigación social Técnicas innovadoras y sus aplicaciones Madrid, Ediciones Síntesis, 2012 Esta obra ofrece una visión de conjunto del panorama emergente y crecientemente diversificado de opciones metodológicas, más allá de la profesión clásica de inves­ tigador social y siguiendo la huella que dejaron Bourdie, Chamboredon y Passe­ ron en su El oficio de sociólogo. …Y al mismo tiempo de vanguar­ dia. Renovar o morir. Este libro “renueva” o, mejor dicho, complementa los ante­ riores. No es manual al uso de los que se encuentra en la literatura, de los de RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 486 • LIBROS / BOOK REVIEWS Mejorando lo presente, como se suele decir, supera anteriores manuales de los que tanto hemos aprendido y/o refe­ renciado, pero olvida partes que estos tienen (ver argumento posterior). Este libro debería catalogarse en esa biblioteca metodológica que hay que (re)generar en nuestras estanterías para seguir nutriendo un área ya consolidada, que no debe/ puede quedar atrapada ni estancada. Estamos ante un texto intergeneracional, tanto para las cohortes jóvenes, para las intermedias o las más decanas. Nadie puede negar que es un texto de prêt-à- porter, de avance de temporada, dado que está preparado para iniciar una etapa convulsa que vivimos y en la que no nos sobran herramientas. Aunque unos capí­ tulos más que otros, en conjunto fascina la sensación de “modernidad” que rezuma su contenido. camino a la refundación y fusión de méto­ dos, recupera reflexiones fundamentales, pone al día o es un buen “estado del arte”. Sin embargo, por eso mismo, es “algo extensa”, muy completa, y podría dar de sí para dos textos o para lo que se denomina una “segunda edición ampliada”.i Muchos manuales, al final de cada capítulo, presentan enunciados de ejer­ cicios con sus respuestas, ejemplos, resumen, conceptos clave o glosario, referencias bibliográficas (o webgrafía) básicas y/o complementarias del tema, links, principalmente. Este texto no des­ cribe estos “trucos” para investigarque sí nos muestran tanto manuales consagra­ dos como los más recientes, por ejemplo el de H. Becker, Trucos del oficio. Cómo conducir su Investigación en Ciencias Sociales (2012, Siglo XXI) o en nuestro contexto español el de D. Guinea-Martín (coord., 2012, Gedisa) Trucos del oficio de investigador. El lector/a de Metodología se puede quedar ávido, tómese como crítica constructiva, de leer más sobre algunos aspectos solo esbozados. Sin embargo, estamos ante un “manual avanzado”, todo esto se presupone, y lo compensan con los puntos excelentes arriba mencionados. RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ Metodología de la investigación social Técnicas innovadoras y sus aplicaciones Madrid, Ediciones Síntesis, 2012 Recomendable sin reservas. Por todo ello, nos encontramos ante una obra recomendable tanto para el alum­ nado como para colegas y/o compañeros (académicos o profesionales). El público destinatario trasciende el ámbito acadé­ mico. Puede incluso convertirse en un libro de cabecera o “manual” de los de tener “a mano”; a mano para consultarlo como compilación de lo importante o para bajar al detalle de capítulos por separado. Cuando se recomienda una obra es señal de que convence, aporta algo más y no va a defraudar. Diferencias en la extensión y organiza­ ción. Cada capítulo sigue una estructura (véase el índice) y longitud. Ello podría justificarse con la mayor/menor utilización de determinadas técnicas pero quizás no estaría de más unificar el formato y que algunos tuvieran una estructura similar y clásica: introducción, fases, partes, con­ clusiones, referencias, ejercicios, glosario, por ejemplo. Aun así, pensamos que la diversidad o hibridación es más recomen­ dable, al igual que enunciaba el novelista Aun con todo lo positivo, y con objeto de realizar una evaluación más ponde­ rada, también se percibe alguna debili­ dad o, mejor dicho, aspecto mejorable para una próxima edición que podría demandarse. Metodología se sitúa en el RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 LIBROS / BOOK REVIEWS • 487 Maurois “En literatura, como en genética (o sociología, añadiríamos), los cruces son saludables”. Presentarlo, además, en formato virtual, adjuntar un CD en sus solapas (o una versión en epub, flash, accesible) con el contenido del mismo también facilitaría la difusión e impacto de sus bondades entre las redes sociales de alumnos y profesionales. portamiento individual puede explicarse en función de nuestra posición en la red de relaciones sociales” (pág. 304). Se toma la “red como dato” pero el objeto de estudio son los actores o fenómenos rela­ cionados con los agentes sociales. Ofre­ cen una guía práctica y protocolo para orientar el trabajo de modelado y simu­ lación. Nos facilitan las principales plata­ formas y recursos disponibles en la web (pág. 339-342) para seguir profundizando en estos “laboratorios sociales virtuales” que permiten contrastar explicaciones sin tener que recrear en la vida real situa­ ciones de experimentación, etc. La obra coordinada por Arroyo y Sádaba puede dar respuesta a las demandas recurren­ tes del alumnado y colegas sobre últimas tendencias metodológicas. RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ Metodología de la investigación social Técnicas innovadoras y sus aplicaciones Madrid, Ediciones Síntesis, 2012 Algunos de los capítulos resultan más cortos pero ello se suple con los textos que conocemos y que siguen siendo imprescindibles. Junto a la introducción escrita por los coordinadores, se echa en falta, por pedir para la próxima edición (de lo que poco que adolece, insisto), un prólogo que podría resumir y atraer más, si cabe, al alumnado y/o a los lectores/as en gene­ ral. Un análisis diseccionado, a modo de prefacio, del cual carece el texto presen­ tado, podría mostrar de otra manera las fortalezas de cada capítulo que en esta recensión han podido quedar diluidas entre comentarios generales. La que aquí escribe ha realizado este análisis pormenorizado pero que, obviamente por motivos de espacio, no se puede facilitar ahora; sin embargo, podría enviarse al lector/a más motivado. Abrir la edición a otros países sería otra idea a considerar. Aunque los autores no lo mencionan, en el libro sobrevuela el mejor espíritu de los clásicos combinado de manera solven­ tecon las aportaciones de metodólogos y metodologías recientes. Ese espíritu, por ejemplo el de Peter Berger, cuando nos advertía del error (“insensibilidad” por lo social) en el que no incurre, desde luego, esta obra: “Algunos sociólogos… se preocupan tanto de las cuestiones metodo­ lógicas que han dejado de interesarse por la sociedad. Como resultado, nada apa­ rece como significativo en la vida social, ya que en la ciencia, como en el amor, una excesiva concentración en las técnicas lo más probable es que conduzca a la impo­ tencia”. Para cerrar, en pocas palabras, felicitar a los coordinadores y autores, y retomar los argumentos de mayor calado En suma, la parte I, compuesta por 3 capítulos, ofrece un “Análisis del dis­ curso y de datos cualitativos. Perspecti­ vas plurales”. El bloque II también incluye 3 capítulos sobre últimas tendencias en torno al “Desarrollo en la investigación cuantitativa”. La parte IIIsobre “Metodolo­ gías participativas y evaluativas”, resulta breve pero igualmente de gran interés. La IV, “Paradigmas y metodologías emer­ gentes”, quizás es la más extensa no sólo por “moda” sino también por necesidad de mayores y mejores aportaciones actuales. Por ejemplo, subrayan que nuestro “com­ RIS, VOL. 71, Nº 2, MAYO-AGOSTO, 475-499, 2013. ISSN: 0034-9712 488 • LIBROS / BOOK REVIEWS que abren esta reseña: garantía desde la autoría, formato, pertinencia, dinamismo, minuciosidad, vanguardia, rigurosidad, aplicabilidad, reflexión, equilibrio,… obra recomendable sin reservas. María Silveria Agulló Tomás. Universidad Carlos III de Madrid. Millán ARROYO MENÉNDEZ e Igor SÁDABA RODRÍGUEZ Metodología de la investigación social Técnicas innovadoras y sus aplicaciones Madrid, Ediciones Síntesis, 2012 msat@polsoc.uc3m.es María Silveria Agulló Tomás. Universidad Carlos III de Madrid. msat@polsoc.uc3m.es
W3128777554.txt
https://aricjournal.biomedcentral.com/counter/pdf/10.1186/s13756-021-00930-x
en
Genetic relatedness of multidrug resistant Escherichia coli isolated from humans, chickens and poultry environments
Antimicrobial resistance and infection control
2,021
cc-by
8,912
Aworh et al. Antimicrob Resist Infect Control https://doi.org/10.1186/s13756-021-00930-x (2021) 10:58 Open Access RESEARCH Genetic relatedness of multidrug resistant Escherichia coli isolated from humans, chickens and poultry environments Mabel Kamweli Aworh1,2,3,4* , Jacob K. P. Kwaga3, Rene S. Hendriksen5, Emmanuel C. Okolocha3 and Siddhartha Thakur4 Abstract Background: Inappropriate use of antimicrobial agents in animal production has led to the development of antimicrobial resistance (AMR) in foodborne pathogens. Transmission of AMR foodborne pathogens from reservoirs, particularly chickens to the human population does occur. Recently, we reported that occupational exposure was a risk factor for multidrug-resistant (MDR) Escherichia coli (E. coli) among poultry-workers. Here we determined the prevalence and genetic relatedness among MDR E. coli isolated from poultry-workers, chickens, and poultry environments in Abuja, Nigeria. This study was conducted to address the gaps identified by the Nigerian AMR situation analysis. Methods: We conducted a cross-sectional study among poultry-workers, chickens, and poultry farm/live bird market (LBM) environments. The isolates were tested phenotypically for their antimicrobial susceptibility profiles, genotypically characterized using whole-genome sequencing (WGS) and in silico multilocus sequence types (MLST). We conducted a phylogenetic single nucleotide polymorphism (SNPs) analysis to determine relatedness and clonality among the isolates. Results: A total of 115 (26.8%) out of 429 samples were positive for E. coli. Of these, 110 isolates were viable for phenotypic and genotypic characterization. The selection comprised 47 (42.7%) isolates from poultry-workers, 36 (32.7%) from chickens, and 27 (24.5%) from poultry-farm or LBM environments. Overall, 101 (91.8%) of the isolates were MDR conferring resistance to at least three drug classes. High frequency of resistance was observed for tetracycline (n = 102; 92.7%), trimethoprim/sulfamethoxazole (n = 93; 84.5%), streptomycin (n = 87; 79.1%) and ampicillin (n = 88; 80%). Two plasmid-mediated colistin genes—mcr-1.1 harboured on IncX4 plasmids were detected in environmental isolates. The most prevalent sequence types (ST) were ST-155 (n = 8), ST-48 (n = 8) and ST-10 (n = 6). Two isolates of human and environmental sources with a SNPs difference of 6161 originating from the same farm shared a novel ST. The isolates had similar AMR genes and plasmid replicons. Conclusion: MDR E.coli isolates were prevalent amongst poultry-workers, poultry, and the poultry farm/LBM environment. The emergence of MDR E. coli with novel ST in two isolates may be plasmid-mediated. Competent authorities should enforce AMR regulations to ensure prudent use of antimicrobials to limit the risk of transmission along the food chain. *Correspondence: mabelaworh@yahoo.com 1 Department of Veterinary and Pest Control Services, Federal Ministry of Agriculture and Rural Development, Abuja, Nigeria Full list of author information is available at the end of the article © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. The Creative Commons Public Domain Dedication waiver (http://​creat​iveco​ mmons.​org/​publi​cdoma​in/​zero/1.​0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Aworh et al. Antimicrob Resist Infect Control (2021) 10:58 Page 2 of 13 Keywords: Escherichia coli, Antimicrobial resistance, Prevalence, Chicken, Multidrug resistance, Genetic relatedness, One health, Nigeria Background Antimicrobial resistance (AMR), is one of the biggest threats to food safety and considered a One-Health issue with the potential of spreading to other countries since resistant pathogens do not recognize boundaries [1, 2]. Recently, we have shown the transmission of AMR E. coli among chickens, humans, and the poultry environment [3, 4]. Globally, antimicrobial agents are used in food animal production to ensure good health and productivity of the animals [5–7]. Multiple studies have shown that inappropriate use of these antimicrobial agents in food animal production particularly poultry has led to the development of AMR [8–10]. Commensal E. coli are known to be part of the normal flora of the gastrointestinal tracts of man and animals without causing any harm to their host [11, 12]. Several E. coli strains have been used as indicator organisms in various studies on AMR [11, 13]. Although commensal E. coli are harmless to the host, the bacteria can acquire resistance genes and act as a reservoir for the spread of multidrug resistance (MDR) to and from food to humans [13]. The genetic structure of E. coli strains is usually influenced by several factors including the host and environment enabling the bacteria to acquire various AMR mechanisms [13, 14]. In September 2016, 193 member countries including Nigeria signed the United Nations General Assembly resolution to develop national action plans (NAP) on AMR [15]. In November 2016, Nigeria established its AMR coordinating body at the Nigeria Center for Disease Control (NCDC), and in January 2017, a One-Health AMR Technical working group was inaugurated to conduct AMR situation analysis and develop Nigeria’s NAP [16]. One of the data gaps identified from the AMR situation analysis was the paucity of AMR studies done in Nigeria across humans, food-producing animals, and the environment [16]. It has been documented that the continuous use of antimicrobial agents for therapeutic purposes against infections has led to the emergence of drug-resistant bacteria such as MDR E. coli [17]. MDR bacteria have made it difficult to treat certain infections effectively with modern or conventional antimicrobial agents [18]. AMR has resulted in treatment failure in human and animal populations, because of the emergence of MDR foodborne pathogens like E. coli arising from the abuse or misuse of antimicrobial agents [19]. This scenario further deteriorates in Nigeria because of the increasing number of farmers who practice self-prescription as well as selfadministration of antimicrobials to their animals [5, 20]. Poultry farmers have easy access to antimicrobials that are available over-the-counter without prescription [3] and evidence shows that farmers administer the antimicrobials repeatedly against non-responsive infections [20, 21]. These actions by the farmers further promote the emergence and spread of antimicrobial-resistant foodborne pathogens with serious implications on public health [22]. Continuous administration of antimicrobial agents to chickens for prophylaxis, therapeutic, or growth promotion purposes increases the antibiotic selection pressure for resistance in the bacteria [23]. Our recent publication demonstrates that occupational exposure over ten years to chickens on poultry farms or live bird markets (LBMs) was a risk factor for MDR E. coli among poultry workers in Abuja [3]. We hypothesized that chickens harbouring MDR E. coli as well as contaminated poultry farm or LBM environment can become potential sources for transmission of resistance genes to poultry workers exposed to chickens and the environment on poultry farms or markets. To better understand the association between MDR E. coli isolates recovered from humans, chickens and poultry environment, we investigated the genetic relatedness of MDR E. coli isolates from poultry-workers, chickens, and selected poultry farms/LBM environments in Abuja, Nigeria. Methods Study overview Our current study was part of a larger project conducted from December 2018 to February 2020 exploring MDR E. coli in humans, chickens, and the poultry farm/market environment. An aspect of this research exploring the risk factors for MDR E. coli among poultry workers has already been previously published [3]. Characterization of E. coli isolates Of 429 samples collected in the course of the present study, 110 E. coli strains isolated from the stool of apparently healthy poultry workers, faecal samples obtained from chickens as well as from poultry litter and water obtained from farm and LBM environments were characterized. The sample collection procedures, isolation of E. coli from these samples, and antimicrobial susceptibility profiling of E. coli using the disk diffusion method have been described previously [3]. Briefly, suspected dark Aworh et al. Antimicrob Resist Infect Control (2021) 10:58 pink E. coli colonies on MacConkey agar were streaked on Eosin Methylene Blue agar and incubated at 37 °C for 24 h. Isolates were confirmed as E. coli using Microbact GNB 24E (Oxoid, UK). Genotypic Detection of E. coli isolates Whole genome sequencing (WGS) of E. coli isolates All isolates were subjected to WGS as previously described [4]. Briefly, libraries for each E. coli isolates were prepared for WGS using a Nextera XT kit. We processed 0.3 ng/µL of DNA from each isolate using a Nextera XT DNA Sample Prep Kit (Illumina Inc., San Diego, CA), pooled together, and sequenced on an Illumina Miseq platform using a 2 × 250 paired-end approach (Illumina Inc., San Diego, CA). Raw sequencing reads were de-multiplexed and converted to fastq files using CLC Genomics workbench version 9.4 (Qiagen bioinformatics, Valencia, CA). The DNA sequences for each isolate were transferred to the National Center for Biotechnology Information (NCBI) database after which each isolate was assigned an accession number. Bioinformatic analysis of WGS data Antimicrobial susceptibility determinants of E. coli isolates High-quality Illumina paired-end reads were assembled de novo into the draft genome sequence for each isolate using SPAdes assembler v.3.13.1 [24]. In silico detection and typing of resistance genes was done using ResFinder 3.2, a Center for Genomics Epidemiology (CGE) bioinformatics tool (database version 2020–02-11), to determine the acquired AMR genes as well as assess chromosomal point mutations [25]. For each isolate, we used between 95–100% identity to match individual genes to an annotated resistance gene. [25]. In silico determination of the existing plasmid replicon types of each E. coli isolate was done by submitting the assembled genomes to PlasmidFinder 2.1, a CGE bioinformatics tool (database version 2020–04-02). The selected threshold for minimum percentage identity was 95% while the minimum coverage of the contig was set at 60% [26]. The in silico plasmid MLST typing of replicons (IncHI2 and IncF) were determined by submitting the assembled genome to pMLST 2.0 (database version: 2020–04-20) bioinformatics tool on the CGE website [26]. Multilocus sequence typing (MLST) of MDR E. coli isolates As previously described [4] in silico MLST-analyses of the E. coli isolates were determined using schemes demonstrated by Achtman which made use of allelic variation amongst seven housekeeping genes (adk, fumC, gyrB, icd, mdh, purA, and recA) to assign sequence types (STs) [27]. We used whole-genome sequence data to generate the E. coli MLST assignment for each isolate that perfectly Page 3 of 13 matched the alleles in the MLST database. MLST Finder 2.0, a CGE bioinformatics tool was used to assign STs to the isolates with 100% match against known MLST alleles while those without perfect matches were identified as unknown [28]. Some isolates were assigned as a new type after matching with MLST alleles of unknown ST in the MLST database. Determination of E. coli Phylogroups, SNPs calling and Phylogeny Phylogroups of E. coli genomes were determined using an in silico Clermont typing method [29]. The Clermont Typer web interface is hosted by CATIBioMed (IAME UMR 1137) and accessible at http://​clerm​ontyp​ing.​iame-​ resea​rch.​center/. Phylogenetic trees were constructed to determine the phylogenetic relatedness of the E. coli isolates using the technique known as SNP calling described by Kaas et al. [30]. Briefly, the tool CSI Phylogeny, a CGE bioinformatics tool accessed online at https://​cge.​cbs.​dtu.​dk/​servi​ ces/​CSIPh​yloge​ny/ was used for SNP calling. The CSI phylogeny uses BWA to map raw reads to a reference sequence and uses Samtools for SNP calling. E. coli strain NCTC11129 was used as the reference strain for SNPs calling to identify variants present in the chromosome of each isolate. The selected thresholds used were: cut-offs for depth = 10x; SNP quality = 30; mapping quality = 25 and Z score = 1.96. The phylogenetic SNP-based maximum likelihood tree were annotated and visualized using the programs Figtree (http://​tree.​bio.​ed.​ac.​uk/​softw​are/​ figtr​ee/) and interactive Tree of Life tool—iTOL (http://​ itol.​embl.​de/​itol.​cgi). Pairwise SNP differences between genomes were computed to determine if isolates of different origins were related. Data analyses Antimicrobial susceptibility data were analyzed using Epi Info 7 software by computing frequencies and proportions. The 108 assembled E. coli genomes of the present study have been deposited by the Thakur Molecular Epidemiology Laboratory, NC State University (GenomeTrakr Project) in the NCBI database under the Bioproject ID number PRJNA293225. The remaining two isolates have accession obtained from the DNA Data Bank of Japan (DDBJ) as previously reported [4]. Results Antimicrobial susceptibility profile of E. coli isolates A total of 110 E. coli strains were isolated from 122 human stool samples obtained from poultry workers on farms and LBMs; 111 faecal samples obtained from chickens on farms and LBMs; and 196 poultry litter and water samples obtained from farm and LBM Aworh et al. Antimicrob Resist Infect Control (2021) 10:58 Page 4 of 13 environments. Of the 110 E. coli strains 42.7% (n = 47) were recovered from humans; 37.7% (n = 36) from chickens and 24.5% (n = 27) from poultry environment. High resistance rates were observed for tetracycline, trimethoprim/ sulfamethoxazole, streptomycin, ampicillin, nalidixic acid and gentamicin. On the contrary resistance to colistin, imipenem, ceftazidime, amoxicillin/clavulanic acid, cefuroxime, cefotaxime and ceftriaxone were quite low although colistin resistance rate of 11.8% in commensal E. coli is quite worrisome (Table 1). Analysis of resistance profiles of the 110 isolates showed that a single isolate (0.9%) from a poultry farmer was susceptible to all antimicrobial drugs tested; 4 (3.6%) were resistant to only one antimicrobial drug, 4 (3.6%) were resistant to two antimicrobial drugs and interestingly 101 (91.8%) were MDR (resistant to three or more classes of antimicrobial drugs). The number of antimicrobials against which each isolate showed resistance was between one and thirteen. Surprisingly, a single isolate from a poultry farm was resistant to 13 out of 16 antimicrobials tested. The AMR phenotypes with AMP, CEP, CHL, CT, GEN, NAL, S, SXT, and TET profile had the highest frequency of 13.6% (n = 15). Figure 1 summarizes the multiple AMR patterns exhibited by the isolates. Prevalence of MDR E. coli in humans, chickens and poultry farm/LBM environment The overall prevalence of E. coli from all sources was 26.8% (n = 115), however, only 110 were further characterized due to viability as the remaining five isolates were mistakenly discarded. Of the 110 E. coli isolates, 91.8% (n = 101) were MDR E. coli. Of these MDR E. coli isolates 38.6% (n = 39), 34.7% (n = 35), and 26.7% (n = 27) were recovered from humans, chickens and poultry environment respectively (Fig. 2). Surprisingly, all the poultry environment isolates were MDR. Of the 101 MDR E. coli isolates 47.5% (n = 48) were MDR5 (resistant to more than 5 classes) and 38.6% (n = 39) were classified as XDR (resistant to 8 or more classes i.e. extensively drug-resistant isolates). Overall, 36.6% (n = 37) of the isolates originated from the LBMs while 63.4% (n = 64) originated from farms. Of the 39 XDR E. coli isolates 41% (n = 16), 33.3% (n = 13), and 25.6% (n = 10) were recovered from chickens, humans and the poultry environment respectively. In silico AMR gene analysis of MDR E. coli isolates in humans, chickens and poultry environment This study identified 57 different resistance determinants from 101 MDR E. coli isolates. Genes encoding resistance to aminoglycosides accounted for the majority with about 14 different determinants (aadA1, Table 1 Antimicrobial resistance profiles of E. coli isolates from humans, chickens and farm/market environments in Abuja—Nigeria, 2019 Drug class Drug Tetracyclines Tetracycline Folate Pathway antagonists Sulfamethoxazole/Trimethoprim Penicillins Ampicillin Quinolones Nalidixic acid Aminoglycosides Streptomycin Gentamicin Phenicols Chloramphenicol 1st Generation Cephalosporins Cephalothin Nitrofurans Nitrofurantoin Carbapenems Imipenem B-lactam inhibitors Amoxicillin-clavulanate 3rd and 4th Generation Cephalosporins Ceftriaxone Cefuroxime Cefotaxime Ceftazidime Polymyxin Colistin Resistance to 3 or more classes MDR of antibiotics Resistance break point µg/mL ≤ 11 ≤ 10 ≤ 13 ≤ 13 ≤ 11 ≤ 12 ≤ 12 ≤ 14 ≤ 14 ≤ 19 ≤ 13 ≤ 19 ≤ 14 ≤ 22 ≤ 17 ≤ 11 n/a Human n = 47 (%) Chicken n = 36 (%) Environment n = 27 (%) Total n = 110 (%) 39 (83.0) 35 (97.2) 27 (100.0) 101 (91.8) 39 (83.0) 31 (86.1) 24 (88.9) 94 (85.5) 36 (76.6) 31 (86.1) 20 (74.1) 87 (79.1) 26 (55.3) 27 (75.0) 19 (70.4) 72 (65.5) 35 (74.5) 30 (83.3) 22 (81.5) 87 (79.1) 20 (42.5) 27 (75.0) 16 (59.3) 63 (57.3) 15 (31.9) 17 (47.2) 7 (25.9) 39 (35.5) 13 (27.7) 15 (41.7) 5 (18.5) 33 (30.0) 5 (10.6) 13 (36.1) 8 (29.6) 26 (23.6) 3 (6.4) 6 (16.7) 3 (11.1) 12 (10.9) 2 (4.3) 5 (13.9) 3 (11.1) 10 (9.1) 3 (6.4) 1 (2.8) 1 (3.7) 5 (4.6) 4 (8.5) 3 (8.3) 0 (0) 7 (6.4) 4 (8.5) 1 (2.8) 1 (3.7) 6 (5.5) 4 (8.5) 2 (5.6) 5 (18.5) 11 (10.0) 7 (14.9) 3 (8.3) 3 (11.1) 13 (11.8) 39 (82.9) 35 (97.2) 27 (100) 101(91.8) Aworh et al. Antimicrob Resist Infect Control (2021) 10:58 Page 5 of 13 Fig. 1 Antimicrobial resistance pattern of E. coli strains from humans, chickens, and poultry farm or market environment in Abuja-Nigeria, 2019. *DR means drug resistance; 1DR means the E. coli isolate was only resistant to one antimicrobial agent while > 10DR means the E. coli isolate was resistant to more than ten different antimicrobial drugs tested. The minimum number of antimicrobial drugs the human and chicken E. coli isolates were resistant to was one while the poultry environmental E. coli isolates were resistant to a minimum of three antimicrobial agents. Hence, all the poultry environmental E. coli isolates were multidrug-resistant 30 Live bird Market Poultry Farm 25 25 Frequency 21 20 15 18 14 14 10 9 5 0 Human Chicken Environment Source of MDR E. coli isolates Fig. 2 Distribution of MDR E. coli isolates based on isolation sources. The bars represent the number of MDR E. coli isolates from humans working on the poultry farm or selling chickens at the live bird market (LBM); the number of MDR E. coli isolates from chickens at the poultry farm or LBM and the number of MDR E. coli isolates from poultry farm or LBM environment aadA2, aadA2b, aadA5, aadA16, armA, aac(3)-IIa, aac(3)-IId, aac(3)-Ib, aac(6)-Ib-cr, aph(3)-Ia, aph(3)Ib, aph(6)-Id, ant(2)-Ia) detected. A high prevalence (70.3%) of aph(6)-Id, which is a plasmid-encoded gene, was also observed. About two-thirds of the isolates (67.3%) exhibited aph(3)-Ib gene, a metabolic enzyme that confers aminoglycoside resistance. The aac(3)-IId gene responsible for conferring gentamicin resistance was observed in 27.7% of the MDR E. coli isolates. We also detected aac(6)-Ib-cr gene, responsible for the reduction in ciprofloxacin activity in two MDR E. coli isolates. Six different variants of β-lactam resistance genes were detected (blaTEM-1, blaOXA-1, blaOXA-10, blaOXA-129, blaCTX-M-15, blaCTXM-65) out of which blaCTX-M type was classical of the ESBL producing E. coli. Ten different fluoroquinolone resistance determinants were observed, an important antimicrobial on the WHO list, (qnrB1, qnrB19, qnrB52, qnrS1, qnrS2, qnrS3, qnrS7, qnrS11, qnrS13, aac(6)-Ib-cr) and associated with mutations in the gyrA, parC, and parE genes. We detected other important resistance determinants such as trimethoprim resistance (dfrA1, dfrA8, dfrA12, dfrA14, dfrA15, dfrA17, dfrA21, and dfrA27), macrolide resistance (mdfA, mphA, mefB, ermB, ereA, mphE and msrE), phenicol resistance (cmlA1, catA1, catA2, catB3, floR), rifampicin resistance (ARR-2 and ARR-3), sulphonamide resistance (sul1, sul2, sul3), tetracycline resistance (tetA, tetB, tetM) and plasmid-mediated colistin resistance gene (PMCR)—mcr-1.1. Aworh et al. Antimicrob Resist Infect Control (2021) 10:58 Page 6 of 13 Multi‑locus sequence determination of MDR E. coli isolates The 101 MDR E. coli isolates belonged to 66 different sequence types (ST), out of which one (1) was non-conclusive and eight (8) were new types. In the in silico MLST analysis of E. coli isolates, the following were observed to appear more than once: ST155 (7.9%; n = 8), ST48 (7.9%; n = 8), ST10 (5.9%; n = 6), ST1638 (4%; n = 4), ST398 (3%; n = 3), ST216 (3%; n = 3), ST226 (3%; n = 3), ST101 (2%; n = 2), ST117 (2%; n = 2), ST165 (2%; n = 2), ST206 (2%; n = 2), ST4663 (2%; n = 2), ST1286 (2%; n = 2), and ST1196 (2%; n = 2). The most prevalent STs are shown in Fig. 3. Phylogroups of E. coli isolates from humans, chickens and poultry environment A majority of the isolates belonged to phylogroup A (n = 61, 55.5%) followed by phylogroup B1 (n = 36, 32.7%) while the rest belonged to phylogroup G (n = 3, 2.7%); D (n = 2, 1.8%); E (n = 2, 1.8%); F (n = 2, 1.8%); B2 (n = 1, 0.9%); C (n = 1, 0.9%); clade I (n = 1, 0.9%) and clade IV (n = 1, 0.9%). Isolates with phylogroup A originated from workers (n = 36) and poultry environment (n = 13) while 6 Human isolates recovered from chickens mostly belonged to phylogroup B1 (Fig. 4). Of the 36 E. coli isolates, belonging to phylogroup B1, 22.2% (n = 8); 50% (n = 18) and 27.8% (n = 10) were recovered from humans, chickens and the poultry environment respectively. All isolates assigned ST10 (n = 6), ST218 (n = 3), ST398 (n = 3) and ST1638 (n = 4) belonged to phylogroup A. However, all but one isolate assigned ST48 (7/8) and ST226 (2/3) also belonged to phylogroup A while a majority with ST155 (7/8) and novel ST (5/8) belonged to phylogroup B1. Plasmid replicon profiles of MDR E. coli isolates from humans, chickens and poultry environment Forty (40) different plasmid replicon types were detected among 97 MDR E. coli isolates however, 4% (n = 4) did not harbour any plasmid replicons. The most prevalent plasmid replicons detected in descending order were p0111 (36.6%, n = 37); IncFIB(AP001918) (33.7%, n = 34); IncFII (18.8%, n = 19); ColpHAD28 (14.9%, n = 15); IncQ1 (13.9%, n = 14); IncFIB(K) (13.9%, n = 14); ColpVC (12.9%, n = 13); IncFIC(FII) (12.9%, n = 13); IncR (9.9%, Enviroment Chicken 5 Frequency 4 3 2 1 0 ST-1638 ST- 398 ST- 218 ST- 226 ST-10 ST- 48 ST-155 Novel Multilocus Sequence Types Fig. 3 Multilocus Sequence Types for E. coli isolates from humans, chickens, and poultry farm/market environment, Abuja-Nigeria, 2019. Each bar represents the various E. coli sequence types for isolates obtained from humans, chickens, and poultry farm/LBM environments Aworh et al. Antimicrob Resist Infect Control Human Chicken 40 Clade IV (2021) 10:58 Page 7 of 13 Environment A 35 B1 30 25 20 15 Clade I B2 10 5 0 G C F D E Fig. 4 Phylogenetic classification of E. coli isolates from humans, chickens and poultry farm/market environments, Abuja-Nigeria, 2019. The peak of the blue triangle denotes the highest frequency of human E. coli isolates in phylogroup A. The orange triangle denotes the highest frequency of chicken E. coli isolates in phylogroup B1. The black triangle peaks in the same direction as the blue triangle indicating that the phylogroup A has the highest frequency for the E. coli isolates from the poultry farm/LBM environment n = 10); IncFII(pCoo) (9.9%, n = 10); IncY (9.9%, n = 10); IncX1 (8.9%, n = 9) and IncI1-I(gamma) (8.9%, n = 9). The plasmid replicons recovered from human isolates were more genetically diverse than those recovered from chickens and the poultry environment. Eighteen replicon types were common to isolates from all sources: p0111, IncFIB(AP001918), IncFII, ColpHAD28, IncQ1, IncFIB(K), ColpVC, IncFIC(FII), IncX1, IncFII(pCoo), IncI1-I (gamma), IncFII (29), IncFII(pHN7A8), IncFIA, Col156, IncHI2, IncHI2A and IncX4. IncFIB(AP001918) was the most common among human isolates (n = 12) while p0111 was commonly detected in both chicken (n = 15) and poultry environment isolates (n = 14). Interestingly, IncFIB (pLF82), a phage plasmid was detected in one isolate recovered from the LBM environment. Eight different plasmids were observed to harbour AMR genes. The following AMR genes were carried on plasmid replicons: mcr-1.1 + IncX4 (n = 2); tetA + IncX1 (n = 1); qnrB19 + Col440I (n = 7); sul2 + IncQ1 (n = 5); aph(3)-Ib + IncQ1 (n = 1); ­blaTEM-1 + IncFIC(FII) (n = 1); mdf(A) + IncFIB (n = 1); qnrS13 + IncFII (n = 1) and aac(3)-IIa + IncHI1B (n = 1). The plasmid replicons harbouring the AMR genes was commonly detected in commensal E. coli isolates recovered from poultry workers, chickens and the poultry environment. Determination of pMLST for IncHI2 and IncF plasmid replicons In silico pMLST identification and typing of IncHI2 and IncF plasmid replicons, were based on the combination of the alleles identified for the genes. For the IncHI2 the assigned ST was ST4 for isolates (MA_251 and MA_252) originating from a poultry farmworker and poultry litter on the same farm. The pMLST analysis assigned the two IncF plasmids for isolates MA_251 and MA_252 with ST[F18:A-B1]. It is interesting to note that although the plasmid structures of the two isolates were so similar, there was no clonal relationship between them. Phylogenetic analysis of E. coli isolates from humans, chickens and poultry environments All isolates assigned a phylogenetic group and ST were used to construct phylogenetic trees to determine if the isolates were genetically related or very diverse. Three phylogenetic trees were constructed: one for all the isolates (Fig. 5), one focusing on isolates with novel STs (Fig. 6a) and one with isolates of different origins assigned the same ST (Fig. 6b). Overall, 110 isolates used to construct a maximum likelihood phylogenetic tree showed that the isolates were genetically diverse. The isolates were grouped based on similarities among them. Whole-genome (wg) SNPsbased phylogenetic analysis showed that some isolates sharing the same ST and phylogroups were not clonally related. The strains were in completely different clades in the SNP tree, separated by strains belonging to other STs. Three isolates with ST-1638 recovered from human, chicken and poultry environment were clustered together on the same clade. Pairwise SNP differences between the (See figure on next page.) Fig. 5 SNP-based phylogeny of MDR E. coli isolates from humans, chickens, and poultry environments in Abuja, 2019. SNP-based maximum likelihood phylogeny of E. coli isolates visualized in iterative Tree of life tool (iTol). The tree was rooted in a reference isolate E. coli strain NCTC11129. Clustering of isolates was found to be following the core genome and SNP-based phylogenies. The clustering of isolates belonging to the same phylogenetic group and sequence type was consistent. Shown for each isolate is the source/origin: farm (F) or live bird market (LBM) and phylogroup. AMR genes cluster for 110 E. coli strains are displayed on the phylogenetic tree. The presence (orange) and absence (white) of 12 AMR genes that were most prevalent are represented in the image while the presence (gray) and absence (white) of 10 prevalent plasmid replicons are also represented in the image Aworh et al. Antimicrob Resist Infect Control (2021) 10:58 Page 8 of 13 Aworh et al. Antimicrob Resist Infect Control (2021) 10:58 Page 9 of 13 a b Fig. 6 a Phylogenetic SNP-based maximum likelihood tree for E. coli isolates with Novel ST from humans, chickens and poultry farm or market environments. The phylogenetic SNP-based maximum likelihood tree was rooted in a reference isolate E. coli strain NCTC11129. For each isolate, the source and origin: farm (F) or live bird market (LBM) as well as the phylogenetic group is displayed. The phylogenetic tree has several clades with a common ancestor however the red clade has two isolates from the same farm belonging to the same phylogroup and sharing a novel ST. These two isolates from human and poultry farm environments although quite diverse had similar plasmid replicons harbouring AMR genes. b Phylogenetic maximum likelihood tree for E. coli isolates with ST 1638. The SNP-based maximum likelihood tree was rooted in a reference isolate E. coli strain NCTC11129. Two isolates of human and avian origin although not clonally related acquired similar AMR genes genomes of the isolates showed that they were not clonally related (Fig. 6b). Two isolates of human and environmental origin with SNPs difference of 6161 were not clonally related although the isolates shared a novel ST and belonged to phylogroup B1 (Fig. 6a). The two isolates originating from the same farm had similar AMR gene profile (qnrB19, qnrS1, mdfA, mefB, sul 2, sul 3, blaTEM1, tetA, tetM, floR); as well as plasmid replicons (p0111, IncFIC(FII), IncHI2A, IncHI2, Col(pHAD28). Discussion To the best of our knowledge, this is the first study to investigate the prevalence of MDR E. coli in poultry workers, chickens, and the poultry farm/market environments in Nigeria. The first objective of this study was to characterize E. coli from poultry workers, chickens, and poultry environments. The unhygienic LBM environment where these chickens are sold acts as a reservoir of antimicrobialresistant bacteria and eventually poses a health risk to people working in such an environment. A similar study done in the Netherlands reported a lower prevalence of MDR E. coli in chickens (23%) and chicken farmers (22%) when compared with the present study where a prevalence of 34.7% and 38.6% was detected in chickens and poultry workers respectively [31]. Access to antimicrobials is better regulated in the Netherlands as well as the implementation of antimicrobial stewardship programs when compared to Nigeria and could explain the differences observed in both studies. A related study conducted in Bangladesh among poultry and poultry environment reported a much higher prevalence of E. coli (82%) from chicken faecal samples when compared with the findings from this study, with a much lower prevalence of 32.2% [32]. Two similar studies performed among chickens from poultry farms in northern Nigeria also reported a much higher E. coli prevalence of 67.7% [33] and 69.8% [34] from cloacal swabs obtained from chickens on the farm. A possible explanation for the difference between studies carried out in northern Nigeria and our study could be due to the sample types collected as our study Aworh et al. Antimicrob Resist Infect Control (2021) 10:58 isolated E. coli from freshly dropped chicken faecal samples as opposed to cloacal swabs. A study conducted in Pakistan, reported a slightly higher E. coli prevalence of 36% from the poultry farm environment when compared to 26.1% obtained from the poultry environment in the present study [35]. Our study findings are consistent with the reports of a related study carried out in Egypt where E. coli prevalence of 26.8% was obtained from the poultry environment [36]. The similarity observed between our study findings and that of the Egyptian study may be due to similarities in poultry farming practices. Our study examined AMR in E. coli isolates from poultry farm workers and chicken sellers and compared them to resistance rates of E. coli isolates from chickens and poultry farm/market environment. The patterns of resistance were similar for human and chicken isolates. High resistance rates were observed in isolates recovered from humans, chickens, and poultry farm/market environments for tetracycline, trimethoprim/ sulfamethoxazole, ampicillin, and streptomycin. This is in agreement with the findings of a study conducted in southwest Nigeria, where high resistance rates of E. coli isolates to beta-lactams, tetracyclines, macrolides, and sulfonamides were reported [37]. This finding is not surprising as these antimicrobials are easily accessible and commonly used in poultry production in Nigeria for therapeutic purposes especially in the absence of antimicrobial stewardship programs [38]. Our study revealed a very high proportion (91.8%) of MDR E. coli isolates from all the sources. Interestingly, 83% of human, 97% of chicken, and 100% of poultry environment isolates were MDR E. coli. A possible explanation for this very high level of resistance observed could be because of the lack of prudent use of antimicrobials and the required regulation to support it resulting in over-the-counter availability often without prescription as reported in many studies [16, 38–40]. The potential transmission of the drug-resistant strains between different hosts could also be responsible for this observation because E. coli is a known zoonotic bacteria [13]. The most common beta-lactamase gene observed in this study was the blaTEM-1 gene, which confers ampicillin resistance in E. coli isolates and is in agreement with a previous study that reported ampicillin-resistant E. coli isolates in food, humans, and healthy animals [41]. Our study however, did not detect any genes encoding carbapenem-hydrolyzing enzymes in any of the isolates although phenotypic characterization showed that 10.9% of the isolates were carbapenemresistant. This may possibly be as a result of borderline interpretation of breakpoint settings between resistance and susceptibility. The present study identified one of the most important AMR genes [42], being the Page 10 of 13 PMCR gene—mcr 1.1 harboured on IncX4 plasmids in two isolates recovered from the poultry environment. Evidence shows that the IncX4 plasmids harbouring mcr-1 genes have been detected in human and animal E. coli isolates however, our study recovered these plasmids from the poultry environment [43]. Another study conducted in China also detected PMCR genes—mcr 1 in E. coli isolates sourced from the aquatic environment [44] however, the mcr 3.1 gene was detected in a human Salmonella case in the US [45]. This further buttresses that mcr gene has spread across multiple pathogens. Our study highlights that poultry workers, chickens, and the poultry environments share identical plasmid replicons and this is consistent with the literature [46, 47]. The IncF plasmids reported as one of the epidemic plasmids were observed in humans, chickens, and the poultry environments to harbour different AMR genes; blaTEM-1, mdf(A) and qnrS13 in the present study and these are consistent with the literature [43]. The IncQ1 plasmids were detected in isolates with ST48 recovered from chickens and poultry farm environments harbouring the sul2 genes that confer sulphonamide resistance and this is consistent with reports of other studies [43, 48]. The poor biosecurity measures, unhygienic practices in poultry farms and LBMs, and occupational exposure of over ten years are factors that predispose these humans to get infected with these drug-resistant bacterial strains [3]. To determine the genetic relatedness of the isolates, we analyzed by WGS, E. coli recovered from humans, chickens, and poultry environments. Our results revealed that these isolates showed very diverse genetic profiles. Common STs were assigned based on MLST including ST155, ST48, ST10, ST1638, and ST398 in isolates from humans, chickens, and poultry environments, although ST155 was mostly detected in isolates of poultry origin at the LBM. The most common ST detected among isolates recovered from the poultry farm environment was ST48. Previous studies have reported that E. coli with ST48 in phylogroup A has been detected in healthy volunteers, seafood, and water [49–51]. Our study detected ST48 in E. coli recovered from healthy people, chickens, and the poultry environment. E. coli strains with ST10 have previously been reported as being emerging and pathogenic as implicated in human infections although MDR strains with ST10 have also been detected in poultry and other animal sources [52]. Our study detected MDR E. coli strains with ST10 in healthy individuals, poultry manure, and water. A possible explanation could be that this is becoming an emerging public health issue arising due to possible mutations in the bacteria. The majority of E. coli isolates in this present study belonged to phylogroup A (55.5%) and phylogroup B1 Aworh et al. Antimicrob Resist Infect Control (2021) 10:58 (32.7%). Most human and poultry environment isolates belonged to phylogroup A while majority of the chicken isolates belonged to phylogroup B1. Our study findings are in agreement with the results of a similar study conducted in Pakistan that reported that phylogroups B1 and A were the most prevalent detected among human and animal E. coli isolates [53]. Interestingly, a study carried out in south-west Nigeria reported that chicken E. coli isolates were evenly distributed into phylogroups A and B1 while phylogroup B1 was the most prevalent among human isolates [37]. Previous studies also showed that E. coli isolates belonging to phylogroup B2 are usually the most virulent, hence MDR [54–56]. However, our study observed that majority of the isolates, which belonged to either phylogroups A, and B1 were MDR. This is consistent with findings from a similar study conducted in south-west Nigeria which reported that isolates belonging to phylogroups B1 and A were MDR [37]. Our study findings are not surprising and consistent with the literature that most commensal E. coli belong to phylogenetic groups A and B1 [57, 58]. However, it is worrisome that these indicator bacteria have become MDR with a negative impact on public health since they could be transferred to more virulent strains or species thus causing disease. The phylogenetic SNP tree rooted using NCTC11129 reference strain revealed that the isolates were genetically diverse among the identified STs. Two unrelated isolates of human and environmental origin belonging to phylogroup B1 and sharing a novel ST, had Col440I replicons harbouring the qnrB19 genes that confer quinolone resistance and consistent with the literature [43]. In silico pMLST typing of the two isolates further confirmed that the isolates shared the same plasmids: IncHI2[ST-4] and IncF[ST-F18:A-:B1]. The two isolates although not clonally related, shared the same plasmids (Col440I) harbouring AMR genes (qnrB19) possibly due to horizontal gene transfer. Studies have shown that the IncF and IncHI2 plasmids mainly found in E. coli strains, are frequently detected in humans and animals serving as reservoirs for the spread of AMR genes and have been associated with MDR E. coli [43, 59]. This evidence supports our study results and explanation of a possibility of horizontal gene transfer of AMR genes harboured in the plasmids. Our study did not find evidence of the clonal spread of MDR E. coli at the human-animal-environment interface; however, our findings suggest that mobile genetic elements may have facilitated the horizontal transfer of MDR genes between the plasmids among commensal E. coli which could potentially mutate into real pathogens with serious public health implications [47]. Page 11 of 13 Conclusion MDR E.coli isolates were found to be prevalent amongst poultry-workers, chickens, and poultry farm/market environments in Abuja, Nigeria. The highest resistance rates among MDR E. coli isolates were observed to tetracycline, sulphonamides, penicillins, aminoglycosides, and quinolones which are classes of antimicrobials commonly used in poultry production for treating avian diseases in Abuja. ST-155, ST-48, and ST-1638 were the only STs detected in humans, chickens, and poultry farm/LBM environments in our study. Our findings showed the emergence and spread of MDR E. coli with novel-ST from a poultry farm environment to a poultry farmer, which may have resulted from horizontal transfer of AMR genes harboured in plasmids. Consequent upon these, healthcare and poultryworkers should be educated on the fact that people in proximity with poultry are a high-risk group for faecal carriage of MDR E. coli. Competent authorities should enforce AMR regulation to ensure prudent use of antimicrobials to limit the risk of transmission along the food chain and to poultry workers. Farmers should be discouraged from indiscriminate use of antimicrobials in poultry production and encouraged to adopt preventive measures by observing biosecurity as well as good management practices on their farms. Abbreviations AMR: Antimicrobial resistance; CGE: Center for Genomics Epidemiology; DDBJ: DNA Data Bank of Japan; DNA: Deoxyribonucleic acid; E. coli: Escherichia coli; iTOL: Interactive Tree of Life; LBM: Live bird market; MDR: Multidrug resistance; MLST: Multilocus sequence typing; NAP: National Action Plan; NCBI: National Center for Biotechnology Information; NCDC: Nigeria Center for Disease Control; pMLST: Plasmid multilocus sequence typing; PMCR: Plasmid-mediated colistin resistance; SNPs: Single nucleotide polymorphisms; SSR: Simple sequence repeat; ST: Sequence type; WGS: Whole-genome sequencing; Wg: Whole genome. Supplementary Information The online version contains supplementary material available at https://​doi.​ org/​10.​1186/​s13756-​021-​00930-x. Additional file1: Supplementary Data. Acknowledgements The authors would like to appreciate the support of Dr. Chikwe Ihekweazu, Director General, Nigeria Center for Disease Control, Abuja for providing laboratory space towards this research at the National Reference Laboratory, NCDC. Special appreciation goes to Dr. Adebayo Adedeji, Mrs. Mba Nwando, Dr. Abiodun Egwuenu, Miss Eme Ekeng, Mr. Akinpelu Afolabi, Mr. Micheal Popoola and Mr. Chris Chukwu of the NCDC, Abuja, towards the success of this research. The authors appreciate the efforts of members of Thakur Molecular laboratory, North Carolina State University; Lyndy Harden, Erin Harrell, Nigatu Atlaw, Ayanna Glaize, Dawn Hall, Morgan Young, Luke Raymond, Bryson Staley Aworh et al. Antimicrob Resist Infect Control (2021) 10:58 and Steven Branz towards the success of the research. Special appreciation goes to Dr. Muhammad Shakir Balogun and Dr. Bola Biliaminu Lawal of Nigeria FELTP for their contributions to the success of this research. We also acknowledge the contributions of Judit Szarvas and Pimlapas Leekitcharoenphon at the National Food Institute, Denmark Technical University towards the success of this research. Authors’ contributions MA was the principal investigator, designed data collection tools, collected data, isolated the organism, performed antibiotic sensitivity testing on the isolates, analyzed and interpreted the data and wrote the first draft of the manuscript. JK made substantial contributions to conception and design. JK, and ST supervised the laboratory aspect of the research. MA performed bioinformatic analysis and RSH assisted with interpretation. JK, EO, RSH, and ST revised the article critically for important intellectual content. All authors read and approved the final manuscript. Funding The author(s) received funding from FDA GenomeTrakr program grant 1U18FD00678801 for whole-genome sequencing of the isolates. Availability of data and materials The datasets used and analyzed during the present study are available upon reasonable request from the corresponding author. All data generated or analyzed during this study are also included in this published article [and Additional file 1]. Raw sequence data have been submitted to NCBI (https://​ www.​ncbi.​nlm.​nih.​gov/) under accession no PRJNA293225. Page 12 of 13 2. 3. 4. 5. 6. 7. 8. 9. 10. Declarations Ethics approval and consent to participate Ethics approval for this study was obtained from the FCT Health Research Ethics Committee in July 2018 (Approval Number: FHREC/2018/01/84/16–0718). Permission was obtained from farm and LBM managers before the commencement of the study. We assured participants of confidentiality for the information obtained. An informed consent form clearly stating the study details and benefits was duly signed by participants who were willing to participate in addition to the farm and LBM managers before sample collection. Ethics approval for this study was also obtained from the Scientific and Ethical Committee of the Ahmadu Bello University Committee on Animal Use and Care (Approval Number: ABUCAUC/2020/35). 11. 12. 13. 14. Consent for publication Not applicable. 15. Competing interests The authors declare that they have no competing interests. 16. Author details 1 Department of Veterinary and Pest Control Services, Federal Ministry of Agriculture and Rural Development, Abuja, Nigeria. 2 Nigeria Field Epidemiology and Laboratory Training Programme, Abuja, Nigeria. 3 Department of Veterinary Public Health and Preventive Medicine, Ahmadu Bello University, Zaria, Nigeria. 4 Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA. 5 WHO, FAO, EU, Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark. Received: 19 June 2020 Accepted: 19 March 2021 17. 18. 19. 20. 21. References 1. Parmley J, Leung Z, Léger D, Finley R, Irwin R, Pintar K, et al. One Health and Food Safety—The Canadian Experience: A Holistic approach toward enteric bacteria pathogens and antimicrobial resistance surveillance. Natl Acad Press. 2012. 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First clinical case of in vivo acquisition of DHA-1 plasmid-mediated AmpC in a Salmonella enterica subsp. Enterica Isolate. Antimicrob Agents Chemother. 2019. https://​doi.​org/​10.​1128/​AAC.​00992-​19. 49. Ben Sallem R, Ben Slama K, Estepa V, Jouini A, Gharsa H, Klibi N, et al. Prevalence and characterisation of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates in healthy volunteers in Tunisia. Eur J Clin Microbiol Infect Dis. 2012;31:1511–6. 50. Said LB, Hamdaoui M, Jouini A, Boudabous A, Slama KB, Torres C, et al. First detection of CTX-M-1 in extended-spectrum b-lactamase-producing Escherichia coli in seafood from Tunisia. J Food Prot. 2017;80:1877–81. 51. Madec JY, Haenni M, Ponsin C, Kieffer N, Rion E, Gassilloud B. Sequence type 48 Escherichia coli carrying the blaCTX-M-1 IncI1/ST3 plasmid in drinking water in France. Antimicrob Agents Chemother. 2016;60:6430–2. 52. Manges AR, Johnson JR. Food-borne origins of escherichia coli causing extraintestinal infections. Clin Infect Dis. 2012;55:712–9. 53. Umair M, Mohsin M, Ali Q, Qamar MU, Raza S, Ali A, et al. Prevalence and genetic relatedness of extended spectrum-β-lactamase-producing Escherichia coli among humans, cattle, and poultry in Pakistan. Microb Drug Resist. 2019;25:1374–81. 54. Iranpour D, Hassanpour M, Ansari H, Tajbakhsh S, Khamisipour G, Najafi A. Phylogenetic groups of escherichia coli strains from patients with urinary tract infection in Iran based on the new Clermont phylotyping method. Biomed Res Int. 2015;2015:5–12. 55. Yang F, Zhang S, Shang X, Wang L, Li H, Wang X. Characteristics of quinolone-resistant Escherichia coli isolated from bovine mastitis in China. J Dairy Sci. 2018;101:6244–52. 56. Moreno E, Prats G, Sabaté M, Pérez T, Johnson JR, Andreu A. Quinolone, fluoroquinolone and trimethoprim/sulfamethoxazole resistance in relation to virulence determinants and phylogenetic background among uropathogenic Escherichia coli. J Antimicrob Chemother. 2006;57:204–11. 57. Clermont O, Bonacorsi S, Bingen E, Bonacorsi P. Rapid and Simple Determination of the Escherichia coli Phylogenetic Group Rapid and Simple Determination of the Escherichia coli Phylogenetic Group Downloaded from http://​aem.​asm.​org/ on January 18 , 2013 by University of Pretoria : Academic Information S. Appl Environ Microbiol. 2000;66:4555–8. 58. Ramadan HH, Jackson CR, Taha SA, Moawad AA, Barrett JB, Woodley TA. Contribution of healthy chickens to antimicrobial-resistant Escherichia coli associated with human extraintestinal infections in Egypt. VectorBorne Zoonotic Dis. 2018;18:408–16. 59. Yang Q-E, Sun J, Li L, Deng H, Liu B-T, Fang L-X, et al. IncF plasmid diversity in multi-drug resistant Escherichia coli strains from animals in China. Front Microbiol. 2015;6:964. https://​doi.​org/​10.​3389/​fmicb.​2015.​00964. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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Correction: Non-Secreted Clusterin Isoforms Are Translated in Rare Amounts from Distinct Human mRNA Variants and Do Not Affect Bax-Mediated Apoptosis or the NF-κB Signaling Pathway
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Abstract (2013) Non-Secreted Clusterin Isoforms Are Translated in Rare Amounts from Distinct Human mRNA Variants and Do Not Affect Bax-Mediated Apoptosis or the NF-κB Signaling Pathway. PLoS ONE 8(9): e75303. doi:10.1371/ journal.pone.0075303 Editor: Guillermo Velasco, Complutense University, Spain Editor: Guillermo Velasco, Complutense University, Spain Received April 22, 2013; Accepted August 14, 2013; Published September 20, 2013 Copyright: © 2013 Prochnow et al. This is an open-access article distributed under the terms of the Creative Commons Attribu unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Competing interests: The authors have declared that no competing interests exist. * E-mail: mbaiersdoerfer@gmx.de Non-Secreted Clusterin Isoforms Are Translated in Rare Amounts from Distinct Human mRNA Variants and Do Not Affect Bax-Mediated Apoptosis or the NF-κB Signaling Pathway Hans Prochnow1, Rene Gollan2, Philipp Rohne1, Matthias Hassemer1, Claudia Koch-Brandt1, Markus Baiersdörfer1* Hans Prochnow1, Rene Gollan2, Philipp Rohne1, Matthias Hassemer1, Claudia Koch Baiersdörfer1* 1 Institute of Pharmacy and Biochemistry, Therapeutical Life Sciences, Johannes Gutenberg - University, Mainz, Mainz, Germany, 2 Department of Neurology University Medical Center Mainz, Johannes Gutenberg-University, Mainz, Mainz, Germany Abstract Clusterin, also known as apolipoprotein J, is expressed from a variety of tissues and implicated in pathological disorders such as neurodegenerative diseases, ischemia and cancer. In contrast to secretory clusterin (sCLU), which acts as an extracellular chaperone, the synthesis, subcellular localization and function(s) of intracellular CLU isoforms is currently a matter of intense discussion. By investigating human CLU mRNAs we here unravel mechanisms leading to the synthesis of distinct CLU protein isoforms and analyze their subcellular localization and their impact on apoptosis and on NF-κB-activity. Quantitative PCR-analyses revealed the expression of four different stress-inducible CLU mRNA variants in non-cancer and cancer cell lines. In all cell lines variant 1 represents the most abundant mRNA, whereas all other variants collectively account for no more than 0.34% of total CLU mRNA, even under stressed conditions. Overexpression of CLU cDNAs combined with in vitro mutagenesis revealed distinct translational start sites including a so far uncharacterized non-canonical CUG start codon. We show that all exon 2- containing mRNAs encode sCLU and at least three non-glycosylated intracellular isoforms, CLU1‑449, CLU21‑449 and CLU34‑449, which all reside in the cytosol of unstressed and stressed HEK‑293 cells. The latter is the only form expressed from an alternatively spliced mRNA variant lacking exon 2. Functional analysis revealed that none of these cytosolic CLU forms modulate caspase-mediated intrinsic apoptosis or significantly affects TNF-α-induced NF- κB-activity. Therefore our data challenge some of the current ideas regarding the physiological functions of CLU isoforms in pathologies. Citation: Prochnow H, Gollan R, Rohne P, Hassemer M, Koch-Brandt C, et al. (2013) Non-Secreted Clusterin Isoforms Are Translated in Rare Amounts from Distinct Human mRNA Variants and Do Not Affect Bax-Mediated Apoptosis or the NF-κB Signaling Pathway. PLoS ONE 8(9): e75303. doi:10.1371/ journal.pone.0075303 Editor: Guillermo Velasco, Complutense University, Spain Received April 22, 2013; Accepted August 14, 2013; Published September 20, 2013 Copyright: © 2013 Prochnow et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The authors have no funding or support to report. Competing interests: The authors have declared that no competing interests exist. * E-mail: mbaiersdoerfer@gmx.de Citation: Prochnow H, Gollan R, Rohne P, Hassemer M, Koch-Brandt C, et al. Citation: Prochnow H, Gollan R, Rohne P, Hassemer M, Koch-Brandt C, et al. (2013) Non-Secreted Clusterin Isoforms Are Translated in Rare Amounts from Distinct Human mRNA Variants and Do Not Affect Bax-Mediated Apoptosis or the NF-κB Signaling Pathway. PLoS ONE 8(9): e75303. doi:10.1371/ journal.pone.0075303 Editor: Guillermo Velasco Complutense University Spain Introduction However, in some studies sCLU has also been reported to exert anti-proliferative activity leading to an arrest in the G0-phase of the cell cycle or to even induce apoptosis [26,30,31]. expression of CLU isoforms with pro-apoptotic functions would be inhibited in cancer cells, this could undermine the ultimate goal of this strategy. To limit such therapeutic risks a stringent analysis of CLU mRNA expression profiles and of the encoded secreted and intracellular proteins is fundamental. Data gathered from such investigations will not only support further studies on CLU-based cancer therapy but will also help to unravel the contradictory data on the protein’s role in pathologies such as brain ischemia [4,47,48], Alzheimer’s disease [49,50], atherosclerosis [7,8,22,51] and cancer [41,42,52,53]. For the first time we here present a quantitative analysis of distinct CLU mRNA variants and a characterization of the encoded CLU isoforms. We use non-malignant HEK‑293 cells as well as prostate cancer (PC‑3), mammary gland carcinoma (MCF‑7) and colorectal adenocarcinoma cells (Caco‑2) since expression of intracellular CLU isoforms and/or different CLU mRNA variants has been reported in these cells and for these types of cancer [14,39,54]. By using the proteasome inhibitor MG‑132, we induced proteotoxic stress leading to the induction of distinct CLU mRNA variants and the concomitant appearance of non-secreted CLU isoforms. In vitro mutagenesis and overexpression of individual CLU forms from engineered cDNAs allowed us to characterize the biogenesis, the subcellular location and the impact of distinct isoforms on Bcl-2-associated X protein (Bax)-mediated apoptosis and on NF-κB signaling. Apart from sCLU non-secreted, intracellular forms of CLU have been found within stressed cells. The functions, properties, subcellular localization and the biogenesis of these CLU proteins are not clear, yet. Several mechanisms as to their biogenesis are being discussed: 1) Retrotranslocation of a post-translationally modified sCLU precursor form from the endoplasmic reticulum (ER) to the cytosol after stress induction presumably by the ER-associated protein degradation pathway [32,33]. 2) Internal translation initiation at AUG codons downstream the ER signal sequence coding region (SSCR) would generate non-secreted CLU isoforms [34,35]. 3) Translational initiation at AUG codons upstream of the SSCR on exon 1 of individual CLU mRNA variants could result in the synthesis of N‑terminally elongated CLU proteins with presumably impaired functionality of the ER signal sequence [36]. 4) Alternative splicing of CLU mRNA could generate an mRNA lacking exon 2 which includes the SSCR. Introduction cancer [9]. Common to these diverse pathological disorders is the induction of a cellular stress response due to injury, increased oxidative or proteotoxic stress or dysregulation of particular signal transduction pathways [10]. This in turn poses a severe threat for cells but can be antagonized by upregulation of a “defense machinery” including proteolytic, metabolic and DNA/RNA modifying enzymes, detoxifying proteins and molecular chaperones altogether known as heat shock proteins [11]. Clusterin (CLU), also known as Apolipoprotein J, is a secreted glycoprotein constitutively expressed from a broad spectrum of tissues, especially in brain, neuronal tissue, liver, adrenal glands and testis. It is found in body fluids including serum, cerebrospinal fluid, mother’s milk, semen and urine. CLU has been identified and characterized by virtue of its upregulation in degenerative conditions. Thus its expression has been shown to be induced in a broad range of pathologies such as Alzheimer’s disease [1,2], spongiform encephalopathies [3], ischemic injury of the hippocampus and the heart [4,5], myocarditis [6], atherosclerosis [7,8] as well as As part of this cellular stress program, CLU mRNA expression is induced. This transcriptional response is mediated by different elements in the CLU promoter region like AP‑1 elements [12,13], TCF-binding sites [14], putative binding PLOS ONE | www.plosone.org September 2013 | Volume 8 | Issue 9 | e75303 1 1 Non-Secreted CLU Forms Translated in Rare Amounts sites for NF-κB and Stat1 [15] and a CLE (Clusterin element), a sequence with high similarity to HSEs (heat shock elements) [16,17,18] resulting in a concomitant increase in CLU protein synthesis and secretion. Secreted CLU (sCLU) has been shown to bind a whole set of target proteins via interaction with hydrophobic domains and exhibits properties similar to small heat shock proteins (sHsps) i.e. binding to unfolding client proteins, preventing their aggregation as well as initiating their disposal by uptake into non-professional phagocytic cells, thereby exerting a cytoprotective function in the affected tissue [19,20,21,22]. This is exemplified by various studies reporting increased proliferation rates, cell-viability and invasiveness of cells upon CLU overexpression under stress conditions [23,24,25,26]. In accordance, siRNA- or antisense oligodeoxynucleotide-mediated CLU knockdown results in opposite effects i.e. in a decrease in cell proliferation and viability as well as in an increase in the sensitivity of cells to chemotherapeutic drugs [16,27,28,29]. For a detailed description, please refer to Protocol S1. For a detailed description, please refer to Protocol S1. Introduction Translation of this mRNA would initiate at an AUG on exon 3 leading to synthesis of an N-terminal truncated, non-secreted CLU isoform. Such a splicing event has been observed in the human mammary gland carcinoma cell line MCF‑7 subjected to ionizing radiation. Owing to the presence of a putative nuclear localization sequence this CLU isoform - termed nuclear Clusterin (nCLU) - has been suggested to translocate into the nucleus of cells where it might act as a pro-death factor [37,38,39]. Functions for these intracellular CLU isoforms are still debated; both, the activation and inhibition of the intrinsic apoptotic pathway [40,41,42,43] as well as the NF-κB signaling cascade have been reported [44,45]. Cell culture HEK-293, PC-3, MCF-7 and Caco-2 cell lines were grown in the presence of 10% FBS at 37 °C in a humidified atmosphere with 5% CO2. Proteasome activity was inhibited by incubation of the cells in presence of 10 µM N-(benzyloxycarbonyl) leucinylleucinylleucinal (MG-132) (Calbiochem) for the indicated times. For heat-shock HEK-293 cells were kept at 37°C as control for 24 hours or subjected to 45°C for 1 hour followed by regeneration for 23 hours at 37°C. Generation and transfection of expression plasmids The cDNAs of the different CLU mRNA variants as well as Bax and Bcl-xL cDNAs were cloned into expression vector pcDNA6-V5/6×His (Life Sciences). For recombinant cDNA expression 4 × 106HEK-293 cells were grown in 6-well plates and transfected for 6 hours with 2 µg of plasmid DNA using OptiMem® (Life Technologies) and Turbofect™ in vitro transfection reagent (Thermo Scientific) according to the manufacturer’s protocol. Prior to Western blot analyses transfected cells were incubated for 24 hours in serum-free medium. Despite the controversial data on the function of different CLU isoforms, modulating their expression is currently considered an attractive strategy in cancer treatment. Thus, therapies combining conventional chemotherapeutic drugs with an antisense oligonucleotide strategy targeting CLU to block its cytoprotective effect have been developed for the treatment of non-small cell lung cancer and prostate cancer, of which the latter is currently in phase III of clinical trials [9,46]. If, however, Reverse transcription, real-time PCR and 5’ RACE analyses Clusterin induction upon cell stress such as heat-shock or proteasome inhibition is a well-established phenomenon [41]. Here we focus on CLU expression in normal and in cancer cells after treatment with MG‑132, a peptide-aldehyde blocking proteasome function. First we monitored by Western blot analysis CLU expression patterns in whole cell lysates and culture supernatants of four different cell lines. Secretory CLU is synthesized as a pre-pro-protein comprising 449 amino acids (aa) with an N-terminal 22 aa signal sequence. In the ER the protein is present as a high mannose single chain precursor (psCLU) that is terminally glycosylated in the Golgi, where it is further cleaved by a furin-like protease in an N-terminal α-chain and a C-terminal β-chain. Mature sCLU is secreted as a heterodimeric protein with an apparent molecular weight (MW) of 75-80 kDa in non-reducing SDS-PAGE analyses. Under reducing conditions the α- and β-chains appear as 34-36 kDa and 37-39 kDa protein bands, respectively [55,56]. In lysates of untreated cells the antibody sc‑6419 exclusively detects psCLU (60 kDa) and the β-chain of mature sCLU (37-39 kDa). The latter is also observed in the culture medium as expected for sCLU (Figure 1). In all cell lines treatment with MG‑132 results in increased CLU protein levels in the cell lysates, however processing and secretion are modulated to various extents. Interestingly in all cell lines tested MG‑132 gives rise to additional protein bands present in minor amounts in the cell lysates: a 50 kDa band in all cell lines examined and a 45 kDa band in HEK‑293 cells. The 50 and 45 kDa bands are also observed in heat stressed HEK‑293 cells indicating that their appearance is not restricted to MG‑132 treatment but appears to be a general stress-induced phenomenon (Figure 1). The absence of these protein bands from the culture media suggests that they represent stress-induced intracellular CLU isoforms. Total cellular RNA was isolated using the innuPrep RNA Mini Kit (Analytic Jena). Quantitative real-time PCRs were performed using 20 ng/µl of oligo dT-reverse transcribed RNA and the SYBR green / ROX based RealQ PCR Master Mix (Biomol). Quantification of mRNAs was performed in triplicates using the 7500 Fast System and SDS Software (Applied Biosystems). Plasmids carrying the respective CLU cDNAs at concentrations ranging from 103-10-5 pg/µl served as standards for the calculation of mRNA copy numbers per ng of total RNA. For primer sequences refer to Table S1. Modulation of CLU mRNAs and proteins in response to proteasome inhibition Modulation of CLU mRNAs and proteins in response to proteasome inhibition Preparation of cell lysates and Western blot analysis Cells were lysed in ice-cold lysis buffer (50 mM Tris/HCl [pH 8], 150 mM NaCl, 1% (v/v) Triton® X-100) containing protease inhibitor (Complete mini, Roche). Deglycosylation of proteins PLOS ONE | www.plosone.org September 2013 | Volume 8 | Issue 9 | e75303 2 Non-Secreted CLU Forms Translated in Rare Amounts was carried out by incubation of 40 µg total protein with 1,000 units PNGase F (NEB) according to the manufacturer’s protocol. For Western blot analyses 40-150 µg of total protein or 30-40 µl of culture medium were subjected to reducing SDS- PAGE and blotted onto nitrocellulose membranes. The polyclonal antibody sc‑6419 (1:1,000 dilution, Santa Cruz) was used for detection of human CLU and monoclonal anti‑V5 antibody (Life Technologies) for detection of recombinant CLU‑V5. Human α-Tubulin was analysed via a monoclonal antibody (Sigma). Reactive bands were visualized by chemiluminescence. ng/ml TNF-α (Sigma, diluted in 1 mg/ml BSA-solution) or an equivalent volume of 1 mg/ml BSA-solution. Cells were lysed in 100 µl Luciferase Assay Buffer (Promega). Luciferase activity was determined using the Luciferase Assay System (Promega) according to the manufacturer’s protocol and the FLUOstar Omega luminometer. Measured values were expressed relative to protein concentrations of respective wells as determined by Bradford assay. Reverse transcription, real-time PCR and 5’ RACE analyses 5’ RACE-PCR was performed according to the protocol “5’ RACE System for Rapid Amplification of cDNA Ends, Version 2.0” (Life Technologies). Determination of caspase‑3/7 activity 1.5 × 104 HEK‑293 cells were cultivated in 96-wells and transfected with 0.2 µg of plasmid DNA. After 18 hours cells were treated under serum-free conditions for 10 hours with 10 µM MG‑132 or an equivalent volume of DMSO. Caspase activity was determined using the Caspase-Glo®-3/7 Assay (Promega) according to the manufacturer’s protocol and a FLUOstar Omega luminometer with Omega-Data Analysis Mars software (BMG Labtech). To investigate the biogenesis of these CLU forms we first analyzed the properties and expression of CLU mRNAs. The CLU gene (8p21-p12) encodes at least three different mRNA variants as currently listed in the NCBI database: variant 1 (NM_001831.3), variant 2 (NR_038335.1) and variant 3 (NR_045494.1). Since we and others revealed by 5’ RACE that the 5’-end of variant 1 differs from NM_001831.3 [14], which contains a 5’-extended exon 1 sequence, but is highly similar to the mRNA database entry BC010514.1 (Figure S1A), we hereafter refer to this sequence as mRNA variant 1. All variants are transcribed as pre-mRNAs each comprising 9 exons and 8 introns. Exon 1 sequences are unique to each of the mRNA Immunocytochemistry HEK‑293 cells were grown on coverslips (Ø 1 cm) and transfected with recombinant CLU cDNAs. If indicated, the cells were treated with 10 µM MG‑132 as described above. Paraformaldehyde-fixed cells were incubated with Alexa Fluor® 488 conjugated lectins ConA or WGA (Life Technologies). After blocking cells were incubated consecutively with anti‑V5 antibody (Life Sciences) and Cy3-conjugated secondary antibody (Dianova) followed by chromatin staining with DAPI. Cells were imaged by confocal laser scanning microscopy (LSM) at a Z‑stack step size of 0.13 µm with a 63× oil immersion objective (1.4 optical aperture) using the LSM SP5 microscope (Leica) and Imaris software (Bitplane). NF-κB-Luciferase reporter assay 4 × 105 HEK‑293 cells were cultivated in 24-wells and cotransfected with 0.3 µg of pNF-κB-Luc (Clontech) together with 0.7 µg of recombinant CLU cDNA. After 18 hours cells were treated under serum-free conditions for 24 hours with 10 September 2013 | Volume 8 | Issue 9 | e75303 PLOS ONE | www.plosone.org 3 Non-Secreted CLU Forms Translated in Rare Amounts Figure 2. Overview of the human CLU gene and mRNA variants. The human CLU gene encodes at least 3 different pre- mRNAs which contain unique exons 1 but share exons 2-9. Alternative splicing of variant 1 pre-mRNA generates an mRNA (variant 1 [Δex2]) that lacks exon 2 and the SSCR (black box). The position of the sCLU start codon (framed) is defined as nt = 1. Notice the additional in-frame AUG codons on exon 3 of all mRNAs and on exon 1c of variant 3. doi: 10.1371/journal.pone.0075303.g002 Figure 2. Overview of the human CLU gene and mRNA variants. The human CLU gene encodes at least 3 different pre- mRNAs which contain unique exons 1 but share exons 2-9. Alternative splicing of variant 1 pre-mRNA generates an mRNA (variant 1 [Δex2]) that lacks exon 2 and the SSCR (black box). The position of the sCLU start codon (framed) is defined as nt = 1. Notice the additional in-frame AUG codons on exon 3 of all mRNAs and on exon 1c of variant 3. doi: 10.1371/journal.pone.0075303.g002 SSCR on exon 2 (hereafter referred to as the sCLU start codon). A putative downstream in-frame start codon resides on exon 3. This codon represents the first AUG present on the previously reported alternatively spliced mRNA of variant 1 that lacks exon 2 (variant 1 [Δex2]) [38]. Translation initiation at this AUG will result in a CLU protein lacking the signal sequence, hence yielding an intracellular isoform corresponding to aa 34– 449 (CLU34‑449) of the full-length pre-pro-protein. Variant 3 mRNA also carries a potential upstream in-frame start codon on exon 1 (Figure 2). Figure 1. Proteasomal inhibition and heat stress modulate sCLU and intracellular CLU protein expression in cancer and non-cancer cells. HEK‑293, PC‑3, MCF‑7 and Caco-2 cells were treated with DMSO as control (C), 10 µM MG-132 (MG) or subjected to heat shock (45°C). Whole cell lysates (upper panel) and cell culture media (lower panel) of cells were analyzed for CLU expression by Western blot. NF-κB-Luciferase reporter assay 45-50 kDa CLU protein bands were detected primarily in stressed cells (*). Data shown are representative of three independent experiments. doi: 10.1371/journal.pone.0075303.g001 Using variant-specific primer sets for RT‑PCR we could demonstrate the expression of all CLU mRNAs in all cell lines tested (Figure 3A). However, the copy numbers of the individual CLU mRNAs differ considerably as determined by quantitative real-time PCR (qPCR). In untreated HEK‑293 cells, variant 1 fundamentally accounts for the total amount of CLU mRNA with about 3,500 copies/ng total RNA. However, the copy numbers of variant 2 and variant 3 only add up to 0.009% of the total CLU mRNA amount. Similar ratios of CLU mRNA variants were observed in untreated MCF‑7 and PC‑3 (Figure 3B, C, D, light gray bars). Using specific primer sets for variant 1 [Δex2] we show that all four cell lines express this mRNA (Figure 3; Figure S1D, E), although in very low amounts (0.008%-0.01% of total CLU mRNA). Further, we detected minor expression of the 5’-extended variant 1 (NM_001831.3) in HEK‑293, MCF‑7 and Caco‑2 cells (Figure S1B, C). Incubation of the cells in presence of MG‑132 leads to an increase in CLU mRNAs variant 1 [Δex2], variant 2 and Figure 1. Proteasomal inhibition and heat stress modulate sCLU and intracellular CLU protein expression in cancer and non-cancer cells. HEK‑293, PC‑3, MCF‑7 and Caco-2 cells were treated with DMSO as control (C), 10 µM MG-132 (MG) or subjected to heat shock (45°C). Whole cell lysates (upper panel) and cell culture media (lower panel) of cells were analyzed for CLU expression by Western blot. 45-50 kDa CLU protein bands were detected primarily in stressed cells (*). Data shown are representative of three independent experiments. doi: 10.1371/journal.pone.0075303.g001 variants arguing for distinct transcription start sites (exons 1a, 1b, and 1c). Variant 1 is known to encode sCLU that is translated from an AUG start codon located upstream of the September 2013 | Volume 8 | Issue 9 | e75303 4 PLOS ONE | www.plosone.org Non-Secreted CLU Forms Translated in Rare Amounts Figure 3. Expression of CLU mRNA variants in cancer and non-cancer cells upon proteotoxic stress. (A) Semi-quantitative RT‑PCR analyses of the expression of different CLU mRNA variants in control and MG‑132-treated HEK‑293, MCF‑7, Caco-2 and PC‑3 cells. The different numbers of amplification cycles performed reflect the varying amounts of individual CLU mRNA variants expressed. NF-κB-Luciferase reporter assay Analysis of Hsp27 mRNA indicates the induction of a heat-shock response upon MG‑132 treatment. GAPDH RT‑PCR served as control to ensure the use of equal amounts of reverse transcribed mRNA. Data shown are representative of at least 3 independent experiments. (B, C, D) Quantification of CLU mRNA expression in control and MG‑132-treated HEK‑293 (B), MCF‑7 (C) and PC‑3 cells (D) by qPCR. The amounts of individual transcripts are expressed as copy number per ng of total RNA (mean ± SD, n = 3). Variant 1 is the pre-dominant CLU mRNA in all cell lines conforming to the amounts of total CLU mRNA. The other variants represent low abundant CLU mRNAs. doi: 10.1371/journal.pone.0075303.g003 3. Expression of CLU mRNA variants in cancer and non-cancer cells upon proteotoxic stress. (A) Figure 3. Expression of CLU mRNA variants in cancer and non-cancer cells upon proteotoxic stress. (A) Semi-quantitative RT‑PCR analyses of the expression of different CLU mRNA variants in control and MG‑132-treated HEK‑293, MCF‑7, Caco-2 and PC‑3 cells. The different numbers of amplification cycles performed reflect the varying amounts of individual CLU mRNA variants expressed. Analysis of Hsp27 mRNA indicates the induction of a heat-shock response upon MG‑132 treatment. GAPDH RT‑PCR served as control to ensure the use of equal amounts of reverse transcribed mRNA. Data shown are representative of at least 3 independent experiments. (B, C, D) Quantification of CLU mRNA expression in control and MG‑132-treated HEK‑293 (B), MCF‑7 (C) and PC‑3 cells (D) by qPCR. The amounts of individual transcripts are expressed as copy number per ng of total RNA (mean ± SD, n = 3). Variant 1 is the pre-dominant CLU mRNA in all cell lines conforming to the amounts of total CLU mRNA. The other variants represent low abundant CLU mRNAs. doi: 10.1371/journal.pone.0075303.g003 Figure 3. Expression of CLU mRNA variants in cancer and non-cancer cells upon proteotoxic stress. (A) Semi-quantitative RT‑PCR analyses of the expression of different CLU mRNA variants in control and MG‑132-treated HEK‑293, MCF‑7, Caco-2 and PC‑3 cells. The different numbers of amplification cycles performed reflect the varying amounts of individual CLU mRNA variants expressed. Analysis of Hsp27 mRNA indicates the induction of a heat-shock response upon MG‑132 treatment. GAPDH RT‑PCR served as control to ensure the use of equal amounts of reverse transcribed mRNA. Data shown are representative of at least 3 independent experiments. NF-κB-Luciferase reporter assay (B, C, D) Quantification of CLU mRNA expression in control and MG‑132-treated HEK‑293 (B), MCF‑7 (C) and PC‑3 cells (D) by qPCR. The amounts of individual transcripts are expressed as copy number per ng of total RNA (mean ± SD, n = 3). Variant 1 is the pre-dominant CLU mRNA in all cell lines conforming to the amounts of total CLU mRNA. The other variants represent low abundant CLU mRNAs. doi: 10.1371/journal.pone.0075303.g003 secretion of sCLU (Figure 4A, lanes 3-5). Although these variants are expressed from recombinant DNA under the control of the CMV promotor sCLU expression from variant 1 cDNA vastly exceeds the amounts synthesized from variant 2 and variant 3 cDNAs. As shown by in vitro mutagenesis this is attributed to out of frame upstream open reading frames (uORFs) on variant 2 and 3 mRNAs interfering with translation initiation at the sCLU start codon (Figure S2A). Variant 3 mRNA contains an additional upstream in-frame AUG codon on exon 1. It has been speculated that expression from this codon would lead to intracellular CLU by suppressing the function of the signal sequence [36]. However, in vitro mutagenesis of the exon 1 ATG and/or the sCLU start codon on variant 3 cDNA revealed that usage of both start codons results in the synthesis of sCLU (Figure 4B), thus demonstrating that expression from the upstream ATG may occur and does not suppress signal sequence function. Similar results were obtained for the upstream in frame ATG on exon 1 of the 5’ extended variant 1 (NM 001831.3) (Figure S2B). variant 3 as well as in Hsp27 mRNA (Figure 3A), the latter confirming the induction of a heat shock response. The inductions of variant 1 [Δex2], variant 2 and variant 3 range from 5- to 50-fold upon proteasome inhibition in all cells examined, yet they account for no more than 0.34% of total CLU mRNA. The copy number of the major variant 1 mRNA is increased only in HEK‑293 and MCF‑7 cells. As expected, the amount of total CLU mRNA reflects the expression level of variant 1 mRNA (Figure 3B, C, D, dark gray bars). Expression of variant specific cDNAs reveals the biogenesis of distinct CLU isoforms (A) Transfection of cDNA CLU‑V5 protein is also expressed, although to a lesser extent, from variant 1, 2 and 3 cDNAs (Figure 4A, lanes 3-5). As shown by in vitro mutagenesis, translation of this protein initiates at the downstream in-frame ATG on exon 3 (Figure 5B, lanes 2, 4, 6, 8). Therefore the 45 kDa CLU form observed in stressed HEK‑293 cells could arise from variant 1 [Δex2] CLU mRNA and/or internal translation initiation on exon 3 of variant 1, 2 and 3 CLU mRNAs and represents the isoform CLU34‑449. With regard to the endogenous 50 kDa CLU protein band observed within stressed cells it is interesting that a 50 kDa CLU‑V5 form cannot be detected upon expression of variant 1 [Δex2] cDNA but is exclusively synthesized from cDNA variants 1, 2 and 3 (Figure 4A, lanes 3-5). To elucidate the nature of this CLU protein, we asked: 1) whether it could originate from still unknown in-frame start codons on exon 2 downstream the sCLU start codon and/or 2) whether it represents unglycosylated sCLU pre-pro-protein that has not been translocated into the ER. In support of possibility 1, inactivation of the sCLU start codon on variant 1 abrogates sCLU synthesis, but does not impair expression of the 50 kDa CLU‑V5 protein (Figure 5B, lane 5). Therefore we proposed a CTG codon surrounded by an adequate Kozak sequence on exon 2 (Figure 5A, underlined) as an unconventional translation initiation site. Indeed, point-mutation of this CTG codon on a cDNA carrying an inactivated sCLU start codon strongly inhibits the expression of the 50 kDa CLU‑V5 form, demonstrating translational initiation at this site (Figure 5B, lane 7). However, after transfection of a cDNA containing exclusively the sCLU start codon as active translational start site, apart from sCLU also significant amounts of a 50 kDa CLU‑V5 protein are expressed (Figure 5B, lane 4). This indicates that the 50 kDa CLU band actually represents two distinct CLU proteins with a similar apparent molecular weight in SDS-PAGE analyses. One is translated from the proposed CTG codon and corresponds to aa 21–449 (CLU21‑449) therefore lacking the SSCR. Since the other 50 kDa CLU protein depends on translational initiation at the sCLU start codon it could well represent sCLU pre-pro-protein which is not segregated into the ER as proposed above (CLU1‑449). Expression of variant specific cDNAs reveals the biogenesis of distinct CLU isoforms We then aimed to characterize the biogenesis of the distinct CLU forms by overexpressing cDNA constructs of all mRNA variants. To differentiate between endogenously and ectopically expressed CLU forms the recombinant proteins were tagged with a 5 kDa C-terminal V5-epitope (hereafter abbreviated “‑V5”). We chose HEK‑293 cells for these experiments, as they endogenously express all mRNA variants and should therefore be capable to correctly synthesize all recombinant CLU forms. Transfection of CLU cDNAs variant 1, 2 and 3 which contain exon 2, leads to the synthesis and Cells transfected with variant 1 [Δex2] cDNA do not secrete recombinant sCLU but express a 45 kDa CLU‑V5 protein in the lysates (Figure 4A, lane 6). Notably, an intracellular 45 kDa PLOS ONE | www.plosone.org September 2013 | Volume 8 | Issue 9 | e75303 5 Non-Secreted CLU Forms Translated in Rare Amounts Figure 4. Expression of CLU-V5 proteins from recombinant cDNAs. Lysates (upper panels) and culture media (lower panels) of HEK-293 cells transiently expressing the indicated CLU cDNA variants were analyzed by Western blotting. Lanes are labeled with circled numbers. Untransfected cells (HEK‑293) or cells transfected with empty pcDNA6 (mock) served as controls. Data shown are representative of at least three independent experiments. (A) Transfection of cDNA variants 1, 2 and 3 leads to expression and secretion of sCLU (lanes 3-5). Variant 1 [Δex2] produces a non-secreted 45 kDa CLU‑V5 protein corresponding to CLU34‑449 (lane 6). This form is also present in low amounts in the lysates of cells transfected with the cDNA variants 1, 2 and 3. Furthermore, cells transfected with these variants express an additional non- secreted 50 kDa CLU‑V5 protein. (B) A schematic outline of the 5’-end of cDNA variant 3 is shown. Neither point-mutations (crossed out codons) of the sCLU start codon (framed, lane 5) nor the in-frame ATG on exon 1c (lane 4) completely block sCLU expression. Concurrent mutation of both codons eliminates sCLU synthesis (lane 6). doi: 10.1371/journal.pone.0075303.g004 Figure 4. Expression of CLU-V5 proteins from recombinant cDNAs. Lysates (upper panels) and culture media (lower panels) of HEK-293 cells transiently expressing the indicated CLU cDNA variants were analyzed by Western blotting. Lanes are labeled with circled numbers. Untransfected cells (HEK‑293) or cells transfected with empty pcDNA6 (mock) served as controls. Data shown are representative of at least three independent experiments. Expression of variant specific cDNAs reveals the biogenesis of distinct CLU isoforms Furthermore, cells transfected with these variants express an additional non- secreted 50 kDa CLU‑V5 protein. (B) A schematic outline of the 5’-end of cDNA variant 3 is shown. Neither point-mutations (crossed out codons) of the sCLU start codon (framed, lane 5) nor the in-frame ATG on exon 1c (lane 4) completely block sCLU expression. Concurrent mutation of both codons eliminates sCLU synthesis (lane 6). doi: 10.1371/journal.pone.0075303.g004 Expression of variant specific cDNAs reveals the biogenesis of distinct CLU isoforms To scrutinize this notion we treated lysates obtained from HEK‑293 cells overexpressing sCLU–V5/CLU1‑449-V5, CLU21‑449-V5 or CLU34‑449-V5 with PNGase F. The molecular weights of CLU21‑449-V5 and CLU34‑449-V5 proteins remain unaffected by deglycosylation demonstrating that these CLU forms do not contain any polysaccharide moieties (Figure 5C, lanes 5-8). As expected, deglycosylation leads to a drop in molecular weight of psCLU-V5 and sCLU-V5 to 50 kDa and 35 kDa respectively. However, no additional bands, which would correspond to deglycosylated CLU1‑449-V5 are observed after PNGase F-treatment indicating an unglycosylated state of CLU1‑449 (Figure 5C, lanes 3, 4). Figure 4. Expression of CLU-V5 proteins from recombinant cDNAs. Lysates (upper panels) and culture media (lower panels) of HEK-293 cells transiently expressing the indicated CLU cDNA variants were analyzed by Western blotting. Lanes are labeled with circled numbers. Untransfected cells (HEK‑293) or cells transfected with empty pcDNA6 (mock) served as controls. Data shown are representative of at least three independent experiments. (A) Transfection of cDNA variants 1, 2 and 3 leads to expression and secretion of sCLU (lanes 3-5). Variant 1 [Δex2] produces a non-secreted 45 kDa CLU‑V5 protein corresponding to CLU34‑449 (lane 6). This form is also present in low amounts in the lysates of cells transfected with the cDNA variants 1, 2 and 3. Furthermore, cells transfected with these variants express an additional non- secreted 50 kDa CLU‑V5 protein. (B) A schematic outline of the 5’-end of cDNA variant 3 is shown. Neither point-mutations (crossed out codons) of the sCLU start codon (framed, lane 5) nor the in-frame ATG on exon 1c (lane 4) completely block sCLU expression. Concurrent mutation of both codons eliminates sCLU synthesis (lane 6). doi: 10.1371/journal.pone.0075303.g004 Figure 4. Expression of CLU-V5 proteins from recombinant cDNAs. Lysates (upper panels) and culture media (lower panels) of HEK-293 cells transiently expressing the indicated CLU cDNA variants were analyzed by Western blotting. Lanes are labeled with circled numbers. Untransfected cells (HEK‑293) or cells transfected with empty pcDNA6 (mock) served as controls. Data shown are representative of at least three independent experiments. (A) Transfection of cDNA variants 1, 2 and 3 leads to expression and secretion of sCLU (lanes 3-5). Variant 1 [Δex2] produces a non-secreted 45 kDa CLU‑V5 protein corresponding to CLU34‑449 (lane 6). This form is also present in low amounts in the lysates of cells transfected with the cDNA variants 1, 2 and 3. Post-translational mechanisms contribute to the accumulation of both 50 kDa CLU isoforms, but not the 45 kDa CLU isoform in MG-132-treated cells After having revealed the origin of the intracellular CLU isoforms generated within unstressed and stressed cells, we PLOS ONE | www.plosone.org September 2013 | Volume 8 | Issue 9 | e75303 6 Non-Secreted CLU Forms Translated in Rare Amounts Figure 5. Characterization of CLU-isoform biogenesis. (A) Schematic outline of the 5’-sequence of variant 1 showing the sCLU start codon (framed) and the downstream start codon on exon 3 (underlined). A non-canonical CTG start codon is present on exon 2 (underlined). The SSCR (black shaded nucleotides) and the exon 2/exon 3 border (arrow) are indicated. (B) Western blots of recombinant CLU-V5 proteins in lysates (upper panel) and culture media (lower panel) of HEK-293 cells transiently expressing unmodified or point-mutated (crossed out codons) CLU cDNA variant 1. CLU34‑449 is translated from the ATG codon on exon 3 (lanes 2, 7). The 50 kDa CLU‑V5 band consists of the sCLU pre-pro-protein (CLU1‑449) translated from the sCLU start codon and CLU21‑449 translated from the CTG codon (lanes 4, 6). (C) Western blot of recombinant CLU-V5 proteins in lysates of HEK-293 cells transiently expressing sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 from point-mutated variant 1 cDNAs or unmodified variant 1 cDNA (wildtype). Lysates were treated with PNGase F as indicated. The molecular weights of psCLU and sCLU decrease upon deglycosylation (psCLU/sCLU n.g., lanes 3, 4). PNGase F treatment does not alter the molecular weights of CLU1‑449 (lanes 3, 4), CLU21‑449 (lanes 5, 6) and CLU34‑449 (lanes 7, 8). (D) Western blots of untagged CLU proteins in lysates (upper panel) and culture media (lower panel) of control and MG-132-treated HEK-293 cells transiently expressing sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 from point-mutated variant 1 cDNAs or transfected with pcDNA (mock). In contrast to CLU1‑449 and CLU21‑449 which accumulate upon proteasome inhibition (lanes 3-6), the amount of CLU34‑449 is not affected (lanes 7, 8). (B, C, D) Data shown are representative of three independent experiments. Lanes are labeled with circled numbers. Recombinant CLU protein bands with a molecular weight of ~38 kDa presumably originate from even further downstream translation initiation sites on CLU cDNAs. doi: 10 1371/journal pone 0075303 g005 Figure 5. Characterization of CLU-isoform biogenesis. (A) Schematic outline of the 5’-sequence of variant 1 showing the sCLU start codon (framed) and the downstream start codon on exon 3 (underlined). A non-canonical CTG start codon is present on exon 2 (underlined). Post-translational mechanisms contribute to the accumulation of both 50 kDa CLU isoforms, but not the 45 kDa CLU isoform in MG-132-treated cells The SSCR (black shaded nucleotides) and the exon 2/exon 3 border (arrow) are indicated. (B) Western blots of recombinant CLU-V5 proteins in lysates (upper panel) and culture media (lower panel) of HEK-293 cells transiently expressing unmodified or point-mutated (crossed out codons) CLU cDNA variant 1. CLU34‑449 is translated from the ATG codon on exon 3 (lanes 2, 7). The 50 kDa CLU‑V5 band consists of the sCLU pre-pro-protein (CLU1‑449) translated from the sCLU start codon and CLU21‑449 translated from the CTG codon (lanes 4, 6). (C) Western blot of recombinant CLU-V5 proteins in lysates of HEK-293 cells transiently expressing sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 from point-mutated variant 1 cDNAs or unmodified variant 1 cDNA (wildtype). Lysates were treated with PNGase F as indicated. The molecular weights of psCLU and sCLU decrease upon deglycosylation (psCLU/sCLU n.g., lanes 3, 4). PNGase F treatment does not alter the molecular weights of CLU1‑449 (lanes 3, 4), CLU21‑449 (lanes 5, 6) and CLU34‑449 (lanes 7, 8). (D) Western blots of untagged CLU proteins in lysates (upper panel) and culture media (lower panel) of control and MG-132-treated HEK-293 cells transiently expressing sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 from point-mutated variant 1 cDNAs or transfected with pcDNA (mock). In contrast to CLU1‑449 and CLU21‑449 which accumulate upon proteasome inhibition (lanes 3-6), the amount of CLU34‑449 is not affected (lanes 7, 8). (B, C, D) Data shown are representative of three independent experiments. Lanes are labeled with circled numbers. Recombinant CLU protein bands with a molecular weight of ~38 kDa presumably originate from even further downstream translation initiation sites on CLU cDNAs. doi: 10.1371/journal.pone.0075303.g005 treatment does not affect the amounts of psCLU and mature sCLU but selectively leads to an accumulation of CLU1‑449, which comigrates with the endogenous 50 kDa protein band detected in stressed mock-transfected cells (Figure 5D, lanes 3, 4). Likewise, we observed an MG‑132-induced accumulation of recombinant CLU21‑449, but not of recombinant CLU34‑449, which comigrates with the endogenous 45 kDa CLU form observed in MG‑132-treated mock-transfected cells (Figure 5D, lanes 5-8). These results strengthen the idea that the endogenous 50 kDa CLU protein expressed in various cells after proteasome inhibition corresponds to CLU1‑449 and/or investigated whether in addition to transcriptional upregulation also post-translational mechanisms (i.e. reduced proteasomal degradation) contribute to the MG‑132‑induced accumulation of endogenous intracellular CLU forms. Post-translational mechanisms contribute to the accumulation of both 50 kDa CLU isoforms, but not the 45 kDa CLU isoform in MG-132-treated cells We therefore overexpressed sCLU/CLU1‑449, CLU21‑449 and CLU34‑449 as untagged proteins under control of the constitutive CMV- promotor followed by treatment of the cells with MG‑132. By this experimental design we could exclude the involvement of transcriptional regulation in the accumulation of CLU proteins and exactly align recombinantly with endogenously expressed CLU bands. When exclusively sCLU is expressed, MG‑132 7 September 2013 | Volume 8 | Issue 9 | e75303 PLOS ONE | www.plosone.org Non-Secreted CLU Forms Translated in Rare Amounts Figure 6. Subcellular localization of individual CLU isoforms. HEK‑293 cells were transfected with unmodified variant 1, variant 1 [Δex2] or point-mutated versions of variant 1 cDNA encoding only sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 and subjected to LSM. CLU-V5 was detected by the anti‑V5 primary antibody and the Cy3-conjugated secondary antibody (red). Alexa Fluor® 488- conjugated ConA (green) and DAPI (blue) served as counterstains for the nuclear membrane-ER continuum and the nucleus, respectively. Images shown represent the middle plane of the analyzed cells. When unmodified variant 1 cDNA or sCLU/CLU1‑449 are expressed the staining of CLU and ConA shows an overlay (yellow) caused by the presence of psCLU in the ER (variant 1, sCLU/CLU1‑449, control). Expression of variant 1 [Δex2] leads to a mutual exclusive CLU and ConA staining (variant 1 [Δex2], control). A similar staining is observed for CLU21‑449 and CLU34‑449 (CLU21‑449, CLU34‑449, control). The presence of 10 µM MG‑132 does not lead to alterations in the subcellular localization of the individual CLU isoforms when compared to untreated controls. The disruption of intracellular membranes, condensed chromatin and nuclear fragmentation is indicative for apoptotic processes induced by MG‑132 treatment. d i 10 1371/j l 0075303 006 Figure 6. Subcellular localization of individual CLU isoforms. HEK‑293 cells were transfected with unmodified variant 1, variant 1 [Δex2] or point-mutated versions of variant 1 cDNA encoding only sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 and subjected to LSM. CLU-V5 was detected by the anti‑V5 primary antibody and the Cy3-conjugated secondary antibody (red). Alexa Fluor® 488- conjugated ConA (green) and DAPI (blue) served as counterstains for the nuclear membrane-ER continuum and the nucleus, respectively. Images shown represent the middle plane of the analyzed cells. When unmodified variant 1 cDNA or sCLU/CLU1‑449 are expressed the staining of CLU and ConA shows an overlay (yellow) caused by the presence of psCLU in the ER (variant 1, sCLU/CLU1‑449, control). Post-translational mechanisms contribute to the accumulation of both 50 kDa CLU isoforms, but not the 45 kDa CLU isoform in MG-132-treated cells Expression of variant 1 [Δex2] leads to a mutual exclusive CLU and ConA staining (variant 1 [Δex2], control). A similar staining is observed for CLU21‑449 and CLU34‑449 (CLU21‑449, CLU34‑449, control). The presence of 10 µM MG‑132 does not lead to alterations in the subcellular localization of the individual CLU isoforms when compared to untreated controls. The disruption of intracellular membranes, condensed chromatin and nuclear fragmentation is indicative for apoptotic processes induced by MG‑132 treatment. d i 10 1371/j l 0075303 006 doi: 10.1371/journal.pone.0075303.g006 results when the cells were transfected with point-mutated variant 1 cDNA carrying only an active sCLU start codon (Figure 6, Figure S3; sCLU / CLU1‑449 control). In contrast, after transfection with variant 1 [Δex2] cDNA or modified variant 1 cDNA encoding only CLU34‑449 the resulting CLU fluorescence shows no overlay with ConA, WGA or DAPI staining but an almost even distribution throughout the rest of the cell that is characteristic of a soluble cytoplasmic protein (Figure 6, Figure S3; variant 1 [Δex2] control, CLU34‑449 control). The same applies to the subcellular localization of CLU21‑449 in unstressed cells (Figure 6, Figure S3; CLU21‑449 control). CLU21‑449 and, that an impaired proteasomal degradation contributes to the accumulation of these CLU form(s) within stressed cells. In contrast, upregulation of the endogenous 45 kDa CLU form in MG‑132-treated HEK‑293 cells seems to occur exclusively on the transcriptional level probably by induction of CLU mRNAs variant 1 and variant 1 [Δex2]. Distinct CLU isoforms do not affect caspase‑3/7- mediated apoptosis or NF-κB-activity The ability to express distinct CLU isoforms independently allowed us to analyze their impact on cellular processes in which the function of CLU isoforms is intensively discussed. In apoptosis, intracellular CLU isoforms have been reported to act as pro-death factors [34,38]. Therefore we first of all investigated whether overexpression of individual CLU isoforms is sufficient to promote caspase‑3/7 activation. Compared to overexpressed Bax, which served as a positive control, neither expression of sCLU/ CLU1‑449, CLU21‑449 nor CLU34‑449 increases caspase 3/7 activity within unstressed HEK‑293 (Figure 7A) and PC‑3 cells (Figure S4). Since CLU is further suggested to mediate MG-132-induced apoptosis [54] we next investigated the effect of individual CLU isoforms on the extent of caspase‑3/7 activity in MG-132-treated cells. As expected, MG‑132 induces caspase 3/7 activity in mock transfected HEK‑293 cells. Upon overexpression of individual CLU isoforms, however, we observed no significant differences in the extent of MG-132-induced caspase 3/7 activity (Figure 7B) arguing against a CLU-isoform specific modulation of MG-132-induced apoptotic processes. In this context the role of CLU in the regulation of Bax-function is debated since it has been reported to promote as well as to inhibit Bax-mediated intrinsic apoptosis [41,42,43]. In contrast to B-cell lymphoma 2- like 1 (Bcl-xL), a Bax-antagonizing anti-apoptotic protein that was used as positive control, neither sCLU/CLU1‑449, CLU21‑449 nor CLU34‑449 affected caspase 3/7 activation when coexpressed with Bax in HEK‑293 cells (Figure 7C). In summary, we could not detect any pro- or anti-apoptotic functions under normal and stress conditions of either the secretory or the non-secreted intracellular CLU forms. In addition to modulating sCLU expression, cellular stress induces the accumulation of non-glycosylated cytosolic 50 and 45 kDa CLU isoforms (Figure 8A). Here we show that the former actually consists of two distinct proteins translated from variant 1 mRNA: One protein represents unglycosylated sCLU pre-pro-protein (CLU1‑449) that is not translocated into the ER lumen under stress conditions. Very recently, the existence of this CLU isoform has been demonstrated in the cytosol of HeLa cells [58]. Remarkably, similar observations have been made for major prion protein (PrP) that is normally cotranslationally segregated across the ER membrane. However, ER stress favors the ‘mistranslocation’ of a PrP isoform still carrying the signal sequence to the cytosol, where it accumulates as a potentially cytotoxic protein [59]. Discussion In this study we have addressed an issue that has engaged the interest of researchers for a long time; namely the regulation and function of distinct CLU mRNAs and protein isoforms during proteotoxic stress. Here we could show for the first time, that translation of all exon 2-containing CLU mRNAs (BC010514.1, NR_038335.1, NR_045494.1, NM_001831.3) leads to predominant sCLU synthesis. Contrary to previous suggestions [36,57] our data demonstrate that in addition to the sCLU start codon, the initiation of sCLU translation may also occur at in-frame AUGs on exon 1 of variant 3 and the 5’- extended version of variant 1 (NM_001831.3). However, variant 1 (BC010514.1) is the dominant CLU mRNA contributing to the vast majority of extracellular sCLU protein. Variant 2 and variant 3 mRNAs represent low-abundant CLU mRNAs with suppressed sCLU synthesis due to interfering uORFs on their exon 1 sequences. Hence, the translational contribution of these variants to total CLU protein amount is insignificant, therefore challenging their physiological relevance. CLU21–449 and CLU34–449 are located in the cytosol of unstressed and stressed cells To track the subcellular localization of the different CLU forms under physiologic conditions and upon proteotoxic stress we expressed these as V5-tagged proteins. After transfection of corresponding CLU cDNAs in HEK‑293 cells we performed immunocytochemistry followed by laser scanning microscopy (LSM). Upon incubation with MG‑132, the number of cells rounding up and detaching from the culture surface increased. In LSM analyses these cells appear shrunken with nuclear fragmentation and disruption of intracellular compartments like ER and Golgi, which is indicative of advanced stages of apoptosis. Concomitantly, sCLU perinuclear staining becomes spotty throughout the cytoplasm (Figure 6, Figure S3; variant 1 MG‑132, sCLU / CLU1‑449 MG‑132). In contrast, CLU21‑449 and CLU34‑449 keep their cytosolic localization after MG‑132 treatment. However, the slightly spottier distribution of their fluorescence indicates the formation of CLU21‑449- and CLU34‑449- containing protein aggregates upon proteotoxic stress (Figure 6, Figure S3; variant 1 [Δex2] MG‑132, CLU21‑449 MG‑132, CLU34‑449 MG‑132). In none of these experiments, we were able In unstressed cells, expression of variant 1 cDNA results in a vesicular and perinuclear CLU staining. As expected for sCLU, which is the major form expressed from variant 1 cDNA (Figure 4A), CLU staining colocalizes with both, Concanavalin A (ConA) and wheat germ agglutinin (WGA) staining, indicating its localization in the ER and the Golgi compartments (Figure 6, Figure S3; variant 1 control). CLU1‑449, CLU21‑449 and CLU34‑449 which are also synthesized in small amounts upon expression of variant 1 are not detectable in these samples due to the overwhelming sCLU and psCLU staining. We obtained identical PLOS ONE | www.plosone.org September 2013 | Volume 8 | Issue 9 | e75303 8 Non-Secreted CLU Forms Translated in Rare Amounts Non-Secreted CLU Forms Translated in Rare Amounts to detect an unambiguous nuclear localization of CLU. In rare cases we observed individual cells displaying an apparent nuclear spotty CLU staining (Figure S3). Detailed analysis of these cells by animated Z‑stacks of the LSM data revealed that these CLU spots are caused by cytoplasmic/cytosolic invaginations into the nuclear compartment rather than representing a localization of CLU in the nucleoplasm (Video S1). Distinct CLU isoforms do not affect caspase‑3/7- mediated apoptosis or NF-κB-activity HEK‑293 cells were transfected with pcDNA6 (mock), unmodified variant 1 (wildtype), variant 1 [Δex2] (Δex2) or point-mutated versions of variant 1 cDNA encoding only sCLU/CLU1‑449, CLU21‑449 or CLU34‑449. (A) 24 hours after transfection the activity of caspases 3 and 7 was determined. Data are expressed relative to the values obtained from Bax cDNA transfected cells (mean ± SD, n = 3), which served as a positive control. In contrast to Bax, the expression of all CLU protein forms does not activate caspase‑3/7. (B) 24 hours after transfection 10 µM MG‑132 or DMSO (control) was added for 10 hours followed by measurement of caspase 3/7 activity. Data are expressed relative to the values obtained from corresponding control cells (mean ± SD, n = 3). MG‑132 treatment causes an increase in caspase 3/7 activity in all cells analyzed. Neither CLU protein form significantly affects the extent of MG‑132-induced caspase‑3/7 activation. (C) HEK-293 were cotransfected with Bax cDNA together with pcDNA6 (mock +Bax), Bcl-xL or point-mutated versions of variant 1 cDNA. 24 hours after transfection the activity of caspases 3 and 7 was determined. Cells transfected with pcDNA6 alone (mock) served as negative control. Data are expressed relative to the values obtained from mock +Bax transfected cells (mean ± SD, n = 3). While cotransfection with Bcl-xL cDNA, suppresses caspase 3/7 activation demonstrating the validity of the experimental setup, neither of the CLU isoforms significantly modulates Bax-mediated apoptosis. (D) HEK-293 were cotransfected with pNF-κB-Luc and the indicated versions of variant 1. 18 hours after transfection cells were incubated for 24 hours with either 10 ng/ml TNF-α (+TNF) or with BSA solution (-TNF). Cells were lysed and luciferase activity was determined as a measure of NF-κB-activity. Data are expressed as increase in Luciferase activity relative to mock transfected cells incubated with BSA solution (mean ± SD, n=4). A representative Western Blot of cell lysates is embedded showing CLU expression in the samples analyzed. The order is: mock, wildtype, Δex2, sCLU/CLU1‑449, CLU21‑449 and CLU34‑449. Only CLU34‑449 expressed from variant 1 [Δex2] reduces NF-κB activity (Δex2). d i 10 1371/j l 0075303 007 Figure 7. Impact of individual CLU isoforms on apoptosis and on NF-κB-activity. HEK‑293 cells were transfected with pcDNA6 (mock), unmodified variant 1 (wildtype), variant 1 [Δex2] (Δex2) or point-mutated versions of variant 1 cDNA encoding only sCLU/CLU1‑449, CLU21‑449 or CLU34‑449. Distinct CLU isoforms do not affect caspase‑3/7- mediated apoptosis or NF-κB-activity The other 50 kDa CLU protein, CLU21‑449, is generated, by unconventional translation from a well-conserved CUG codon located on exon 2 resulting in an unglycosylated isoform lacking the signal sequence. Interestingly, 10 nucleotides surrounding this CUG codon show a high degree of homology to a CUG translation initiation site found in the internal ribosome entry site of human fibroblast growth factor 2 [60] suggesting that a similar functional sequence on exon 2 of CLU mRNAs could lead to the expression of cytosolic CLU21‑449. The 45 kDa CLU protein represents yet another cytosolic and non-glycosylated CLU isoform lacking the signal sequence (CLU34‑449). It is generated from alternatively spliced variant 1 mRNA in which exon 2 has been removed. Thus far, this mRNA variant 1 [Δex2] has only been reported for gamma-irradiated MCF-7 mammary gland carcinoma cells [39]. We here demonstrate for the first time that this mRNA is present in other cell types, most intriguingly even under normal conditions (HEK-293 cells). Stress-induced alternative mRNA splicing is well-known. It involves canonical splicosome dependent and unconventional cytosolic mechanisms [61,62], thereby increasing the diversity or shifting the balance between stress-related protein isoforms. Interestingly, similar to CLU1‑449 and CLU21‑449 minor amounts of CLU34‑449 are also synthesized from non-spliced variant 1 The regulation of NF-κB-activation is another proposed function of CLU. However, both, NF-κB-stimulatory and - inhibitory properties have been described [44,45], which might be attributed to different CLU isoforms. By using an NF-κB- controlled Luciferase reporter plasmid, we determined the impact of individual CLU isoforms on the TNF-α-induced NF-κB activity. Incubation with TNF-α leads to an 8-fold increase in NF-κB activity in HEK-293 cells cotransfected with pNF-κB-Luc and pcDNA6 (Figure 7D, mock). Neither expression of unmodified variant 1, of sCLU/CLU1‑449 nor of CLU21‑449 does affect TNF-α-induced NF-κB activity. The same is observed for CLU34‑449 when being expressed from point-mutated variant 1 (Figure 7D, CLU34‑449). However, the latter isoform reduces NF- κB activity when being expressed from variant 1 [Δex2] (Figure 7D, Δex2) which might reflect the higher amount of CLU34‑449 expressed from this cDNA. September 2013 | Volume 8 | Issue 9 | e75303 9 PLOS ONE | www.plosone.org Non-Secreted CLU Forms Translated in Rare Amounts Figure 7. Impact of individual CLU isoforms on apoptosis and on NF-κB-activity. doi: 10.1371/journal.pone.0075303.g007 Distinct CLU isoforms do not affect caspase‑3/7- mediated apoptosis or NF-κB-activity (A) 24 hours after transfection the activity of caspases 3 and 7 was determined. Data are expressed relative to the values obtained from Bax cDNA transfected cells (mean ± SD, n = 3), which served as a positive control. In contrast to Bax, the expression of all CLU protein forms does not activate caspase‑3/7. (B) 24 hours after transfection 10 µM MG‑132 or DMSO (control) was added for 10 hours followed by measurement of caspase 3/7 activity. Data are expressed relative to the values obtained from corresponding control cells (mean ± SD, n = 3). MG‑132 treatment causes an increase in caspase 3/7 activity in all cells analyzed. Neither CLU protein form significantly affects the extent of MG‑132-induced caspase‑3/7 activation. (C) HEK-293 were cotransfected with Bax cDNA together with pcDNA6 (mock +Bax), Bcl-xL or point-mutated versions of variant 1 cDNA. 24 hours after transfection the activity of caspases 3 and 7 was determined. Cells transfected with pcDNA6 alone (mock) served as negative control. Data are expressed relative to the values obtained from mock +Bax transfected cells (mean ± SD, n = 3). While cotransfection with Bcl-xL cDNA, suppresses caspase 3/7 activation demonstrating the validity of the experimental setup, neither of the CLU isoforms significantly modulates Bax-mediated apoptosis. (D) HEK-293 were cotransfected with pNF-κB-Luc and the indicated versions of variant 1. 18 hours after transfection cells were incubated for 24 hours with either 10 ng/ml TNF-α (+TNF) or with BSA solution (-TNF). Cells were lysed and luciferase activity was determined as a measure of NF-κB-activity. Data are expressed as increase in Luciferase activity relative to mock transfected cells incubated with BSA solution (mean ± SD, n=4). A representative Western Blot of cell lysates is embedded showing CLU expression in the samples analyzed. The order is: mock, wildtype, Δex2, sCLU/CLU1‑449, CLU21‑449 and CLU34‑449. Only CLU34‑449 expressed from variant 1 [Δex2] reduces NF-κB activity (Δex2). doi: 10.1371/journal.pone.0075303.g007 September 2013 | Volume 8 | Issue 9 | e75303 10 PLOS ONE | www.plosone.org Non-Secreted CLU Forms Translated in Rare Amounts Figure 8. Properties of distinct CLU isoforms and their synthesis in unstressed and stressed cells. (A) A CLU-specific Western blot of cell lysate of MG‑132-treated HEK‑293 cells is shown. All detectable protein bands can be assigned to distinct CLU forms with different properties and subcellular localization (1 determined MWs of secretory CLU forms according to Kapron et al. [55]). Distinct CLU isoforms do not affect caspase‑3/7- mediated apoptosis or NF-κB-activity (B) Model depicting the synthesis of CLU isoforms in unstressed and stressed HEK-293 cells. Under unstressed conditions, the dominant isoform sCLU is translated from variant 1, which accounts virtually for the total CLU mRNA amount. Cytosolic CLU1‑449 (‘mistranlocated’ sCLU pre-pro-protein) and CLU21‑449 (translated from exon 2 CUG) are not detectable due to presumably low expression and proteasomal degradation. CLU34‑449 is translated from exon 3 AUG on variant 1 and from variant 1 [Δex2]. Although CLU34‑449 is not proteasomally degraded, it is not detectable in unstressed cells reflecting its low expression level. Induction of cellular stress (MG-132, heat) induces transcriptional upregulation of variant 1 and its splicing to variant 1 [Δex2] leading to enhanced synthesis of all CLU isoforms. Further, the ‘mistranslocation’ of CLU1‑449 to the cytosol is increased. In the case of proteotoxic stress induced by MG-132, diminished proteasomal degradation of CLU1‑449 and CLU21‑449 further promotes their accumulation. Altogether these events generate amounts of the rare cytosolic CLU isoforms that are detectable in Western Blot analyses. They account for 3.6% ± 1.6% (mean ± SD, n=5) of total cell-associated CLU in stressed cells as determined by densitometric quantification of corresponding bands. Note that different expression levels (from low to high) are indicated by the different line width of arrows (from dashed to bold). Variants 2 and 3 are not illustrated because they are expressed in very low amounts and virtually do not contribute to the synthesis of any CLU isoform. Figure 8. Properties of distinct CLU isoforms and their synthesis in unstressed and stressed cells. (A) A CLU-specific Western blot of cell lysate of MG‑132-treated HEK‑293 cells is shown. All detectable protein bands can be assigned to distinct CLU forms with different properties and subcellular localization (1 determined MWs of secretory CLU forms according to Kapron et al. [55]). (B) Model depicting the synthesis of CLU isoforms in unstressed and stressed HEK-293 cells. Under unstressed conditions, the dominant isoform sCLU is translated from variant 1, which accounts virtually for the total CLU mRNA amount. Cytosolic CLU1‑449 (‘mistranlocated’ sCLU pre-pro-protein) and CLU21‑449 (translated from exon 2 CUG) are not detectable due to presumably low expression and proteasomal degradation. CLU34‑449 is translated from exon 3 AUG on variant 1 and from variant 1 [Δex2]. Although CLU34‑449 is not proteasomally degraded, it is not detectable in unstressed cells reflecting its low expression level. Distinct CLU isoforms do not affect caspase‑3/7- mediated apoptosis or NF-κB-activity Induction of cellular stress (MG-132, heat) induces transcriptional upregulation of variant 1 and its splicing to variant 1 [Δex2] leading to enhanced synthesis of all CLU isoforms. Further, the ‘mistranslocation’ of CLU1‑449 to the cytosol is increased. In the case of proteotoxic stress induced by MG-132, diminished proteasomal degradation of CLU1‑449 and CLU21‑449 further promotes their accumulation. Altogether these events generate amounts of the rare cytosolic CLU isoforms that are detectable in Western Blot analyses. They account for 3.6% ± 1.6% (mean ± SD, n=5) of total cell-associated CLU in stressed cells as determined by densitometric quantification of corresponding bands. Note that different expression levels (from low to high) are indicated by the different line width of arrows (from dashed to bold). Variants 2 and 3 are not illustrated because they are expressed in very low amounts and virtually do not contribute to the synthesis of any CLU isoform. doi: 10.1371/journal.pone.0075303.g008 rties of distinct CLU isoforms and their synthesis in unstressed and stressed cells. (A) A CLU- Figure 8. Properties of distinct CLU isoforms and their synthesis in unstressed and stresse Figure 8. Properties of distinct CLU isoforms and their synthesis in unstressed and stressed cells. (A) A CLU-specific Western blot of cell lysate of MG‑132-treated HEK‑293 cells is shown. All detectable protein bands can be assigned to distinct CLU forms with different properties and subcellular localization (1 determined MWs of secretory CLU forms according to Kapron et al. [55]). (B) Model depicting the synthesis of CLU isoforms in unstressed and stressed HEK-293 cells. Under unstressed conditions, the dominant isoform sCLU is translated from variant 1, which accounts virtually for the total CLU mRNA amount. Cytosolic CLU1‑449 (‘mistranlocated’ sCLU pre-pro-protein) and CLU21‑449 (translated from exon 2 CUG) are not detectable due to presumably low expression and proteasomal degradation. CLU34‑449 is translated from exon 3 AUG on variant 1 and from variant 1 [Δex2]. Although CLU34‑449 is not proteasomally degraded, it is not detectable in unstressed cells reflecting its low expression level. Induction of cellular stress (MG-132, heat) induces transcriptional upregulation of variant 1 and its splicing to variant 1 [Δex2] leading to enhanced synthesis of all CLU isoforms. Further, the ‘mistranslocation’ of CLU1‑449 to the cytosol is increased. In the case of proteotoxic stress induced by MG-132, diminished proteasomal degradation of CLU1‑449 and CLU21‑449 further promotes their accumulation. Distinct CLU isoforms do not affect caspase‑3/7- mediated apoptosis or NF-κB-activity Altogether these events generate amounts of the rare cytosolic CLU isoforms that are detectable in Western Blot analyses. They account for 3.6% ± 1.6% (mean ± SD, n=5) of total cell-associated CLU in stressed cells as determined by densitometric quantification of corresponding bands. Note that different expression levels (from low to high) are indicated by the different line width of arrows (from dashed to bold). Variants 2 and 3 are not illustrated because they are expressed in very low amounts and virtually do not contribute to the synthesis of any CLU isoform. doi: 10.1371/journal.pone.0075303.g008 the CLU promotor [18,63]. Thus, the increased sCLU/CLU1‑449, CLU21‑449 and in part CLU34‑449 expression are attributed to upregulation of variant 1 within stressed cells. mRNA. This supports previous publications which proposed internal initiation at the exon 3 AUG on CLU mRNA, contributing to CLU34‑449 synthesis [34,35]. We here show that in HEK-293, MCF-7 and Caco-2 cells variant 1 mRNA is induced upon MG-132 treatment. This is in accordance to previous studies demonstrating regulation of CLU mRNA by heat-shock factors (HSFs) which bind to the CLE motif within Our data further reveal that in contrast to CLU1‑449 and CLU21‑449, which accumulate upon proteasome inhibition, CLU34‑449 is not subjected to proteosomal degradation. Thus, we suggest that under conditions of impaired proteasomal September 2013 | Volume 8 | Issue 9 | e75303 11 PLOS ONE | www.plosone.org PLOS ONE | www.plosone.org Non-Secreted CLU Forms Translated in Rare Amounts Non-Secreted CLU Forms Translated in Rare Amounts activity, expression of CLU34‑449 is regulated exclusively on the transcriptional level by increased synthesis of variant 1 and variant 1 [Δex2] mRNA, while reduced proteasomal degradation clearly contributes to the accumulation of the endogenous 50 kDa isoforms CLU1‑449 and CLU21‑449 [54,63]. These cytosolic proteins represent rare CLU isoforms altogether accounting for less than 5% of total cell-associated CLU in stressed cells (Figure 8B). Recently, hypoglycosylated psCLU (55-60 kDa) after retrotranslocation from the ER has been reported to represent an additional cytosolic CLU isoform [32,33]. In support of this, we observed a CLU protein band of ~55 kDa in MG-132-treated HEK-293 cells that presumably corresponds to hypoglycosylated CLU (Figure 1, Figure 5D, lane 4, Figure 8A). NF-κB-activity in a dose-dependent manner. However, a physiological relevance of this effect seems unlikely, as respective amounts of CLU34‑449 are not reached endogenously, even under conditions of massive stress. Supporting Information Figure S1. BC010514.1 is the predominantly expressed CLU mRNA variant 1 and can be spliced to produce variant 1 [Δex2]. (A) Different entries for CLU mRNA variant 1 exist in the NCBI database having various lengths at their 5’ ends. 5’ RACE-PCR analyses of 6 different cell lines produces a DNA fragment (upper panel) that is identical to the EST BP211675 and highly similar to the 5’ end of mRNA BC010514.1 but not to that of NM_001831.3 or NM_001831.1 (lower panel). Hence, the canonical transcription start site of CLU mRNA variant 1 is located 23 nucleotides downstream of the TATA promotor element, as expected. (B) Semi-quantitative RT‑PCR analyses of CLU variant 1 mRNA expression in unstressed HEK‑293, PC‑3, MCF‑7 and Caco-2 cells using primer sets specific for BC010514.1 or NM_001831.3. Upon using 22 cycles of PCR- amplification the expression of BC010514.1 is observed in all cell lines. CLU mRNA NM_001831.3, however, is expressed in minor amounts only in HEK‑293 cells. (C) Semi-quantitative RT‑PCR analyses of CLU mRNA NM_001831.3 expression in unstressed and MG‑132 treated HEK‑293, PC‑3, MCF‑7 and Caco-2 cells using 35 cycles of PCR-amplification. CLU mRNA NM_001831.3 shows low abundant expression in HEK‑293, MCF‑7 and Caco-2 cells and a cell line specific pattern of regulation upon MG‑132 treatment. (D) RT‑PCR analysis of CLU variant 1 mRNA and variant 1 [Δex2] mRNA expression in MG‑132 treated PC‑3 cells using variant 1-specific primers and 35 cycles of amplification. Specificity of both resulting PCR products was verified by DNA sequencing. They represent variant 1 mRNA containing exon 2 (+ exon 2) and variant 1 [Δex2] (Δ exon 2). (E) Plasmids carrying variant 1 or variant 1 [Δex2] cDNA served as templates for PCRs performed with a The function of distinct CLU isoforms in intrinsic apoptosis and NF-κB-mediated signaling is unclear. Here, we neither could detect spontaneous induction of apoptosis nor modulation of MG‑132- and Bax-induced apoptosis upon overexpression of sCLU/CLU1‑449, CLU21‑449 or CLU34‑449. Thus we cannot confirm previous studies showing both, anti- apoptotic [41,42] as well as pro-apoptotic [38,43] functions of CLU. We suggest that the reported effects of sCLU and cytosolic CLU isoforms on intrinsic apoptosis may either depend on a specific cellular context or represent responses that are restricted to certain cell types or cell lines. Interestingly, similar possibilities are being discussed regarding the role of cytosolic PrP on cell viability [69]. Distinct CLU isoforms do not affect caspase‑3/7- mediated apoptosis or NF-κB-activity Regardless of the complexity of CLU proteins and functions and their still incompletely understood influence on cell viability and apoptosis, a current strategy to optimize the treatment of androgen-independent prostate cancer is to minimize sCLU synthesis while leaving cytosolic CLU expression unaffected in order to make cancer cells more susceptible to chemotherapeutic drugs. However, on the basis of our results, it may be difficult to accomplish by common antisense oligonucleotide or RNAi strategies. The approach of Essabani and colleagues to force exon 2 skipping of CLU mRNAs by suppressing an exon splicing enhancer using hairpin oligonucleotides seems more promising. This leads to a decrease in sCLU expression and a concomitant increase in the synthesis of CLU34‑449 resulting in a higher mortality of LNCaP prostate cancer cells [70]. On the basis of our results it is reasonable that this strategy would suppress the expression of sCLU, but also CLU1‑449 and CLU21‑449, while increasing CLU34‑449. However, our data indicate that none of the rare cytosolic CLU isoforms reduces cell viability. Therefore, in contrast to sCLU, these isoforms appear likely to be irrelevant in the context of cancer and other pathologies. In summary, alternative splicing (CLU34‑449), internal translation initiation (CLU21‑449, CLU34‑449), ‘mistranslocation’ of sCLU pre-pro-protein (CLU1‑449) as well as impaired proteasomal degradation (CLU1‑449, CLU21‑449) contribute to the biogenesis of cytosolic CLU isoforms. The properties of all individual CLU isoforms are summarized in Figure 8A. Previous works describe a 50 kDa CLU protein band as a post- translationally modified, “activated” form of CLU34‑449 [38,39]. Our results, however, demonstrate that the 50 kDa CLU forms (CLU1‑449 and CLU21‑449) as well as CLU34‑449 are all independently synthesized proteins. The subcellular localization of intracellular CLU has been studied previously by immunofluorescence microscopy. We could confirm the presence of psCLU/sCLU in the ER/Golgi continuum [33,64] and the cytosolic distribution of CLU34‑449 [43,65,66]. However, no nuclear localization of CLU, even in late-stage apoptotic cells was detectable. This does not support previous reports suggesting translocation of CLU34‑449 into nucleus under stress conditions [38,54,67,68]. Furthermore, considering the low endogenous amounts of CLU1‑449, CLU21‑449 and CLU34‑449 (compared to psCLU/sCLU) present within stressed cells, it has to be concluded that none of these cytosolic isoforms can realistically account for the often reported major stressed-induced changes in subcellular distribution of CLU in cells. Supporting Information (A+B) Western blot analysis of whole cell lysates (50 µg total protein) and cell culture media (30 µl) of HEK‑293 cells transiently expressing unmodified or point-mutated versions of the indicated CLU cDNA variants. Recombinant CLU protein was detected using the V5-tag specific antibody. Cells transfected with blank pcDNA6 (mock) served as controls (lanes 1). Analysis of α-tubulin was performed as a loading control. Lanes are labeled with circled numbers. Data shown are representative of three independent experiments. (A) Schematic outlines of the 5’-ends of cDNA variants 2 and 3 are shown. Exon 1 sequences of both variants contain a set of uORFs (indicated by brackets) which differ from the CLU reading frame. On each variant the longest uORF (* or **) overlaps with the CLU reading frame leading to lower expression of sCLU compared to variant 1, which does not contain any uORFs (lanes 2, 3, 5). Point-mutation of the start codons of these uORFs leads to an increase in the amount of sCLU expressed from variant 2 and 3 which is comparable to that synthesized from variant 1 (lanes 4, 6), strongly indicating that these uORFs inhibit translation initiation at the sCLU start codon (framed) as well as the alternative sCLU start codon on variant 3. (B) A schematic outline of the 5’-end of the 5’- extended cDNA variant 1 (NM_001831.3) is shown. Neither point-mutations of the sCLU start codon (framed) nor the in- frame ATG on exon 1, which is part of the 5’-extended exon 1a sequence (dark grey box), do inhibit sCLU expression, indicating that both codons initiate sCLU translation. Concurrent mutation of both codons, however, almost completely blocks sCLU synthesis. Note that ATG on exon 1a also initiates the translation of a 60 kDa CLU protein that likely represents an N-terminal elongated sCLU pre-proprotein corresponding to CLU1‑449 expressed from variant 1 (BC010514.1). Respective mutated start sites of modified cDNAs are indicated above each lane (crossed out). (PDF) Figure S4. Impact of individual CLU isoforms on apoptosis of PC-3 cells. PC-3 cells were transfected with pcDNA6 (mock), unmodified variant 1 (wildtype), variant 1 [Δex2] (Δex2) or point-mutated versions of variant 1 cDNA encoding only sCLU/CLU1‑449, CLU21‑449 or CLU34‑449. 24 hours after transfection the activity of caspases 3 and 7 was determined. Data are expressed as fold changes in caspase activity compared to mock-transfected cells (mean ± SD, n = 3). Supporting Information Luciferase reporter assays revealed a significant inhibitory effect of CLU34‑449 on NF-κB -activity only when overexpressed from variant 1 [Δex2] but not from point-mutated variant 1 cDNA. Since the amount of CLU34‑449 translated from variant 1 [Δex2] vastly exceeds that translated from the point- mutated variant 1 cDNA indicates that this isoform influences PLOS ONE | www.plosone.org 12 September 2013 | Volume 8 | Issue 9 | e75303 Non-Secreted CLU Forms Translated in Rare Amounts and subjected to LSM. CLU-V5 was detected by the anti‑V5 primary antibody and the Cy3-conjugated secondary antibody (red). Alexa Fluor® 488-conjugated WGA (green) and DAPI (blue) served as counterstains for Golgi/plasmamembrane and the nucleus, respectively. Images shown represent the middle plane of the analyzed cells. When unmodified variant 1 cDNA or sCLU/CLU1‑449 are expressed the staining of CLU and WGA shows an overlay (yellow) caused by the presence of psCLU in the ER (variant 1, sCLU/CLU1‑449, control). Expression of variant 1 [Δex2] leads to a mutual exclusive CLU and WGA staining (variant 1 [Δex2], control). A similar staining is observed for CLU21‑449 and CLU34‑449 (CLU21‑449, CLU34‑449, control). The presence of 10 µM MG‑132 does not lead to alterations in the subcellular localization of the individual CLU isoforms when compared to untreated controls. The disruption of intracellular membranes, condensed chromatin and nuclear fragmentation is indicative for apoptotic processes induced by MG‑132 treatment. (PDF) variant 1- (upper panel) or a variant 1 [Δex2]-specific primer set (lower panel). While both cDNAs can be detected by variant 1- specific primers resulting in the amplification of two PCRs with different length, variant 1 [Δex2]-specific primers solely detect variant 1 [Δex2] cDNA. When mixtures of both cDNAs with ratios of variant 1: variant 1 [Δex2] = 100:1 or higher were used as a template, variant 1 [Δex2] cDNA is only detectable by variant 1 [Δex2] primers, but no longer by the variant 1 primer set. Considering that in cells usually amounts of variant 1mRNA exceed those of variant 1 [Δex2] by four orders of magnitude does result in difficulties when detecting the CLU variant 1 [Δex2] mRNA by conventional variant 1 specific primer sets. (PDF) p (PDF) Figure S2. Upstream ORFs impair sCLU translation from variants 2 and 3 whereas an upstream in-frame start codon on NM_001831.3 initiates translation of sCLU. Supporting Information In contrast to Bax-overexpression, which served as positive control, the expression of all CLU protein forms does not activate caspase‑3/7. (PDF) References 17. Michel D, Chatelain G, North S, Brun G (1997) Stress-induced transcription of the clusterin/apoJ gene. Biochem J 328(1): 45-50. PubMed: 9359832. 1. Calero M, Rostagno A, Frangione B, Ghiso J (2005) Clusterin and Alzheimer’s disease. Subcell Biochem 38: 273-298. doi: 10.1007/0-387-23226-5_14. PubMed: 15709484. 2. Nuutinen T, Suuronen T, Kauppinen A, Salminen A (2009) Clusterin: a forgotten player in Alzheimer’s disease. Brain. Res Rev 61: 89-104. doi: 10.1016/j.brainresrev.2009.05.007. 18. Loison F, Debure L, Nizard P, le Goff P, Michel D et al. (2006) Up- regulation of the clusterin gene after proteotoxic stress: implication of HSF1-HSF2 heterocomplexes. Biochem J 395: 223-231. doi:10.1042/ BJ20051190. PubMed: 16336210. 3. Kempster S, Collins ME, Aronow BJ, Simmons M, Green RB et al. (2004) Clusterin shortens the incubation and alters the histopathology of bovine spongiform encephalopathy in mice. Neuroreport 15: 1735-1738. doi:10.1097/01.wnr.0000134990.97051.22. PubMed: 15257138. 19. Humphreys DT, Carver JA, Easterbrook-Smith SB, Wilson MR (1999) Clusterin has chaperone-like activity similar to that of small heat shock proteins. 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PubMed: 20965420. 12. Wong P, Taillefer D, Lakins J, Pineault J, Chader G et al. (1994) Molecular characterization of human TRPM-2/clusterin, a gene associated with sperm maturation, apoptosis and neurodegeneration. Eur J Biochem 221: 917-925. doi:10.1111/j.1432-1033.1994.tb18807.x. PubMed: 8181474. 28. So A, Sinnemann S, Huntsman D, Fazli L, Gleave M (2005) Knockdown of the cytoprotective chaperone, clusterin, chemosensitizes human breast cancer cells both in vitro and in vivo. Mol Cancer Ther 4: 1837-1849. doi:10.1158/1535-7163.MCT-05-0178. PubMed: 16373699. 13. Protocol S1. Trial protocol. (DOCX) Table S1. Sequences of DNA oligomers which were used as primers for semi-quantitative RT PCR, quantitative real- time PCR and 5’ RACE. (DOCX) Video S1. (A) Animated LSM Z stack of MG 132-treated HEK 293 cells expressing sCLU/CLU1-449. CLU-V5 was detected by the anti V5 primary antibody and the Cy3- conjugated secondary antibody (red). Alexa Fluor® 488- conjugated ConA (green) and DAPI (blue) served as counterstains for the nuclear membrane-ER continuum and the nucleus, respectively. Staining of CLU and ConA shows an overlay (yellow). (B) Animated LSM Z stack of MG 132-treated HEK 293 cells expressing CLU21-449. CLU-V5 was detected by the anti V5 primary antibody and the Cy3-conjugated secondary antibody (red). Alexa Fluor® 488-conjugated ConA (green) and DAPI (blue) served as counterstains for the nuclear membrane-ER continuum and the nucleus, respectively. (C) Animated LSM Z stack of MG 132-treated HEK 293 cells expressing CLU34-449 from variant 1 [Δex2] cDNA. CLU-V5 was detected by the anti V5 primary antibody and the Cy3-conjugated secondary antibody (red). Alexa Figure S3. Subcellular localization of individual CLU isoforms. HEK‑293 cells were transfected with unmodified variant 1, variant 1 [Δex2] or point-mutated versions of variant 1 cDNA encoding only sCLU/CLU1‑449, CLU21‑449 or CLU34‑449 13 September 2013 | Volume 8 | Issue 9 | e75303 PLOS ONE | www.plosone.org Non-Secreted CLU Forms Translated in Rare Amounts correcting the manuscript and Prof. Dr. Frauke Zipp for providing the LSM microscope. Fluor® 488-conjugated WGA (green) and DAPI (blue) served as counterstains for the Golgi/plasma membrane and the nucleus, respectively. Fluor® 488-conjugated WGA (green) and DAPI (blue) served as counterstains for the Golgi/plasma membrane and the nucleus, respectively. Author Contributions (ZIP) Conceived and designed the experiments: HP MB. Performed the experiments: HP RG PR MH MB. Analyzed the data: HP RG CKB MB. Contributed reagents/materials/analysis tools: HP RG MB. Wrote the manuscript: HP CKB MB. 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Localization of decorin gene expression in normal human breast tissue and in benign and malignant tumors of the human breast
Histochemistry and cell biology
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Histochem Cell Biol (2013) 139:161–171 DOI 10.1007/s00418-012-1026-0 Histochem Cell Biol (2013) 139:161–171 DOI 10.1007/s00418-012-1026-0 ORIGINAL PAPER ORIGINAL PAPER Localization of decorin gene expression in normal human breast tissue and in benign and malignant tumors of the human breast Sainio  T. Kakko  H. Ja¨rvela¨inen Department of Medical Biochemistry and Genetics, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland e-mail: anorsa@utu.fi Localization of decorin gene expression in normal human breast tissue and in benign and malignant tumors of the human breast Pia Bostro¨m • Annele Sainio • Tanja Kakko • Mikko Savontaus • Mirva So¨derstro¨m • Hannu Ja¨rvela¨inen Accepted: 28 August 2012 / Published online: 25 September 2012  The Author(s) 2012. This article is published with open access at Springerlink.com Abstract The small extracellular matrix proteoglycan decorin which possesses a potent antitumor activity has been shown to be present in various amounts in the stroma of several tumors including those of the breast. Regarding decorin in breast malignancies the published data are conflicting, i.e., whether breast cancer cells express it or not. Here, we first compared decorin gene expression levels between healthy human breast tissue and selected types of human breast cancer using GeneSapiens databank. Next, we localized decorin mRNA in tissue specimen of normal human breast, intraductal breast papillomas and various histologic types of human breast cancer using in situ hybridization (ISH) with digoxigenin-labeled RNA probes for decorin. We also examined the effect of decorin transduction on the behavior of cultured human breast cancer MCF7 cells. Analysis of GeneSapiens databank revealed that in various human breast cancers decorin expression is significant. However, ISH results clearly demonstrated that human breast cancer cells independently of the type of the cancer do not express decorin mRNA. This was also true for papilloma-forming cells of the human breast. Indeed, decorin gene expression in healthy human breast tissue as well as in benign and malignant tumors of human breast was shown to take place solely in cells of the original stroma. Decorin transduction using decorin adenoviral vector in decorin-negative MCF7 cells resulted in a significant decrease in the proliferation of these cells and changed cell cohesion. Decorin-transduced MCF7 cells also exhibited increased apoptosis. In conclu- sion, our study shows that in human breast tissue only cells of the original stroma are capable of decorin gene expression. Our study also shows that transduction of decorin in decorin-negative human breast cancer cells markedly modulates the growth pattern of these cells. P. Bostro¨m and A. Sainio contributed equally to this work. P. Bostro¨m and A. Sainio contributed equally to this work. P. Bostro¨m  M. So¨derstro¨m Department of Pathology, Turku University Hospital, University of Turku, Kiinamyllynkatu 4-8, 20520 Turku, Finland e-mail: pia.bostrom@tyks.fi M S¨d ¨ Keywords Breast cancer  Extracellular matrix  Decorin  In situ hybridization  Cell behavior Keywords Breast cancer  Extracellular matrix  Decorin  In situ hybridization  Cell behavior A. P. Bostro¨m and A. Sainio contributed equally to this work. Introduction In recent years, growing interest has been focused on the role and therapeutic potential of extracellular matrix (ECM) macromolecules in various diseases including the evolution and progression of cancer (Hielscher et al. 2012; Ja¨rvela¨inen et al. 2009; Lu et al. 2012; Marastoni et al. 2008). This is because today we understand that ECM macromolecules form not only an inert, space-filling 3 12 Histochem Cell Biol (2013) 139:161–171 162 et al. 1999; Lu et al. 2012). These alterations in turn are likely to play an important role in the growth and invasion of breast lesions (Brown et al. 1999; Lu et al. 2012). Regarding decorin, its expression has been shown to be increased in the peritumoral stroma of the malignant lesions but decreased within the breast tumor tissue (Brown et al. 1999; Leygue et al. 2000). However, results on decorin expression in human breast cancer have been somewhat conflicting, i.e., whether breast cancer cells express this small proteoglycan or not (Cawthorn et al. 2012; Gu et al. 2010; Leygue et al. 2000; Skandalis et al. 2011). Thus, in the present study, we aimed to localize decorin mRNA in individual cells within normal and malignant human breast tissues using in situ hybridization (ISH) with digoxigenin (DIG)-labeled RNA probes for decorin. In addition, by utilizing cultures of MCF7 human breast adenocarcinoma cells and a decorin producing adenoviral vector, we also examined whether targeted decorin delivery can modulate the behavior of these cells. microenvironment around the cells but they also interact with cells and generate signals that regulate the behavior of the cells (Hynes 2009; Rozario and DeSimone 2010) and control angiogenesis (Hielscher et al. 2012). Indeed, indi- vidual ECM macromolecules display important functional roles in the control of key cellular events of physiologic and pathological processes, namely adhesion, migration, proliferation, differentiation, and survival (Daley et al. 2008; Ja¨rvela¨inen et al. 2009; Marastoni et al. 2008; Rozario and DeSimone 2010). An ECM molecule that has been shown to be involved in the regulation of all the aforementioned cellular events, and thereby markedly contributes to health and disease, is decorin, a small leucine-rich extracellular matrix proteo- glycan (Ferdous et al. 2010; Iozzo and Schaefer 2010; Seidler and Dreier 2008). The evidence suggests that decorin represents a potent antitumor molecule (Iozzo and Sanderson 2011; Theocharis et al. 2010). Introduction For example, early studies with decorin-deficient mice have indicated that although the lack of decorin does not lead to the development of spontaneous tumors (Danielson et al. 1997), it is permissive for tumorigenesis (Iozzo et al. 1999). In concordance with this, we have recently dem- onstrated that there is a striking difference in the expression of decorin between malignant and benign vascular tumors in human, i.e., within Kaposi’s sarcoma, and angiosarcoma, decorin expression is completely lacking; while within hemangiomas, decorin is expressed in abundant amounts (Saloma¨ki et al. 2008). Decorin has also been shown to inhibit tumor growth by antagonizing tumor angiogenesis (Neill et al. 2012). Furthermore, ectopic expression of decorin has been shown to cause generalized growth sup- pression in neoplastic cells of various histologic origin (Santra et al. 1997). As can be expected, several other studies supporting the antitumor and antimetastatic activity for decorin have been published (Biaoxue et al. 2011; Goldoni and Iozzo 2008; Hu et al. 2009; Reed et al. 2005; Shintani et al. 2008; Troup et al. 2003), and low levels of decorin have been found to be associated with a shorter progression time and poorer survival in lymph node- negative invasive human breast carcinomas (Araki et al. 2009; Troup et al. 2003). As such, a lot of interest has been paid to the potential use of decorin as an anticancer agent in the future (Neill et al. 2012; Pucci-Minafra et al. 2008; Theocharis et al. 2010). GeneSapiens database receptors (ER) were determined positive in 56 cases and progesterone receptors (PR) were positive in 53 cases. Ki-67 status was intermediate (16–30 %) or high ([30 %) in 46 cases. Among the 69 cases of invasive breast cancer specimen studied, Her2 chromogenic in situ hybridization (CISH) positivity was found in 11 patients. The GeneSapiens database was used to analyze previous published results of the gene expression levels of decorin in healthy and malignant human breast tissues (Kilpinen et al. 2008). This database (http://www.genesapiens.org/) covers the relative gene expression patterns for 17,330 genes across all the 9,783 annotated healthy and pathological human tissue samples from publicly available Affymetrix microarray experiments. The database contains 15 healthy breast tissue samples and 1,504 different human breast carcinoma samples. Table 1 Patients and tumor characteristics Variable Number of patients (%) Number of the patients 69 (aged 40–94, mean 65.4) Grade I 8 (11.6 %) II 36 (52.2 %) III 25 (36.2 %) Axillary nodal status N0 33 (47.8 %) [N1 33 (47.8 %) Unknown 3 (4.3 %) Tumor size B2 cm 23 (33.3 %) [2 cm 46 (66.7 %) Estrogen receptor status (ER)a Positive 56 (81.2 %) Negative 13 (18.8 %) Progesterone receptor status (PR)a Positive 53 (76.8 %) Negative 16 (23.2 %) Ki-67 statusb Low B15 % 23 (33.3 %) Intermediate 16–30 % 26 (37.7 %) High [30 % 20 (29 %) Histologic type Ductal 49 (71.0 %) Lobular 11 (15.9 %) Subtypes 9 (13.0 %) Her2c IHC positive (2? and 3?) 27 (39.1 %) IHC negative (0 and 1?) 42 (60.9 %) CISH positive 11 (15.9 %) a Cut off point used for ER and PR immunohistochemistry is 10 % of positively stained tumor nuclei. b Proliferation index according to St Gallen Consesus (Goldhirsch et al. 2009) c Scoring of HER2 immunohistochemistry: Score 0 no staining is observed or cell membrane staining is observed in less than 10 % of tumor cells. Score 1? a faint perceptible membrane staining can be detected in more than 10 % of the tumor cells or cells are only stained in part of their membrane. Score 2? a weak-to-moderate complete membrane staining is observed in more than 10 % of the tumor cells. Table 1 Patients and tumor characteristics Immunohistochemistry Five different ready-to-use mouse or rabbit monoclonal antibodies were used from Ventana Medical Systems/ Roche Diagnostics: Estrogen Receptor (SP1, rabbit), Pro- gesterone Receptor (1E2, rabbit), HER-2/neu (4B5, rab- bit), Ki-67 (30-9, rabbit), and p63 (4A4, mouse) with BenchMark XT immunostainer and ultraVIEW Universal DAB Detection Kit (Ventana/Roche, Tucson, Arizona, USA). The percentage of nuclei with immunoreactivity to ER, PR, and Ki-67 was classified as continuous data from 0 to 100 %. ER-positive and PR-positive cases showed staining in at least 10 % of the tumor cell nuclei. Carci- nomas revealing 3? immunohistochemical membrane staining for Her2 or positive gene amplification by CISH were accepted as positive (Bostro¨m et al. 2009). Immu- nostaining for p63 was done to identify myoepithelial cells in some cases. Immunohistochemical analyses for decorin were performed as previously described in detail (Salo- ma¨ki et al. 2008). Patients and tumors Ethical approval for the use of the clinical material of this study was given by Turku University Hospital Ethics committee (no 241/2005) and the Finnish National Authority for Medicolegal Affairs (no 4424/32/300/02). Well-characterized human breast cancer material consisted of tumor samples collected from 69 female breast cancer patients (mean age at surgery 65.4 years, range 40–94 years) who were operated and treated at Turku University Hospital during the years 2004–2007 (Table 1). All patients had over 10 mm invasive breast tumor and were treated with a radical mastectomy. Tissue samples from the invasive border of the tumor were excised within 30 min after the surgical removal of the breast. Normal human female breast tissue (three samples) and intraductal papillomas (three samples) were obtained through reduc- tion mammoplasty of the healthy side. The specimen were fixed in 10 % phosphate buffered formaldehyde and embedded in paraffin. Four lm serial sections were cut and stained with hematoxylin and eosin. The slides were reviewed to confirm the diagnosis of the breast cancer, and the histologic typing and grading of the specimen were performed according to the World Health Organization (WHO) classification (Ellis et al. 2003). Of the 69 patients, 25 cases were grade III tumors, 36 cases were grade II tumors, and 8 cases were grade I tumors. Histologically, the majority were invasive ductal carcinomas (71 %). Lymph node metastases were found in 33 cases. Estrogen Breast cancer is the leading cancer malignancy among women aged 20–59 years (WHO 2009). It comprises a collection of diseases that have different histopathology, genetic, and genomic variations, and prognostic outcomes (Geyer et al. 2009). In both benign and malignant breast tumors, alterations of stromal structure and composition are well-recognized phenomena (Alowami et al. 2003; Brown 123 123 123 Histochem Cell Biol (2013) 139:161–171 163 GeneSapiens database a Cut off point used for ER and PR immunohistochemistry is 10 % of positively stained tumor nuclei. Statistical analysis Statistical analysis Unpaired Student’s t test was employed in statistical analyses. All p values \0.05 were considered statistically significant. Decorin transduction Human breast adenocarcinoma cell line MCF7 was used for transduction with a recombinant replication-deficient adenoviral vector dcn-pxc1c-1. MCF7 cells were main- tained in RPMI-1640 medium containing 10 % fetal bovine serum (FBS), 25 lM insulin, 1 nM b-estradiol, 2 mM L-glutamine, penicillin (100 IU/mL), and strepto- mycin (100 lg/mL) and grown at 37 C with 5 % CO2. The cells were plated on a 24-well plate (Greiner Bio-One, Kremsmuenster, Austria), 30,000 per well. The next day, cells were transduced with 0, 3, 30, 100, 300, and 1000 pfu/cell of dcn-pxc1c-1 or RAdlacZ in reduced medium containing no FBS. Four parallels were made of each vector concentration. After 24-h incubation, the cells were washed twice with reduced medium and incubated in this medium for another 24 h. The cells were trypsinized, pooled, and the RNA was extracted using NucleoSpin RNA II–kit (Macherey–Nagel, Du¨ren, Germany) according to the manufacturer’s instructions. Results Relative decorin gene expression in human breast cancer tissues based on the GeneSapiens in silico transcriptomics data In order to analyze published data on decorin gene expression in different types of human breast cancer, we used an in silico database from the GeneSapiens website (Kilpinen et al. 2008). The analysis indicated that the rel- ative decorin gene expression is significant in both healthy and various malignant conditions of human breast tissue (Fig. 1). Fig. 1 Box plot analysis of decorin gene expression levels using the GeneSapiens in silico database at www.genesapiens.org in healthy human breast tissues and in different types of human breast cancer. Y axis indicates the level of relative decorin gene expression in the tissues. The continuous lines in the box plot images represent the median gene expression level of decorin in breast tissue samples included in the database. Compared to decorin expression in healthy breast tissue decorin expression is decreased in ductal, lobular, and other breast cancers but increased in breast carcinomas not otherwise specified (breast carcinoma NOS) pairs used in qPCR were: 50-GGACCGTTTCAACAGAG AGG-30 (for) and 50-GAGTTGTGTCAGG GGGAAGA-30 (rev) for decorin and 50-GAGTGTGGCCTTCTCCTCTG-30 (for) and 50-GCTTG CAGTTAGCCAGGTTC-30 (rev) for GNB2L1. Reactions were run on an Applied Biosystems 7900HT machine (Applied Biosystems, Carlsbad, CA, USA). The qPCR protocol consisted of initial denaturation at 95 C for 2 min followed by 40 cycles of denaturation at 95 C for 40 s and extension at 60 C for 45 s. The spec- ificity of the reactions was confirmed by melt-curve and agarose gel analysis. Triplicate CT values were analyzed using the comparative CT (2-44CT) method. pairs used in qPCR were: 50-GGACCGTTTCAACAGAG AGG-30 (for) and 50-GAGTTGTGTCAGG GGGAAGA-30 (rev) for decorin and 50-GAGTGTGGCCTTCTCCTCTG-30 (for) and 50-GCTTG CAGTTAGCCAGGTTC-30 (rev) for GNB2L1. Reactions were run on an Applied Biosystems 7900HT machine (Applied Biosystems, Carlsbad, CA, USA). The qPCR protocol consisted of initial denaturation at 95 C for 2 min followed by 40 cycles of denaturation at 95 C for 40 s and extension at 60 C for 45 s. The spec- ificity of the reactions was confirmed by melt-curve and agarose gel analysis. Triplicate CT values were analyzed using the comparative CT (2-44CT) method. pairs used in qPCR were: 50-GGACCGTTTCAACAGAG AGG-30 (for) and 50-GAGTTGTGTCAGG GGGAAGA-30 (rev) for decorin and 50-GAGTGTGGCCTTCTCCTCTG-30 (for) and 50-GCTTG CAGTTAGCCAGGTTC-30 (rev) for GNB2L1. Reactions were run on an Applied Biosystems 7900HT machine (Applied Biosystems, Carlsbad, CA, USA). The qPCR protocol consisted of initial denaturation at 95 C for 2 min followed by 40 cycles of denaturation at 95 C for 40 s and extension at 60 C for 45 s. The spec- ificity of the reactions was confirmed by melt-curve and agarose gel analysis. Triplicate CT values were analyzed using the comparative CT (2-44CT) method. Adenoviral vectors Adenoviral vectors For transduction experiments, a recombinant replication- deficient adenoviral vector dcn-pxc1c-1 was used. This vector harbors the human decorin (DCN) cDNA under the control of cytomegalovirus (CMV) promoter. For the preparation of the vector, full length human decorin cDNA (Fisher et al. 1989) in pGEM plasmids was cloned and inserted into shuttle plasmid pxcJL-1. The viruses were prepared by cotransfecting HEK293–cells with back bone plasmid pBHG10. As a control vector RAdlacZ, which harbors the E. coli b-galactosidase gene (lacZ) under the control of CMV IE promoter was used (Wilkinson and Akrigg 1992). This vector was purchased from the Virus Vector Facility, Centre for Biotechnology, University of Turku, Turku, Finland. Decorin in situ hybridization Decorin ISH was performed on 4 lm breast tissue sec- tions by probing with human decorin antisense and sense single-stranded RNA riboprobes. A 533 bp fragment containing human decorin cDNA was cloned into the Eco RI/Hind III site of pGEM-4Z transcription vector (kindly provided by Dr. Liliana Schaefer, University of Frank- furt, Frankfurt am Main, Germany). Linearized plasmid DNA was purified with QIAquick PCR Purification Kit (QIAGEN, Hilden, Germany) and DIG-labeled sense and antisense RNA probes were synthesized by in vitro transcription with SP6 and T7 polymerases, respectively, using a DIG RNA Labeling Kit (Roche, Applied Science, Mannheim, Germany). Probe quantification was carried out with a DIG Nucleic Acid Detection Kit (Roche), and ISH was performed as described (Saloma¨ki et al. 2008). a Cut off point used for ER and PR immunohistochemistry is 10 % of positively stained tumor nuclei. c Scoring of HER2 immunohistochemistry: Score 0 no staining is observed or cell membrane staining is observed in less than 10 % of tumor cells. Score 1? a faint perceptible membrane staining can be detected in more than 10 % of the tumor cells or cells are only stained in part of their membrane. Score 2? a weak-to-moderate complete membrane staining is observed in more than 10 % of the tumor cells. Score 3? a strong complete membrane staining is observed in more than 10 % of the tumor cells 12 123 Histochem Cell Biol (2013) 139:161–171 164 RT-qPCR RNA concentration from the extractions was determined using a Nano-Drop spectrophotometer (ThermoScientific, Waltham, MA, USA), and the integrity of the RNA was confirmed with agarose gel electrophoresis. One lg of RNA was DNase treated with RQ1 RNase-Free DNase (Promega, Madison, WI, USA) and reverse transcribed into cDNA using M-MLV reverse transcriptase and Oli- go(dT)15 primer (Promega, Madison, WI, USA) according to manufacturer’s instructions. RT-qPCR was performed using GoTaq qPCR Master Mix (Promega, Madison, WI, USA) with 100 nM primer concentrations and final volume of 10 lL according to manufacturer’s protocol. GNB2L1 was chosen as a reference gene (Zhang et al. 2005). Primer Fig. 1 Box plot analysis of decorin gene expression levels using the GeneSapiens in silico database at www.genesapiens.org in healthy human breast tissues and in different types of human breast cancer. Y axis indicates the level of relative decorin gene expression in the tissues. The continuous lines in the box plot images represent the median gene expression level of decorin in breast tissue samples included in the database. Compared to decorin expression in healthy breast tissue decorin expression is decreased in ductal, lobular, and other breast cancers but increased in breast carcinomas not otherwise specified (breast carcinoma NOS) Fig. 1 Box plot analysis of decorin gene expression levels using the GeneSapiens in silico database at www.genesapiens.org in healthy human breast tissues and in different types of human breast cancer. Y axis indicates the level of relative decorin gene expression in the tissues. The continuous lines in the box plot images represent the median gene expression level of decorin in breast tissue samples included in the database. Compared to decorin expression in healthy breast tissue decorin expression is decreased in ductal, lobular, and other breast cancers but increased in breast carcinomas not otherwise specified (breast carcinoma NOS) 123 165 Histochem Cell Biol (2013) 139:161–171 3–1,000 pfu/cell of a decorin expression vector and a viral concentration of 100 pfu/cell was chosen for further experiments. Transduction with a decorin adenoviral vector changed markedly the growth pattern of MCF7 cells. Cell cohesion clearly decreased and decorin-transduced MCF7 cells exhibited abnormal features (Fig. 6a), compared either to the cells transduced with a control vector LacZ (Fig. 6b) or to negative control cells (data not shown), which both grew as large cohesive solid sheets. Discussion Previously, decreased level of decorin expression has been reported in breast cancer (Eshchenko et al. 2007; Gu et al. 2010; Leygue et al. 2000). However, in a recent study, even increased amounts of decorin in breast carcinoma has been observed (Skandalis et al. 2011). In addition to these conflicting results, it has also not been convincingly dem- onstrated whether breast cancer cells themselves express decorin or not (Cawthorn et al. 2012; Gu et al. 2010). In the present study, we have first analyzed previously published data on decorin gene expression using GeneSa- piens databank. Thereafter, we have localized decorin mRNA in tissues samples of normal human breast and selected human breast tumors using ISH with DIG-labeled decorin probes. We have also examined the influence of adenoviral mediated decorin transduction on the behavior of human breast cancer cells in vitro. GeneSapiens data- bank analysis demonstrated that the relative decorin gene expression is significant in both healthy and various malignant conditions of human breast tissue. ISH of heal- thy human breast tissue and selected human breast tumor samples revealed that decorin mRNA can merely be localized to the normal stroma. Indeed, no decorin mRNA could be detected in benign epithelial cells or in malignant cancer cells of the human breast. In previous studies, it has been demonstrated that decorin expression is high in nor- mal human breast tissue stroma adjacent to lobules and reduced in the breast tumor itself (Brown et al. 1999; Leygue et al. 2000). However, these studies have used Localization of decorin mRNA in normal human breast tissue, and in benign and malignant tumors of the human breast Next, we localized decorin mRNA in healthy human breast tissue, and in benign and selected types of malignant human breast tumors. Using ISH with DIG-labeled RNA probes for decorin, we were able to demonstrate that in healthy human breast tissue decorin gene expression takes place only in cells in the stromal area surrounding the lobules and in the intralobular stroma, whereas in cells of the epithelium of ducts or lobules no decorin gene expression was detected (Fig. 2a, b). Identical analysis of intraductal papillomas of the human breast (Fig. 2c) revealed that in these benign ductal tumors no decorin gene expression takes place (Fig. 2d, e). Similarly to the healthy human breast tissue, decorin mRNA was solely localized to the original stroma around the dilated duct of the papillomas and not at all within the papillomas (Fig. 2d, e). There was also no decorin mRNA detected in the area within breast tissue specimen containing malignant proliferation of ductal or lobular epithelial cells with myoepithelium, the so-called ductal carcinoma in situ (DCIS) (Fig. 3a–f), and lobular carcinoma in situ (LCIS) (data not shown). Indeed, in DCIS- and LCIS-containing samples, expression of decorin mRNA was localized merely to the peritumoral stroma. Decorin mRNA was also lacking from the infiltrating can- cer cells of the invasive ductal carcinoma (IDC) (Fig. 4a, b) and the invasive lobular carcinoma (ILC) (data not shown). All decorin mRNA in the above-mentioned invasive human breast cancer samples was localized to the original stromal cells. Furthermore, in invasive mucinous carcinomas cancer cells in the mucin lakes or those within the original stroma did not express decorin mRNA (Fig. 5a, b). In conformity with IDC and ILC described above, the surrounding original stromal cells were highly positive for decorin mRNA. Positive immunoreactivity for decorin was seen in the same original non-malignant stromal area as decorin mRNA (data not shown). RT-qPCR Several of the decorin-transduced MCF7 cells were also found to contain a large vacuole within another larger cell with a crescent-shaped nucleus at its periphery (Fig. 6c). Micro- scopic examination further revealed apoptotic features in many of these internalized cells. These so-called cannibal cells were also sporadically seen among the MCF7 cells transduced with the control vector and among the MCF7 cells without any transduction (data not shown). The mitosis rate was statistically significantly lower in the de- corin-transduced MCF7 cell cultures compared to their counterpart cell cultures treated with the control vector LacZ (Fig. 6d). Localization of decorin mRNA in normal human breast tissue, and in benign and malignant tumors of the human breast Effect of adenoviral decorin transduction on MCF7 cells Arrowheads indicate the borders between intraductal papillomas and normal breast tissue. a, b and d, e scale bar 50 lm, c scale bar 500 lm Fig. 2 Decorin mRNA is localized solely to the stromal cells surrounding the lobulus and to the intralobular stromal cells of normal human breast tissue. a HE staining of normal lobulus and its stroma. b ISH for decorin of a serial section of the same normal lobulus as in (a). Examples of individual stromal cells expressing decorin mRNA are indicated by arrows. In the epithelium of ducts or lobules, no decorin mRNA can be detected (examples indicated by asterisks). c HE staining of human breast tissue containing intraductal Fig. 2 Decorin mRNA is localized solely to the stromal cells surrounding the lobulus and to the intralobular stromal cells of normal human breast tissue. a HE staining of normal lobulus and its stroma. b ISH for decorin of a serial section of the same normal lobulus as in (a). Examples of individual stromal cells expressing decorin mRNA are indicated by arrows. In the epithelium of ducts or lobules, no decorin mRNA can be detected (examples indicated by asterisks). c HE staining of human breast tissue containing intraductal Fig. 2 Decorin mRNA is localized solely to the stromal cells surrounding the lobulus and to the intralobular stromal cells of normal human breast tissue. a HE staining of normal lobulus and its stroma. b ISH for decorin of a serial section of the same normal lobulus as in (a). Examples of individual stromal cells expressing decorin mRNA are indicated by arrows. In the epithelium of ducts or lobules, no decorin mRNA can be detected (examples indicated by asterisks). c HE staining of human breast tissue containing intraductal papillomas. d, e ISH for decorin of a serial section of the same sample as in (c), magnified illustrations of the boxed regions shown in (c). Positive DIG-reaction in ISH can be seen in purple. No decorin mRNA is detected within the intraductal papilloma tissue (indicated by asterisks). Arrowheads indicate the borders between intraductal papillomas and normal breast tissue. a, b and d, e scale bar 50 lm, c scale bar 500 lm clearly shown that human breast cancer cells do not express decorin at all and that in human breast tissue specimen decorin is derived from original stromal cells, not from benign or malignant tumor-forming epithelial cells. Effect of adenoviral decorin transduction on MCF7 cells The ISH results clearly demonstrated that decorin is not expressed by benign or malignant ductal or lobular epi- thelial cells of the human breast. Therefore, next we wanted to examine the effects of targeted decorin trans- duction on the behavior of human breast adenocarcinoma cells. Human breast adenocarcinoma cell line MCF7 and decorin producing adenoviral vector were applied for this purpose. Using RT-qPCR, it was first shown that MCF7 cells do not express decorin mRNA (data not shown). These cells were then transduced with a titer range of 12 3 Histochem Cell Biol (2013) 139:161–171 166 Fig. 2 Decorin mRNA is localized solely to the stromal cells surrounding the lobulus and to the intralobular stromal cells of normal human breast tissue. a HE staining of normal lobulus and its stroma. b ISH for decorin of a serial section of the same normal lobulus as in (a). Examples of individual stromal cells expressing decorin mRNA are indicated by arrows. In the epithelium of ducts or lobules, no decorin mRNA can be detected (examples indicated by asterisks). c HE staining of human breast tissue containing intraductal Fig. 2 Decorin mRNA is localized solely to the stromal cells surrounding the lobulus and to the intralobular stromal cells of normal human breast tissue. a HE staining of normal lobulus and its stroma. b ISH for decorin of a serial section of the same normal lobulus as in (a). Examples of individual stromal cells expressing decorin mRNA are indicated by arrows. In the epithelium of ducts or lobules, no decorin mRNA can be detected (examples indicated by asterisks). c HE staining of human breast tissue containing intraductal papillomas. d, e ISH for decorin of a serial section of the same sample as in (c), magnified illustrations of the boxed regions shown in (c). Positive DIG-reaction in ISH can be seen in purple. No decorin mRNA is detected within the intraductal papilloma tissue (indicated by asterisks). Arrowheads indicate the borders between intraductal papillomas and normal breast tissue. a, b and d, e scale bar 50 lm, c scale bar 500 lm papillomas. d, e ISH for decorin of a serial section of the same sample as in (c), magnified illustrations of the boxed regions shown in (c). Positive DIG-reaction in ISH can be seen in purple. No decorin mRNA is detected within the intraductal papilloma tissue (indicated by asterisks). Effect of adenoviral decorin transduction on MCF7 cells How- ever, the specific cell types responsible for decorin expression in the original stroma compartment still remains to be studied. To the best of our knowledge, this study is the first to exactly localize decorin mRNA at the cellular level in human breast tissue including different types of human breast cancer. radioactive probes use of which is limited, if the purpose is to exactly localize the mRNA at the cellular level. With radioactive probes, all the cellular relationships are lost because of tissue digest and mRNA levels are averaged from all of the cells contained in the original sample (Wilcox 1993). When methods like Northern (Tralha˜o et al. 2003) or western blot analyses (Leygue et al. 2000; Nash et al. 2002; Troup et al. 2003) and more modern methods such as RT-PCR (Eshchenko et al. 2007) are used to evaluate the expression of molecules, e.g., decorin, they are usually performed with pooled samples consisting of the sectioned tumor which also contain its surrounding original stroma. Therefore, these above-mentioned methods including GeneSapiens database used in the present study are unable to tell the cellular origin of a specific molecule. Our results using ISH with DIG-labeled decorin probe have Next, we examined whether by introducing decorin, a known antitumoral molecule, to widely used MCF7 (Bur- dall et al. 2003) human breast adenocarcinoma cells, we could modulate the behavior of these cells. We showed that decorin transduction causes marked changes in the prolif- eration and growth pattern of the MCF7 cells. In particular, 123 Histochem Cell Biol (2013) 139:161–171 167 Fig. 3 Decorin gene expression is lacking in human ductal carci- noma in situ tumor (DCIS). IHC and ISH of serial sections of a representative DCIS GII sample. Tumor tissue in the sections is indicated by an asterisk. a, d HE staining. b, e Immunostaining for p63. Brown color indicates p63 positive myoepithelial cells lining the tumor mass. c, f ISH for decorin. Positive DIG-reaction in ISH indicating the cells expressing decorin mRNA can be seen in purple. Arrows (d–e) indicate the border between DCIS and surrounding tissue. Arrows (f) indicate examples of decorin positive cells. a–c scale bar 100 lm, d–f scale bar 20 lm tumor mass. c, f ISH for decorin. Positive DIG-reaction in ISH indicating the cells expressing decorin mRNA can be seen in purple. Arrows (d–e) indicate the border between DCIS and surrounding tissue. Effect of adenoviral decorin transduction on MCF7 cells Arrows (f) indicate examples of decorin positive cells. a–c scale bar 100 lm, d–f scale bar 20 lm Fig. 3 Decorin gene expression is lacking in human ductal carci- noma in situ tumor (DCIS). IHC and ISH of serial sections of a representative DCIS GII sample. Tumor tissue in the sections is indicated by an asterisk. a, d HE staining. b, e Immunostaining for p63. Brown color indicates p63 positive myoepithelial cells lining the (Winnemo¨ller et al. 1992). It is also possible that altera- tions in the expression of metalloproteinases (MMPs) and their inhibitors (TIMPs) by MCF7 cells are responsible for the observed decreased cell cohesion. Indeed, adenovirus- mediated overexpression of decorin has been shown to modulate the expression of certain MMPs and TIMPs by human gingival fibroblasts (Al Haj Zen et al. 2003). Fur- thermore, the possibility that the decreased cell cohesion of MCF7 cells in response to decorin transduction is mediated via direct interactions between decorin and certain inte- grins remains to be explored (Guidetti et al. 2002). The decreased proliferation of decorin-transduced MCF7 cells, on the other hand, is most likely mediated via decorin’s ability to antagonize receptor tyrosine kinases, particularly the signaling through epidermal growth factor receptor (Hu et al. 2009), the receptor for hepatocyte growth factor called Met (Goldoni et al. 2009), insulin-like growth factor receptor (Iozzo et al. 2011) and/or vascular endothelial growth factor 2 receptor (Khan et al. 2011). In addition, induction of apoptotic features of MCF7 cells due to decorin transduction may also have a role in the finding of this study that decorin-transduced MCF7 human breast cancer cells exhibit decreased proliferation. Interestingly, (Winnemo¨ller et al. 1992). It is also possible that altera- tions in the expression of metalloproteinases (MMPs) and their inhibitors (TIMPs) by MCF7 cells are responsible for the observed decreased cell cohesion. Indeed, adenovirus- mediated overexpression of decorin has been shown to modulate the expression of certain MMPs and TIMPs by human gingival fibroblasts (Al Haj Zen et al. 2003). Fur- thermore, the possibility that the decreased cell cohesion of MCF7 cells in response to decorin transduction is mediated via direct interactions between decorin and certain inte- grins remains to be explored (Guidetti et al. 2002). Effect of adenoviral decorin transduction on MCF7 cells In conclusion, by utilizing ISH with DIG-labeled probes for decorin, we have shown that in human breast cancer, the cancer cells do not express decorin mRNA, but the expression of decorin takes place merely in cells of the original stroma both in healthy human breast tissue and in breast tissues containing benign or malignant breast Fig. 4 Cells of invasive ductal cancer (IDC) of human breast are negative for decorin mRNA. a ISH of an infiltrating ductal breast carcinoma GIII tissue sample. b Magnified illustration of the boxed region shown in (a). Positive DIG-reaction of stromal cells in ISH indicating the localization of decorin mRNA can be seen in purple. Asterisks in (b) indicate areas of infiltrating cancer cells that are negative for decorin gene expression. Note that all decorin mRNA within invasive cancer tissue sample is detected in the original stromal cells, not in the cancer cells. a scale bar 100 lm, b scale bar 50 lm Fig. 5 Invasive mucinous carcinoma cells of human breast lack decorin gene expression. a ISH for decorin of a representative invasive mucinous breast cancer tissue sample. b Magnified illustra- tion of the boxed region shown in (a). Positive DIG-reaction in ISH indicating decorin expressing cells can be seen in purple. Asterisks in (b) indicate areas of invasive cancer cells. Note that these areas do not express decorin mRNA and all detected decorin mRNA is located in the original stromal cells. a scale bar 100 lm, b scale bar 50 lm 168 Histochem Cell Biol (2013) 139:161–171 Fig. 5 Invasive mucinous carcinoma cells of human breast lack decorin gene expression. a ISH for decorin of a representative Fig. 4 Cells of invasive ductal cancer (IDC) of human breast are negative for decorin mRNA. a ISH of an infiltrating ductal breast carcinoma GIII tissue sample. b Magnified illustration of the boxed region shown in (a). Positive DIG-reaction of stromal cells in ISH indicating the localization of decorin mRNA can be seen in purple. Asterisks in (b) indicate areas of infiltrating cancer cells that are negative for decorin gene expression. Note that all decorin mRNA within invasive cancer tissue sample is detected in the original stromal cells, not in the cancer cells. a scale bar 100 lm, b scale bar 50 lm Fig. 5 Invasive mucinous carcinoma cells of human breast lack decorin gene expression. Effect of adenoviral decorin transduction on MCF7 cells The decreased proliferation of decorin-transduced MCF7 cells, on the other hand, is most likely mediated via decorin’s ability to antagonize receptor tyrosine kinases, particularly the signaling through epidermal growth factor receptor (Hu et al. 2009), the receptor for hepatocyte growth factor called Met (Goldoni et al. 2009), insulin-like growth factor receptor (Iozzo et al. 2011) and/or vascular endothelial growth factor 2 receptor (Khan et al. 2011). In addition, induction of apoptotic features of MCF7 cells due to decorin transduction may also have a role in the finding of this study that decorin-transduced MCF7 human breast cancer cells exhibit decreased proliferation. Interestingly, compared to control MCF7 cells, decorin-transduced MCF7 cells exhibited statistically significantly lower mitosis rate, and they also revealed increased apoptotic features such as the formation of the so-called cannibal cells. Earlier, it has been shown in mice that decorin gene delivery decreases the proliferative index (Pucci-Minafra et al. 2008) and alters the architecture and differentiation of the tumor xenografts, thereby retarding the growth of colon and squamous cell carcinomas (Reed et al. 2002). Using an animal model of orthotopic breast carcinoma, decorin has also been shown to slow mammary carcinoma cell motility, induce significant apoptosis and impede cell invasion through a three-dimensional extracellular matrix (Goldoni et al. 2008). The mechanism(s) of action of decorin transduction on the behavior of MCF7 human breast cancer cells was not in our focus in this study and therefore remains to be explored. However, the observed decreased cell cohesion of MCF7 cells in response to decorin transduction could be caused by modulated pericellular matrix around the cells, because previously decorin has been shown to influence cellular adhesion via its capability to interact e.g., with fibronectin (Winnemo¨ller et al. 1991) and thrombospondin 12 3 3 Histochem Cell Biol (2013) 139:161–171 168 exogenous decorin core protein has been shown to inhibit cancer growth by triggering apoptosis via activation of caspase-3 (Seidler et al. 2006). Finally, decorin’s ability to bind and block transforming growth factor-b should be kept in mind (Yamaguchi et al. 1990), although trans- forming growth factors have been shown not to act as major growth regulators of MCF7 cells (Herman and Katzenellenbogen 1994). Effect of adenoviral decorin transduction on MCF7 cells a, b scale bar 50 lm, c scale bar 10 lm, **p \ 0.001, Student’s t test Histochem Cell Biol (2013) 139:161–171 169 t c Magnified illustration of cannibal cells from figure (a). Arrows indicate the presence of cannibal cells after Ad-Dcn transduction of MCF7 cells. d Number of observed mitoses per 100 cells, 2 days after in vitro incubation with Ad vectors. a, b scale bar 50 lm, c scale bar 10 lm, **p \ 0.001, Student’s t test Fig. 6 Decorin gene transduction mediated by a recombinant adenovirus has a significant effect on the growth pattern and proliferation of MCF7 cells. HE staining of MCF7 cell cultures transduced with human decorin cDNA-containing adenovirus (Ad- Dcn) (a) and lacZ gene-contaning adenovirus (Ad-LacZ) (b). c Magnified illustration of cannibal cells from figure (a). Arrows indicate the presence of cannibal cells after Ad-Dcn transduction of MCF7 cells. d Number of observed mitoses per 100 cells, 2 days after in vitro incubation with Ad vectors. a, b scale bar 50 lm, c scale bar 10 lm, **p \ 0.001, Student’s t test the early stages of this study. Financially, this study was supported by Medical Research Fund (EVO) of Turku University Hospital, Cancer Foundation of South-Western Finland, and by grant from the Finnish Breast Cancer Group. epithelial tumors. By introducing a decorin producing adenoviral vector to the MCF7 human breast adenocarci- noma cells, we have also shown that decorin transduction in these decorin-negative cells results in marked changes in their behavior. Specifically, we have shown that decorin- transduced MCF7 cells exhibit decreased cell cohesion and statistically significantly lower mitosis rate and increased apoptotic features. Thus, our study provides evidence that targeted decorin transduction to breast cancer cells could be used as a novel adjuvant therapy in the treatment of human breast cancer in the future. Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, dis- tribution, and reproduction in any medium, provided the original author(s) and the source are credited. Al Haj Zen A, Lafont A, Durand E et al (2003) Effect of adenovirus- mediated overexpression of decorin on metalloproteinases, tissue inhibitors of metalloproteinases and cytokines secretion by human gingival fibroblasts. Matrix Biol 22:251–258 Effect of adenoviral decorin transduction on MCF7 cells a ISH for decorin of a representative invasive mucinous breast cancer tissue sample. b Magnified illustra- tion of the boxed region shown in (a). Positive DIG-reaction in ISH indicating decorin expressing cells can be seen in purple. Asterisks in (b) indicate areas of invasive cancer cells. Note that these areas do not express decorin mRNA and all detected decorin mRNA is located in the original stromal cells. a scale bar 100 lm, b scale bar 50 lm Fig. 5 Invasive mucinous carcinoma cells of human breast lack decorin gene expression. a ISH for decorin of a representative invasive mucinous breast cancer tissue sample. b Magnified illustra- tion of the boxed region shown in (a). Positive DIG-reaction in ISH indicating decorin expressing cells can be seen in purple. Asterisks in (b) indicate areas of invasive cancer cells. Note that these areas do not express decorin mRNA and all detected decorin mRNA is located in the original stromal cells. a scale bar 100 lm, b scale bar 50 lm exogenous decorin core protein has been shown to inhibit cancer growth by triggering apoptosis via activation of caspase-3 (Seidler et al. 2006). Finally, decorin’s ability to bind and block transforming growth factor-b should be kept in mind (Yamaguchi et al. 1990), although trans- forming growth factors have been shown not to act as major growth regulators of MCF7 cells (Herman and Katzenellenbogen 1994). In conclusion, by utilizing ISH with DIG-labeled probes for decorin, we have shown that in human breast cancer, the cancer cells do not express decorin mRNA, but the expression of decorin takes place merely in cells of the original stroma both in healthy human breast tissue and in breast tissues containing benign or malignant breast 123 169 Histochem Cell Biol (2013) 139:161–171 Fig. 6 Decorin gene transduction mediated by a recombinant adenovirus has a significant effect on the growth pattern and proliferation of MCF7 cells. HE staining of MCF7 cell cultures transduced with human decorin cDNA-containing adenovirus (Ad- Dcn) (a) and lacZ gene-contaning adenovirus (Ad-LacZ) (b). c Magnified illustration of cannibal cells from figure (a). Arrows indicate the presence of cannibal cells after Ad-Dcn transduction of MCF7 cells. d Number of observed mitoses per 100 cells, 2 days after in vitro incubation with Ad vectors. References Acknowledgments The authors are grateful to Ms. Minnamaija Lintunen, PhD, for the validation of the immunohistochemical sta- inings. The expert technical assistance of Ms. Sinikka Kollanus is gratefully acknowledged. Ms. Henriikka Saloma¨ki, MSc, is also gratefully acknowledged for her excellent technical assistance during Al Haj Zen A, Lafont A, Durand E et al (2003) Effect of adenovirus- mediated overexpression of decorin on metalloproteinases, tissue inhibitors of metalloproteinases and cytokines secretion by human gingival fibroblasts. 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Breast Cancer Res 5:89–95 Iozzo RV, Buraschi S, Genua M et al (2011) Decorin anatagonizes IGF-IR function by interfering with IGF-IR activity and attenuating downstream signaling. References J Biol Chem 286:34712– 34721 Cawthorn TR, Moreno JC, Dharsee M et al (2012) Proteomic Analyses reveal high expression of decorin and endoplasmin (HSP90B1) are associated with breast cancer metastasis and decreased survival. PLoS One 7:e30992 Ja¨rvela¨inen H, Sainio A, Koulu M et al (2009) Extracellular matrix molecules: potential targets in pharmacotherapy. Pharmacol Rev 61:198–223 Daley WP, Peters SB, Larsen M (2008) Extracellular matrix dynamics in development and regenerative medicine. J Cell Sci 121: 255–264 Khan GA, Girish GV, Lala N et al (2011) Decorin is a novel VEGFR- 2-binding antagonist for the human extravillous trophoblast. 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Partial trisomy 21 map: Ten cases further supporting the highly restricted Down syndrome critical region (HR‐DSCR) on human chromosome 21
Molecular genetics & genomic medicine
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O R I G I N A L A R T I C L E O R I G I N A L A R T I C L E © 2019 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals, Inc. Correspondence Correspondence Allison Piovesan, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, via Belmeloro 8, 40126 Bologna (BO), Italy. Email: allison.piovesan2@unibo.it Abstract Background: Down syndrome (DS) is characterized by the presence of an extra full or partial human chromosome 21 (Hsa21). An invaluable model to define geno- type‐phenotype correlations in DS is the study of the extremely rare cases of partial (segmental) trisomy 21 (PT21), the duplication of only a delimited region of Hsa21 associated or not to DS. A systematic retrospective reanalysis of 125 PT21 cases described up to 2015 allowed the creation of the most comprehensive PT21 map and the identification of a 34‐kb highly restricted DS critical region (HR‐DSCR) as the minimal region whose duplication is shared by all PT21 subjects diagnosed with DS. We reanalyzed at higher resolution three cases previously published and we accu- rately searched for any new PT21 reports in order to verify whether HR‐DSCR limits could prospectively be confirmed and possibly refined. This is an open access article under the terms of the Creat​ive Commo​ns Attri​bution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2019 Th A h M l l G i & G i M di i bli h d b Wil P i di l I Received: 15 October 2018  |  Accepted: 22 May 2019 DOI: 10.1002/mgg3.797 Received: 15 October 2018  |  Accepted: 22 May 2019 DOI: 10.1002/mgg3.797 Received: 15 October 2018  |  Accepted: 22 May 2019 Maria Chiara Pelleri1  | Elena Cicchini1  | Michael B. Petersen2,3  | Lisbeth Tranebjærg4,5  | Teresa Mattina6  | Pamela Magini7  | Francesca Antonaros1  | Maria Caracausi1  | Lorenza Vitale1  | Chiara Locatelli8  | Marco Seri9  | Pierluigi Strippoli1  | Allison Piovesan1   | Guido Cocchi10 Maria Chiara Pelleri1  | Elena Cicchini1  | Michael B. Petersen2,3  | Lisbeth Tranebjærg4,5  | Teresa Mattina6  | Pamela Magini7  | Francesca Antonaros1  | Maria Caracausi1  | Lorenza Vitale1  | Chiara Locatelli8  | Marco Seri9  | Pierluigi Strippoli1  | Allison Piovesan1   | Guido Cocchi10 Maria Chiara Pelleri1  | Elena Cicchini1  | Michael B. Petersen2,3  | Lisbeth Tranebjærg4,5  | Teresa Mattina6  | Pamela Magini7  | Francesca Antonaros1  | Maria Caracausi1  | Lorenza Vitale1  | Chiara Locatelli8  | Marco Seri9  | Pierluigi Strippoli1  | Allison Piovesan1   | Guido Cocchi10 1Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna (BO), Italy Bologna (BO), Italy 2Department of Genetics, Aalborg University Hospital, Aalborg, Denmark 3Department of Clinical Genetics, Aalborg University, Aalborg, Denmark 4Department of Clinical Genetics/Rigshospitalet, The Kennedy Centre, Glostrup, Denmark 5University of Copenhagen, Institute of Clinical Medicine, The Panum Institute, Copenhagen N, Denmark 6Department of Pediatrics, Medical Genetics University of Catania, Italy 7Medical Genetics Unit, St. Orsola‐Malpighi Polyclinic, Bologna (BO), Italy 8Neonatology Unit, St. Orsola‐Malpighi Polyclinic, Bologna (BO), Italy 9Medical Genetics Unit, Department of Medical and Surgical Sciences (DIMEC), St. Orsola‐Malpighi Polyclinic, University of Bologna, Bologna (BO), Italy 10Neonatology Unit, Department of Medical and Surgical Sciences (DIMEC), St. Orsola‐Malpighi Polyclinic, University of Bologna, Bologna (BO), Italy rms of the Creat​ive Commo​ns Attri​bution License, which permits use, distribution and reproduction in any medium, provided the original 1  |  INTRODUCTION Following multiple case reports of individuals with PT21 in the 70s–90s, the concept of "Down syndrome critical re- gion" (DSCR) arose, with different grades of support from different authors (reviewed in (Pelleri et al. (2016)). Systematic attempts were then published in 2009 to identify "critical re- gions" on Hsa21 for several distinct phenotypes observed in DS, exploiting the availability of a larger number of cases (Korbel et al., 2009; Lyle et al., 2009). We have recently pro- posed a systematic reanalysis of all described PT21 cases (from 1973 to 2015) by building an integrated, comparative map of 125 cases with or without DS fulfilling stringent cyto- genetic and clinical criteria (Pelleri et al., 2016). An innova- tion was also the use of the diagnosis of DS as the phenotype to be mapped, thus focusing on the Hsa21 minimal duplicated region shared by all the subjects diagnosed with DS, whose most constant features are ID and some facial phenotypes, that is oblique eyes and flat nasal bridge. The thorough re- analysis and comparison of the data available over several de- cades required the correction and update of cytogenetic band boundaries as well as of relative order and exact position of many genomic markers, integration of analyses subsequently performed in the course of years on the same identifiable subjects even if reported by different authors, corrections of incongruencies in clinical classification or cytogenetic characterization, and removal of cases with any residual un- certainty in the presentation of data. This approach finally allowed the inclusion or exclusion of fine Hsa21 sequence intervals as candidates for DS, also integrating duplication copy number variants (CNVs) data. The main result was the identification of a highly restricted DSCR (HR‐DSCR) of only 34 kilobases (kb) on distal 21q22.13 as the minimal region whose duplication is shared by all DS subjects and is absent in all non‐DS subjects, containing no known gene and with relevant homology only to the chimpanzee genome (Pelleri et al., 2016). In 1959 Lejeune, Gautier, and Turpin showed that human chromosome 21 (Hsa21) is present in an extra copy (tri- somy 21) in the cells of subjects with Down syndrome (DS, OMIM #190685) (Lejeune, Gauthier, & Turpin, 1959), the most common constitutional form of intellectual disability (ID) (Gardiner et al., 2010; Menghini, Costanzo, & Vicari, 2011; Tolksdorf & Wiedemann, 1981). K E Y W O R D S computational biology, Down syndrome, highly restricted Down syndrome critical region, human chromosome 21, intellectual disability, partial trisomy 21 Radius S.r.l.—Technology for life (www. radiu​stech.it). Radius S.r.l.—Technology for life (www. radiu​stech.it). Results: The PT21 map now integrates fine structure of Hsa21 sequence intervals of 132 subjects onto a common framework fully consistent with the presence of a duplicated HR‐DSCR, on distal 21q22.13 sub‐band, only in DS subjects and not in non‐DS individuals. No documented exception to the HR‐DSCR model was found. Conclusions: The findings presented here further support the association of the HR‐ DSCR with the diagnosis of DS, representing an unbiased validation of the original model. Further studies are needed to identify and characterize genetic determinants presumably located in the HR‐DSCR and functionally associated to the critical mani- festations of DS. Funding information Funding information MCP's fellowship has been co‐funded by a donation from Fondazione Umano Progresso, Milano, Italy and by donations following the international fundraising initiative by Vittoria Aiello and Massimiliano Albanese. The fellowship for EC has been funded by Centro Universitario Cattolico, Italy. The fellowship for FA has been funded by Illumia S.p.A. (Bologna, Italy). The fellowships for MC and AP have been funded by the Fondazione Umano Progresso, Matteo and Elisa Mele and Methods: Hsa21 partial duplications of three PT21 subjects were refined by adding array‐based comparative genomic hybridization data. Seven newly described PT21 cases fulfilling stringent cytogenetic and clinical criteria have been incorporated into the PT21 integrated map. |  1 of 14 wileyonlinelibrary.com/journal/mgg3 Mol Genet Genomic Med. 2019;7:e797. https://doi.org/10.1002/mgg3.797 2 of 14 PELLERI et al. 1  |  INTRODUCTION Although Hsa21 has the smallest number of genes among the human autosomal chromosomes (Piovesan, Caracausi, Antonaros, Pelleri, & Vitale, 2016), it has been difficult to link the function of spe- cific Hsa21 genes to distinct phenotypic features of subjects with DS, whose more constant manifestations are a typical facies (oblique eyes, flat nasal bridge) and ID, together with other variable signs and symptoms (Epstein, 1989; Gardiner et al., 2010; Hickey, Hickey, & Summar, 2012; Letourneau & Antonarakis, 2012; Megarbane et al., 2009; Roizen & Patterson, 2003; Strippoli et al., 2013). An invaluable model for linking genotype and phenotype in DS is the study of the extremely rare cases of partial (seg- mental) trisomy 21 (PT21), the duplication of only a delim- ited segment of Hsa21 associated or not to DS. PT21 was first reported by Ilbery and coll. (Ilbery, Lee, & Winn, 1961) as "incomplete trisomy" and has been widely studied by meth- ods with an increasing power of resolution in order to estab- lish correlations between the gene content of the duplicated segment and the associated signs and symptoms (reviewed in (Pelleri et al., 2016)). These studies have strongly supported the concept that not all Hsa21 loci are required for the mani- festation of DS, as anticipated by Lejeune who hypothesized the presence of a few "culprits among so many innocents" on Hsa21 because if most of the genes would produce harm when in triplicate, "trisomic children would not survive at all. Few of the accelerated reactions are dangerous" (Lejeune, 1990). 3 of 14 PELLERI et al. TABLE 1  Summarized data about partial trisomy 21 cases mapped here. Cases 1–3 were reanalyzed here, cases 4 and 7–10 were newly described and reviewed here, cases 5 and 6 were the two additionally retrieved cases. Sex and age: as in the first report about the subject; M: male; F: female. Map ID here: identification numbers as reported in Tables S1 and S2 Case no. Subject Diagnosis Sex Age Karyotype Method Country Reference Map ID in Pelleri et al. (2016) Map ID here 1 MP01 DS M 6.5 yrs 46,XY,dup(21)(q22.1‐‐>qter) de novo Banding Southern Blot Array‐CGH (here) Denmark McCormick et al. (1989), Petersen et al. (1990) #043 #044 2 MP03 Non‐DS F 25 yrs 46,XX,dup(21)(q11.2‐‐>q21.2) pat de novo Banding Southern Blot Array‐CGH (here) Denmark McCormick et al. (1989), Petersen et al. When a similar systematic approach has been applied to congenital heart disease (CHD) in subjects with DS, a more distal region has been shown to be associated to CHD in DS, possibly with different limits according to the specific type of CHD, in the context of a multifactorial model (Pelleri et al., 2017). These findings further support the specificity of the results previously obtained for the HR‐DSCR that appears to be more proximal, well‐delimited, and monofactorial in its association to the diagnosis of DS. in the previous map. These three reanalyzed cases are num- bered here from 1 to 3 (Table 1); the correspondence with previous map identifiers ("Map ID" in (Pelleri et al., 2016)) and with updated map identification numbers ("Map ID here") is reported in Table 1. Array–based comparative genomic hybridization (array‐ CGH) analysis was performed on DNA from three patients by using two different Agilent Technologies platforms (Agilent Technologies, Santa Clara, CA), following the manufacturer's protocol: SurePrint G3 Unrestricted CGH ISCA v2, with an average resolution of 60 kb, for MP01 and MP03 (cases 1 and 2, Table 1), and Human Genome CGH 60k Oligo Microarray Kit, with a median spatial res- olution of 41.5 Kb, for proband case number 3 (Table 1). A graphical visualization of the results was provided by the Genomic Workbench software v.7.0 for the three patients and aberrations were called by the ADM1 algorithm with threshold at 6.0. Further studies are needed to confirm that HR‐DSCR is really functionally associated to the critical manifestations of DS, and in particular to ID. While research is in progress to identify functioning loci still unknown but possibly pres- ent in the HR‐DSCR, it is also fundamental to continue the study of any new cases of PT21 and to refine the limits of the trisomic Hsa21 portions in cases already studied at low resolution. The confirmation that there is no documented exception to the HR‐DSCR model would further encourage molecular studies in this small segment of Hsa21 as well as high resolution analysis to investigate some very interesting cases reported in 90s: they are five phenocopies (people with DS phenotype and no evidence of cytogenetic/molecular alteration) (Ahlbom et al., 1996; Anneren & Edman, 1993; McCormick et al., 1989) and the opposite condition of appar- ent full trisomy 21 without DS phenotype (Avramopoulos et al., 1997). No marker through high resolution techniques was analyzed within the HR‐DSCR, therefore the possibility that a very small Hsa21 region might be involved in the expres- sion of basic DS features cannot be excluded. 2.2  |  Bibliographic searches and case selection We accurately searched for any reports of PT21 to integrate the new data in the previous PT21 map. Bibliographic searches performed to build the starting map (Pelleri et al., 2016) were repeated in order to identify newly reported cases of PT21. "Mirror duplication chromosome 21" was used as additional PubMed query on the National Center for Biotechnology Information (NCBI) site (https​:// www.ncbi.nlm.nih.gov/pubme​d/) and references cited in turn in the retrieved reports were examined. In addition, a search for "partial trisomy 21" through Google web search engine (https​://www.google.com/) was performed. Due to the rarity of these particular cases as well as of PT21 cases, an international collaborative effort would be de- sirable in order to perform cutting‐edge analysis and collect new data. Only new PT21 subjects with sufficient and unambiguous descriptions at the cytogenetic, molecular, and clinical levels were included in the study, following inclusion and exclu- sion criteria as previously described in detail (Pelleri et al., 2016). Briefly, the main cytogenetic inclusion criterion was the presence of a 21q partial duplication, excluding from the analysis cases presenting translocations and ring Hsa21 with a complete 21q, tetrasomies of Hsa21, mosaic trisomy 21, chromosomal rearrangements involving the X chromosome, and chromosomal alterations described in leukemic cell clones. For the molecular analysis criteria, the condition was a detailed and unambiguous description of the duplicated seg- ment boundaries. At the clinical level, subjects were classi- fied as "DS" or "non‐DS" according to the following criteria: (a) explicit statements found in the study; (b) whether authors judged recognizable DS as present or absent, irrespectively of other symptoms or signs associated to possibly concur- rent aneuploidies of non‐Hsa21 chromosomal segments; (c) assessment of detailed phenotype description when present in the article. In this light, the aim of this study was to reanalyze at higher resolution three cases already included in the PT21 integrated map in order to verify whether this analysis could help in confirming and refining the limits of the HR‐DSCR. In addition, we accurately searched for any new reports of PT21 subsequent to the original study to integrate the new data in the existing PT21 map searching again for confirma- tion or rejection of the original model. This second approach is of particular relevance because, being a prospective study started after the first description of HR‐DSCR, it represents an unbiased validation of the original model that could also be performed in the future. 1  |  INTRODUCTION (1990) #045 #046 3 Proband Non‐DS F 1 yr 47,XX,+der(21),t(9;21) (34.1;q22.1)mat Banding FISH Array‐CGH (here) Italy Mattina et al. (1997) #076 #077 4 B.B. DS M 6 yrs t(15;21) Banding Array‐CHG Alabama (US) Finley et al. (1965), Hamm et al. (2015) — #002 5 Proband DS M 5 yrs 46,XY, idic(21)(q22.3) FISH India Sheth et al. (2007) — #105 6 Patient DS F 2 yrs 46,XX, psu idic(21) (q22.3) Banding FISH Japan Egashira et al. (2008) — #108 7 Proband DS M 2 mos 46,XY,der20t(20,21) (21qter‐>21q22::20p13‐>21qter) Banding FISH Array‐CGH Poland Biaduń‐Popławska et al. (2014) — #127 8 Patient Non‐DS F 5 yrs 46,XX, dup21q22.11(chr21:32,583,901‐ 35,355,969;hg19) Array‐CGH Colorado (US) Weisfeld‐Adams et al. (2016) — #130 9 Case 1 Non‐DS F 2 yrs 46,XX, dup(21) q22.2q22.3 Banding Array‐CGH Taiwan Su et al. (2016) — #131 10 Case 2 Non‐DS F 14 mos 46, XX, dup(21)q11.2q21 Banding Array‐CGH Taiwan Su et al. (2016) — #132 4 of 14 PELLERI et al. 2.4 We revised and updated all the sequence features of Hsa21 reported to build the starting map (Pelleri et al., 2016) (here Table S1): known Hsa21 genes, coordinates for single nu- cleotide polymorphisms (SNPs), sequence‐tagged sites, bacterial artificial chromosome clones, nucleotide posi- tions determined by array‐CGH as limits of altered regions in individual subjects and cytogenetic band limits. All the genomic coordinates refer to the current Genome Reference Consortium (GRC) human genome assembly GRCh38, or hg38 (December 2013). ( ) The third reanalyzed case (case 3 in Table 1) was first reported in 1997 (Mattina et al., 1997) and we present clini- cal data from the follow‐up of the patient here. The proband is the only child of nonconsanguineous parents, born at the 40th week of gestation with eutocic delivery after an un- complicated pregnancy; low‐risk triple test; birth weight was 3,020 g. The child was admitted to hospital for the first time at birth due to neonatal asphyxia and dysmorphic signs. The traditional karyotype through fluorescence in situ hybridiza- tion (FISH) was: 47, XX, +der21, t(9;21), but the patient was recognized as affected by a chromosomal syndrome due to a double partial trisomy 9q34.1‐>qter, 21pter‐>21q22.11. She was repeatedly admitted to the polyclinic due to frequent bronchopneumonic episodes and apnea crises. She is cur- rently followed by annual follow‐up at the Medical Genetics Clinic. In agreement with the parents, clinical controls are carried out only within the limits of the "availability" of the girl. The girl shows a clinical picture with characteristics in agreement with partial trisomy 9q. Apparently, there are no clinical signs attributable to partial trisomy 21. Dysmorphic signs include brachycephaly, small anteverted ears with sim- ple pavillon, straight forehead, divergent strabismus, propto- sis, beak nose deviated to the left with narrow bridge, short philtrum, and "carp" mouth with thin lips. Prognathism, long and thin arms, hands and feet with arachnodactyly, and bi- lateral patella dislocation were also observed. Congenital malformations involved the heart (ventricular sept defect), brain (hypoplasia of the corpus callosum and subarachnoid space dilation), eyes (proptosis, nystagmus, divergent stra- bismus, pupil optic nerve pallor and hypoplasia, the patient underwent surgery to correct ectopia of crystalline lens and cataracts developed over years), skeleton (additional thoracic metameres with corresponding costal segments) and kidneys (hypoplasia‐dysplasia of the left kidney). 2.4 During neonatal period and the first year of life, the patient did not thermo- regulate and showed significant apnea crises, serious psychic In summary, each spreadsheet row corresponds to a spe- cific and relevant sequence feature on Hsa21 for a total of 724 sequence intervals (rows), providing anchor points useful to homogeneously map each cytogenetic feature described in the reports of PT21. 2.3 Descriptions of seven cases (summary in Table 1, cases 4–10) retrieved by the new bibliographic search performed and mapped here have been reported in detail in the respec- tive reports (Biaduń‐Popławska et al., 2014; Egashira et al., 2008; Finley, Finley, Rosecrans, & Phillips, 1965; Hamm, Carroll, Mikhail, Korf, & Finley, 2015; Sheth et al., 2007; Su et al., 2016; Weisfeld‐Adams, Tkachuk, Maclean, Meeks, & Scott, 2016). Main clinical data of the reanalyzed or reviewed cases are summarized in Table 1. Briefly, the first two reanalyzed cases were subjects MP01 and MP03 (cases 1 and 2, Table 1). They were firstly reported in 1989 (McCormick et al., 1989) and 1990 (Petersen et al., 1990). According to the checklist of Jackson et al. (Jackson, North, & Thomas, 1976), a pheno- typic score consistent with the clinical diagnosis of DS was reported for patient MP01, while patient MP03's pheno- typic score is below the threshold for the clinical diagnosis of DS (Petersen et al., 1990). 2.1  |  Molecular cytogenetic characterization 2.1  |  Molecular cytogenetic characterization 2.1  |  Molecular cytogenetic characterization In order to update the PT21 map (125 PT21 cases with or without DS) previously published (Pelleri et al., 2016), we reanalyzed at higher resolution three cases already included In order to update the PT21 map (125 PT21 cases with or without DS) previously published (Pelleri et al., 2016), we reanalyzed at higher resolution three cases already included 5 of 14 PELLERI et al. The cases thus retrieved were numbered starting from 4 to 10 following chronological order of first description in literature. and motor deficits, muscle hypotonia and hypotrophy, and afinalistic and uncoordinated hand movements. She pro- nounces "mom" and "dad", does not deambulate. Menarche was reported in September, 2009; irregular menstrual cycle. She presents with hand tremor. 2.5 For each subject studied, a column on the map file built as explained above was added, representing the structure of his/ her Hsa21. Each row represents a specific sequence inter- val on Hsa21. Starting from the 125 PT21 cases previously described (Pelleri et al., 2016), we added refined limits of the duplicated portion for cases 1–3 to the map and mapped the additionally retrieved cases found with additional biblio- graphic searches performed here (Table 1, cases 4–10). Each row represents a specific sequence interval on Hsa21 and for each subject with DS the corresponding cell was col- ored following this code: red = trisomic, therefore possible candidate as causing DS; green = disomic, therefore excluded as causing DS; blue = monosomic, considered as "not dupli- cated", therefore excluded as candidate; white = information not available with certainty. A complementary reasoning was used to color the cells representing sequence intervals when the subject presented cytogenetically with a segmental trisomy 21 in absence of a typical DS picture. In particular: red = disomic in non‐DS, therefore not excluded as causing 6 of 14 PELLERI et al. DS; green = trisomic in non‐DS, therefore excluded as caus- ing DS; blue = monosomic, considered as "not duplicated", therefore indirectly not excluded as candidate; white = in- formation not available with certainty. Headings of non‐DS cases are highlighted in yellow. 2.6  |  Scoring system Using "mirror duplication chromosome 21" as additional PubMed query (Pelleri et al., 2016) and examining references cited in turn in the retrieved reports led to the retrieval of two additional PT21 cases (Egashira et al., 2008; Sheth et al., 2007) to be included here according to selection criteria detailed above (Table 1, cases 5 and 6). A score was assigned to each interval sequence substantially following the scoring system applied by Lyle and coll. (Lyle et al., 2009), but attributing a lower score to not excluded regions in non‐DS subjects due to the fact that these regions would only be candidate regions indirectly. A score of +1 was assigned to each trisomic (candidate) sequence interval in DS subjects, while +0.5 was assigned to disomic (not excluded) intervals in non‐DS subjects. A score of −1 was assigned to each sequence interval that was ex- cluded as candidate for DS, being disomic in DS or trisomic in non‐DS subjects. Monosomic regions are considered as "not duplicated", therefore they should be excluded as candi- dates in DS subjects (score = −1) and indirectly not excluded in non‐DS (score = +0.5). For each sequence interval, the algebraic sum of the scores is calculated, generating the final score for the interval. The Excel macro and the Python scripts implementing the described algorithms for the calculations of the scores and for summarizing scores along Hsa21 regular intervals, respectively, are available upon request. In addition, a search for "partial trisomy 21" through Google web search engine revealed a new described PT21 report case (Biaduń‐Popławska et al., 2014) not included in PubMed to be included according to matching selection cri- teria (Table 1, case 7) detailed above. In total, seven cases were added to the map (Table S1) following the new bibliographic search performed and inclu- sion/exclusion criteria described in Materials and Methods section. A complete list of all retrieved included and excluded reports of PT21 cases is available in the Supplementary References file. The complete description of all these PT21 cases is available in the Table S2, along with reasons for in- clusion and exclusion. Higher scores indicate increased probability of associa- tion to DS. Detailed partial and final scores for each interval are reported in Table S1 at the right of the columns represent- ing mapping for the 132 analyzed cases. 3  |  RESULTS Scores for association with DS for each sequence interval are graphed in Figure 4. Complete data for each distinct se- quence interval placed in the map are given in Table S1. 3.3 The updated integrated comparative map obtained as de- scribed in the Materials and Methods section showing the localization of segmental anomalies of Hsa21 includes a total of 132 PT21 DS or non‐DS cases. 3.2  |  Bibliographic searches Bibliographic searches performed to build the starting map (Pelleri et al., 2016) were repeated in order to identify newly reported cases of PT21, resulting in four newly described PT21 cases to be included (Table 1, cases 4 and 8–10) (Finley et al., 1965; Hamm et al., 2015; Su et al., 2016; Weisfeld‐ Adams et al., 2016). These new limits have been recorded in the Table S1. 3.1  |  Molecular cytogenetic characterization The array‐CGH analysis of DNA from patient MP01 (case 1, Map ID here #044) revealed a duplication of Hsa21 from 36,760,100 to 46,329,175 bp (GRCh38) (Figure 1). Analysis of the PT21 comparative map confirmed the ex- clusion of several regions of Hsa21 as associated to DS, in particular 21p, 21q11, and 21q21. Highest scores were found in the 21q22.13 and 21q22.2 sub‐bands (Figure 4). The 34‐kb interval from 37,929,229 to 37,963,130 previously described as the minimal region associated to DS and located on distal 21q22.13 (Pelleri et al., 2016), still has the highest scores, even when considering pure positively candidate scores not integrated with penalization/exclusion scores (Table S1). In addition, the duplication of this region is shared by all 92 DS subjects with available data about it and is absent in all 40 non‐DS subjects with available data about it, thus confirming consistency with the HR‐DSCR. The array‐CGH analysis of DNA from patient MP03 (case 2, Map ID here #046) revealed trisomy of Hsa21 from 14,112,687 to 28,015,203 bp (GRCh38) (Figure 2). The array did not allow evaluation of the Hsa21 portion upstream the proximal limit. Regarding case 3 (Map ID here #077), duplications of about 13.4 megabases (Mb) in the 9q33.3‐q34.3 chro- mosome region, of about 0.45  Mb in the 9q34.3 chromo- some region, and of about 19  Mb in the 21q11.2‐q22.11 chromosomal region have been highlighted. According to ISCN 2016 nomenclature, the alterations may be described as: arr[GRCh38] 9q33.3‐q34.3(123265569_136502696) x3, 9q34.3(137666340_138059636)x3, 21q11.2‐ q22.11(13268071_32197958)x3 (Figure 3). A concise, sample outlook of a portion of the map is de- picted in Figure 5a, showing in particular the three reana- lyzed cases (Table 1, cases 1–3; #044, #046, #077 Map ID These new limits have been recorded in the Table S1. 7 of 14 PELLERI et al. |  7 of 14 PELLERI et al. FIGURE 1  Array‐CGH analysis of DNA from patient MP01. Profile of chromosome 21 showing the duplication from 36,760,100 to 46,329,175 bases present in MP01 (reanalyzed case 1). Genomic coordinates refer to the current GRCh38 human assembly FIGURE 1  Array‐CGH analysis of DNA from patient MP01. Profile of chromosome 21 showing the duplication from 36,760,100 to 46,329,175 bases present in MP01 (reanalyzed case 1). 3.1  |  Molecular cytogenetic characterization Genomic coordinates refer to the current GRCh38 human assembly here), two additionally retrieved cases (Table 1, cases 5 and 6; #105 and #108 Map ID here), and the five newly described cases (Table 1, cases 4 and 7–10; #002, #127, #130, #131, #132 Map ID here). PT21 cases has turned into the study of distinct phenotypic features, in order to associate each of them to a specific re- gion most constantly duplicated in subjects presenting with the feature (Korbel et al., 2009; Korenberg et al., 1994; Lyle et al., 2009). This approach has certainly been successful in suggesting that specific Hsa21 subregions of various sizes are mostly associated to hypotonia (Lyle et al., 2009), to acute megakaryoblastic leukemia and transient myeloproliferative disorder (Korbel et al., 2009; Pelleri et al., 2014), and to CHD (Pelleri et al., 2017), among others. Due to high frequency of an Alzheimer‐like disease in DS and the location of the APP (amyloid beta precursor protein) gene on Hsa21, this pheno- type represents a particularly suggestive example of the use- fulness of PT21 study in defining genetic determinants for a phenotypic feature. Recently, it has been possible to confirm 4  |  DISCUSSION Over time, the concept of a "Down syndrome critical region" on Hsa21 has assumed different meanings. It was mainly criticized observing that a certain single duplicated region is not responsible for all or most DS features, that is, it is not sufficient to cause the full DS phenotype (Korbel et al., 2009; Lyle et al., 2009; Papoulidis et al., 2014). From this point of view, modeling the genotype‐phenotype correlations using 8 of 14 PELLERI et al. 8 of 14  |      PELLERI et al. FIGURE 2  Array‐CGH analysis of DNA from patient MP03. Profile of chromosome 21 showing the duplication from 14,112,687 to 28,015,203 bases present in MP03 (reanalyzed case 2). Genomic coordinates refer to the current GRCh38 human assembly FIGURE 2  Array‐CGH analysis of DNA from patient MP03. Profile of chromosome 21 showing the duplication from 14,112,687 to 28,015,203 bases present in MP03 (reanalyzed case 2). Genomic coordinates refer to the current GRCh38 human assembly observed in DS may be absent in a proportion of the subjects, even at a high extent, ID and the typical facies are virtually universal, if cases with mosaicism are excluded. The genetic marker associated to these features should be, in principle, robust as the extra copy of the whole Hsa21. Dissection of small regions allowed by the variety of breakpoints delimit- ing duplicated regions in subjects with PT21 has repeatedly pointed to 21q22 band as associated to DS. Our systematic reanalysis of cytogenetic maps from 125 subjects with PT21, integrating them under a common and updated framework, has suggested that the duplication of a small 34‐kb region on distal 21q22.13 (HR‐DSCR) is fully coherent with the diag- nosis of DS, while the disomic state of this region is consis- tent with a non‐DS phenotype (Pelleri et al., 2016). the obligatory role of APP in the clinical, biochemical, and neuropathological findings of Alzheimer‐like disease study- ing a case of PT21 with DS and without Alzheimer disease, lacking the APP duplication (Doran et al., 2017). In addition to the search for genotype‐phenotype correla- tions aimed at dissecting single phenotypes, a few features regularly present at the highest frequency in subjects with DS can be considered so that the DSCR is viewed as the re- gion which "suffices to induce the main phenotypic symp- toms of the classic syndrome of trisomy 21" (Rethore, 1981). |  9 o PELLERI et al. FIGURE 3  Array‐CGH analysis of DNA from patient #077. Profile of chromosomes 9 and 21 showing the duplication of chromosome 9 from 123,265,569 to 136,502,696 and from 137,666,340 to 138,059,636 bases and the duplication of chromosome 21 from 13,268,071 to 32,197,958 present in case #077 (reanalyzed case 3). Genomic coordinates refer to the current GRCh38 human assembly FIGURE 3  Array‐CGH analysis of DNA from patient #077. Profile of chromosomes 9 and 21 showing the duplication of chromosome 9 from 123,265,569 to 136,502,696 and from 137,666,340 to 138,059,636 bases and the duplication of chromosome 21 from 13,268,071 to 32,197,958 present in case #077 (reanalyzed case 3). Genomic coordinates refer to the current GRCh38 human assembly In this work, we have tested if the HR‐DSCR limits could be refined by reanalyzing PT21 cases already included in the integrated map, and also if this model is prospectively consis- tent with additional PT21 cases not described at the moment of building the original map. Regarding the reanalysis, we were successful in delineating duplicated regions from subjects MP01 (case 1, Map ID here #044), MP03 (case 2, Map ID here #046), and proband case number 3 (Map ID here #077), whose DNA was originally investigated by McCormick and coll. (McCormick et al., 1989), Petersen and coll. (Petersen et al., 1990), and Mattina and coll. (Mattina et al., 1997), respectively, and in this work has been subjected to array‐CGH. The array‐CGH analysis was able to clarify the breakpoints of the trisomic portions. The refinement of the limits in these reanalyzed cases was fully consistent with the previous reports and was fully consistent with the trisomic state of HR‐DSCR in the subject with DS and its disomic state in the subjects without a diagnosis of DS. FIGURE 4  Genotype–phenotype correlation in 132 cases of partial trisomy 21. The X‐axis displays the score for association with DS for each sequence interval of 50 kb, shown as median of the values assigned to each map row (Table S1) that is comprised in each interval. The Y‐axis represents the position along Hsa21 (scale in megabases, Mb) FIGURE 4  Genotype–phenotype correlation in 132 cases of partial trisomy 21. The X‐axis displays the score for association with DS for each sequence interval of 50 kb, shown as median of the values assigned to each map row (Table S1) that is comprised in each interval. 4  |  DISCUSSION Therefore, using the diagnosis of DS itself as the phenotype to be mapped, the PT21 approach should point to the "mini- mal" Hsa21 region associated to the DS core features, notably ID. Actually, while any of the long list of symptoms and signs 9 of 14 PELLERI et al. | A zoom‐in (b) of the case (#116 here and #113 in the previous study (Pelleri et al., 2016)) and the CNV (nsv1060057) strictly defining HR‐DSCR limits are shown here. Rows: Hsa21 sequence intervals (only those centered on HR‐DSCR are represented here). Red = candidate or not excluded regions; green = excluded regions. Levels of overlapping among intervals are indicated by increasingly darker violet color of the coordinates; blue italics indicate coordinates overlapping (Start or End) or nesting (Start and End) with the immediately previous interval (row). HR‐DSCR coordinates: 37,929,229–37,963,130. Complete map is available as Table S1 Interestingly, the girl with a duplication of 2.78  Mb of chromosome 21q22.11 (Table 1, case 8) (Weisfeld‐Adams et al., 2016) was considered borderline and without a clear diagnosis of DS. Regarding the two most constant features, the typical facies and the characteristic ID, the observation of the girl's picture (Figure 1 in (Weisfeld‐Adams et al., 2016): absence of oblique eyes and of gestalt recognition of the typi- cal DS facies assessed through blind, independent evaluation by the clinicians involved in this work) and the phenotypic description lead to the non‐DS classification of the patient. In addition, the author reporting the case stated that, although showing some grade of developmental delay, the patient "lacked the happy, sociable affect observed in many children with DS". These findings are consistent with the lack of HR‐ DSCR in this subject. Regarding the verification of new cases, we accurately checked for any new reports published in the last two years and thus not considered in the original PT21 map. We further found five recent detailed descriptions (Table 1, cases 4 and 7–10) and two previously described cases not included in the original PT21 map (Table 1, cases 5 and 6) fulfilling criteria for the inclusion on the PT21 integrated map. Each of them deserved a specific publication due to the extreme rarity of each of these cases. The stringent criteria that we have defined for the establishment of genotype‐phenotype correlations in this type of study (Pelleri et al., 2016) have been very use- ful to guide the analysis of these new cases. The Y‐axis represents the position along Hsa21 (scale in megabases, Mb) In this work, we have tested if the HR‐DSCR limits could be refined by reanalyzing PT21 cases already included in the integrated map, and also if this model is prospectively consis- tent with additional PT21 cases not described at the moment of building the original map. investigated by McCormick and coll. (McCormick et al., 1989), Petersen and coll. (Petersen et al., 1990), and Mattina and coll. (Mattina et al., 1997), respectively, and in this work has been subjected to array‐CGH. The array‐CGH analysis was able to clarify the breakpoints of the trisomic portions. The refinement of the limits in these reanalyzed cases was fully consistent with the previous reports and was fully consistent with the trisomic state of HR‐DSCR in the subject with DS and its disomic state in the subjects without a diagnosis of DS. Regarding the reanalysis, we were successful in delineating duplicated regions from subjects MP01 (case 1, Map ID here #044), MP03 (case 2, Map ID here #046), and proband case number 3 (Map ID here #077), whose DNA was originally 4  | 10 of 14 PELLERI et al. 10 of 14  |      PELLERI et al. 10 of 14  |      PELLERI et al. FIGURE 5  Concise outlook (a) of a portion of the partial trisomy 21 map. Each column represents the chromosome 21 structure (in megabases, Mb) of partial trisomy 21 subjects with or without Down syndrome (DS or non‐DS). For each subject the case number (n.), the updated map identifier (ID) and the corresponding previous map ID if present (Pelleri et al., 2016) are reported. The ten cases reanalyzed or reviewed here are reported together with Map ID #116 and the duplication coded as structural variant nsv1060057 which delimited the proximal and distal highly restricted DS critical region (HR‐DSCR, red continuous line) boundaries, respectively. Red boxes, candidate or not excluded regions; green boxes, excluded regions; white boxes: information not available with certainty; blue boxes, monosomic regions. A zoom‐in (b) of the case (#116 here and #113 in the previous study (Pelleri et al., 2016)) and the CNV (nsv1060057) strictly defining HR‐DSCR limits are shown here. Rows: Hsa21 sequence intervals (only those centered on HR‐DSCR are represented here). Red = candidate or not excluded regions; green = excluded regions. Levels of overlapping among intervals are indicated by increasingly darker violet color of the coordinates; blue italics indicate coordinates overlapping (Start or End) or nesting (Start and End) with the immediately previous interval (row). HR‐DSCR coordinates: 37,929,229–37,963,130. Complete map is available as Table S1 | FIGURE 5  Concise outlook (a) of a portion of the partial trisomy 21 map. Each column represents the chromosome 21 structure (in megabases, Mb) of partial trisomy 21 subjects with or without Down syndrome (DS or non‐DS). For each subject the case number (n.), the updated map identifier (ID) and the corresponding previous map ID if present (Pelleri et al., 2016) are reported. The ten cases reanalyzed or reviewed here are reported together with Map ID #116 and the duplication coded as structural variant nsv1060057 which delimited the proximal and distal highly restricted DS critical region (HR‐DSCR, red continuous line) boundaries, respectively. Red boxes, candidate or not excluded regions; green boxes, excluded regions; white boxes: information not available with certainty; blue boxes, monosomic regions. A zoom‐in (b) of the case (#116 here and #113 in the previous study (Pelleri et al., 2016)) and the CNV (nsv1060057) strictly defining HR‐DSCR limits are shown here. Rows: Hsa21 sequence intervals (only those centered on HR‐DSCR are represented here). Red = candidate or not excluded regions; green = excluded regions. Levels of overlapping among intervals are indicated by increasingly darker violet color of the coordinates; blue italics indicate coordinates overlapping (Start or End) or nesting (Start and End) with the immediately previous interval (row). HR‐DSCR coordinates: 37,929,229–37,963,130. Complete map is available as Table S1 FIGURE 5  Concise outlook (a) of a portion of the partial trisomy 21 map. Each column represents the chromosome 21 structure (in megabases, Mb) of partial trisomy 21 subjects with or without Down syndrome (DS or non‐DS). For each subject the case number (n.), the updated map identifier (ID) and the corresponding previous map ID if present (Pelleri et al., 2016) are reported. The ten cases reanalyzed or reviewed here are reported together with Map ID #116 and the duplication coded as structural variant nsv1060057 which delimited the proximal and distal highly restricted DS critical region (HR‐DSCR, red continuous line) boundaries, respectively. Red boxes, candidate or not excluded regions; green boxes, excluded regions; white boxes: information not available with certainty; blue boxes, monosomic regions. that variability both in Hsa21 (Sailani et al., 2013) or in other chromosomes (Priest et al., 2012) originating from CNVs or SNPs also contributes to both normal and DS phenotypes (Antonarakis, 2017). Moreover, the HR‐DSCR might function as a long‐range interactor with other chromosomes, although preliminary analysis of databases derived from high‐throughput chromo- some conformation capture data (Hi‐C) (Durand et al., 2016) was not able to retrieve useful results (data not shown). An interesting possibility is to generate trisomy 21 cells with the selective deletion of a single copy of the HR‐DSCR to com- pare the features of fully trisomic, HR‐DSCR deleted and normal cells to prove that the critical region is exerting some function, for example, modifying the metabolic profile that has recently been found to be specifically altered in DS by metabolome analysis (Caracausi et al., 2018). The descrip- tion of the CRISPR/Cas9 method (Bauer, Canver, & Orkin, 2015) may make the realization of such a sophisticated study model realistic (Harrison, Sanz, & Hollywood, 2016). ( , ) A relevant problem remains to be the identification and characterization of the genetic determinants presumably lo- cated in the HR‐DSCR. Gene databases, as well as accurate transcriptome maps based on the use of known probes to ob- tain gene expression profiling data for organs involved in DS phenotypes such as hippocampus (Caracausi et al., 2016) or heart (Caracausi, Piovesan, Vitale, & Pelleri, 2017) might be of limited help in the hypothesis that the genetic determinants are presently uncharacterized. It is still possible that, due to the possible extremely low size of human introns (Piovesan et al., 2015), one or more spliced transcripts originate from this small region. RNA high‐throughput sequencing (Wang, Gerstein, & Snyder, 2009) or ENCODE (Encyclopedia of DNA Elements) project (ENCODE Project Consortium, 2012) data may offer the possibility to identify novel func- tional elements; however, we have not had to date success in using them to the aim of a better characterization of the HR‐ DSCR. Other possibilities include the presence of unknown microRNA in the HR‐DSCR (Kozomara & Griffiths‐Jones, 2014), as the field of non‐coding RNA involved in DS patho- genesis has been recently explored (Karaca et al., 2017; Xu et al., 2013; Zhao, Jaber, Percy, & Lukiw, 2017) revealing the functions of several microRNA located on other Hsa21 regions with the capability to potentially regulate over 3,600 protein‐encoding genes (Alexandrov, Percy, & Lukiw, 2017; Li et al., 2012; Quinones‐Lombrana & Blanco, 2015). Therefore, while a relevant body of cytogenetic data ob- tained from the analysis of PT21 cases strongly suggests that there should be some critical elements for the pathogenesis of DS present in the distal part of the 21q22.13 sub‐band, further studies are needed for additional verification of the limits of the region in any case of PT21 reported in the future as well as for the characterization of functional loci within it. The success of these objectives might be critical to build a rational foundation for a treatment of DS ID. In conclusion, the findings presented here represent the most comprehensive study on PT21 and further support the association of the HR‐DSCR with the diagnosis of DS, rep- resenting an unbiased validation of the original model that could be performed also in the future. Further studies are needed to identify and characterize genetic determinants pre- sumably located in the HR‐DSCR and functionally associ- ated to the critical manifestations of DS. , ; Q , ) While this work was in revision, an update in the Ensembl and UCSC genome browsers actually mapped two small new exons on the KCNJ6 locus (OMIM # 600877) encoding po- tassium voltage‐gated channel subfamily J member 6, based on automated parsing of high throughput RNA sequencing (RNA‐Seq) data. Remarkably, this predicts a size extension for the KCNJ6 locus from 292,216 bp as currently reported in NCBI Gene database (coordinates 37,624,223–37,916,438 in human genome map GRCh38.p12) to 497,787  bp (37,623,559–38,121,345). This transcript allows the predic- tion of a new intron which totally encompasses HR‐DSCR and preliminary experimental data confirm the existence of this intron. Interestingly, according to RNA‐Seq Expression Data from GTEx as reported in the UCSC browser, this tran- script appears to be expressed at a high level in the brain and in the pituitary gland, in particular in the cerebellum, hip- pocampus, and cortex within the brain, regions well known for their specific alteration in DS (Stagni, Giacomini, Emili, Guidi, & Bartesaghi, 2018). While this update suggests the presence of transcribed DNA in the HR‐DSCR for the first time, further work will be necessary to characterize structure and function of this complex locus. ACKNOWLEDGMENTS As DIMES and Neonatology Unit group, we are profoundly grateful to the Fondazione Umano Progresso, Milano, Italy for their fundamental support to the research on trisomy 21 and to this study. We also wish to sincerely thank Matteo and Elisa Mele; Illumia S.p.A., Bologna, Italy; Radius S.r.l.— Technology for life (www.radiu​stech.it); the community of Dozza (Bologna, Italy): "Comitato Arzdore di Dozza", "Parrocchia di Dozza", and "Pro‐Loco di Dozza" as well as the Costa family for their support to our research. Very spe- cial thanks to the newlyweds Leonardo Costa and Camilla Casadio for the donation in occasion of their holy matrimony in Dozza. We are grateful to Kirsten Welter for her kind and expert revision of the manuscript. Correlation of the clinical data to the cytogenetic map was consistent with the notion that all the subjects lacking the duplication of the HR‐DSCR were not diagnosed with DS, although these new cases did not allow further refinement of the region because the breakpoints of the duplicated portions were not within it. Remarkably, cases 1 and 9 (Figure 5a) alone would be suffi- cient to exclude very large portions of Hsa21 as associated to the diagnosis of DS delimiting a region of about 2.8 Mb (36,760,100–39,605,955) in which the HR‐DSCR is located in the center. Taken together, all the findings presented here further support the concept that the distal part of the 21q22.13 sub‐ band is strongly associated to diagnosis of DS while other regions are not, and they were all consistent with the HR‐ DSCR model, although the limits of the reported duplications did not allow further refinement of the region or the con- firmation of its narrowest extension. It should also be noted 11 of 14 PELLERI et al. REFERENCES org/10.1111/j.1442-200X.2008.02680.x Ahlbom, B. E., Goetz, P., Korenberg, J. R., Pettersson, U., Seemanova, E., Wadelius, C., … Anneren, G. (1996). Molecular analysis of chro- mosome 21 in a patient with a phenotype of Down syndrome and ap- parently normal karyotype. American Journal of Medical Genetics, 63(4), 566–572. https​://doi.org/10.1002/(sici)1096-8628(19960​ 628)63:4<566:aid-ajmg1​0>3.0.co;2-g ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57–74. https​://doi.org/10.1038/natur​e11247 Epstein, C. J. (1989). Down syndrome, trisomy 21. Metabolic basis of inherited disease (pp. 291–326). New York, NY: McGraw‐Hill. Finley, S. C., Finley, W. H., Rosecrans, C. J., & Phillips, C. (1965). Exceptional intelligence in a Mongoloid child of a family with a 13–15/partial 21 (D/partial G) translocation. 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General Medicine: Open Access, 02(04), https​://doi. org/10.4172/2327-5146.1000149 MCP designed the study. MCP, EC, and FA collected the data, built the integrated map, and performed the analy- sis. MBP, LT, and TM obtained and interpreted clinical and molecular data for the three cases reanalyzed here. PM performed the array‐CGH analysis for two cases and inter- preted the data. GC and CL performed case selection and discussed the clinical data. MS analyzed and discussed the cytogenetic data. LV and MC performed the bibliographic data search and contributed to mapping data collection and analysis. AP developed the scoring system, the pertinent software and graphed the data. MCP, AP, and PS wrote the manuscript draft. AP and GC supervised the project. All authors contributed to the discussion of the data and to the Discussion section and read and approved the final manuscript. Caracausi, M., Ghini, V., Locatelli, C., Mericio, M., Piovesan, A., Antonaros, F., … Cocchi, G. (2018). 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Partial trisomy of chromosome 21 without the Down syndrome phenotype. Prenatal Diagnosis, 36(5), 492–495. https​:// doi.org/10.1002/pd.4796 Tolksdorf, M., & Wiedemann, H. R. (1981). Clinical aspects of Down's syndrome from infancy to adult life. In G. R. Burgio, M. Fraccaro, L. Tiepolo, & U. Wolf (Eds.), Trisomy 21 (pp. 3–32). Berlin, Germany: Springer‐Verlag. How to cite this article: Pelleri MC, Cicchini E, Petersen MB, et al. Partial trisomy 21 map: Ten cases further supporting the highly restricted Down syndrome critical region (HR‐DSCR) on human chromosome 21. Mol Genet Genomic Med. 2019;7:e797. https​://doi.org/10.1002/mgg3.797 How to cite this article: Pelleri MC, Cicchini E, Petersen MB, et al. Partial trisomy 21 map: Ten cases further supporting the highly restricted Down syndrome critical region (HR‐DSCR) on human chromosome 21. Mol Genet Genomic Med. 2019;7:e797. https​://doi.org/10.1002/mgg3.797 Wang, Z., Gerstein, M., & Snyder, M. (2009). RNA‐Seq: A revolution- ary tool for transcriptomics. Nature Reviews Genetics, 10(1), 57–63. https​://doi.org/10.1038/nrg2484 Weisfeld‐Adams, J. D., Tkachuk, A. K., Maclean, K. N., Meeks, N. L., & Scott, S. A. (2016). A de novo 2.78‐Mb duplication on chromo- some 21q22.11 implicates candidate genes in the partial trisomy 21
https://openalex.org/W2989777713
http://www.scielo.br/pdf/reben/v72n6/0034-7167-reben-72-06-1519.pdf
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Tecnologia educativa para manejo da fadiga relacionada à quimioterapia antineoplásica
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cc-by
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ORIGINAL ARTICLE RESUMO Objetivo: Construir e validar tecnologia educativa (TE) sobre fadiga e estratégias não farmacológicas para manejo desse sintoma em pessoas com câncer em tratamento quimioterápico antineoplásico ambulatorial. Método: Estudo metodológico composto por três etapas: 1) elaboração da TE, utilizando o modelo teórico-metodológico de Doak, Doak e Root; 2) validação de conteúdo e aparência por sete juízes enfermeiros, por meio do índice de validade de conteúdo (IVC); e 3) realização de teste piloto com 10 pacientes. Resultados: A TE “Conhecendo e lidando com a fadiga” contempla a definição de fadiga, suas causas e as intervenções de prática de exercícios físicos, higiene do sono, conservação de energia e intervenção comportamental. O IVC global obtido com os juízes foi de 0,95. Conclusão: A TE apresentou validade de conteúdo e aparência para a educação em saúde com relação à fadiga relacionada à quimioterapia antineoplásica em pacientes oncológicos ambulatoriais. Descritores: Pacotes de Assistência ao Paciente; Enfermagem Oncológica; Fadiga; Estudos de Validação; Tecnologia Educacional. Patrícia Peres de OliveiraIII ORCID: 0000-0002-0325-4917 I Universidade Federal do Ceará. Fortaleza, Ceará, Brazil. II Universidade Estadual do Ceará. Fortaleza, Ceará, Brazil. III Universidade Federal de São João Del Rei. Divinópolis, Minas Gerais, Brazil. Fernanda Macedo Cartaxo FreitasI ORCID: 0000-0002-2944-0291 Descriptors: Patient Care Bundles; Oncology Nursing; Fatigue; Validation Studies; Educational Technology. Lia Guedes BravoII ORCID: 0000-0002-0974-7931 How to cite this article: Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. Educational technology for fatigue management related to antineoplastic chemotherapy. Rev Bras Enferm. 2019;72(6):1519-25. doi: http://dx.doi.org/10.1590/0034-7167-2018-0505 Marcela Maria de Melo PerdigãoI ORCID: 0000-0001-9084-1249 Andrea Bezerra RodriguesI ORCID: 0000-0002-2137-0663 Tayanne de Lima MagalhãesI ORCID: 0000-0003-2511-3901 Fernanda Macedo Cartaxo FreitasI ORCID: 0000-0002-2944-0291 ABSTRACT Objective: To construct and validate an educational technology (ET) on fatigue and non- pharmacological strategies for the management of this symptom in people with cancer undergoing outpatient antineoplastic chemotherapy. Method: This is a methodological study composed of three stages: 1) elaboration of the ET using the theoretical-methodological model of Doak, Doak and Root; 2) validation of content and appearance by seven nurses via the content validity index (CVI); and 3) a pilot test with 10 patients. Results: The ET “Knowing and coping with fatigue” contemplates the definition of fatigue, its causes and the interventions of physical exercise practice, sleep hygiene, energy conservation and behavioral intervention. The overall CVI obtained with the judges was 0.95. Conclusion: The ET presented content and appearance validity for health education regarding fatigue related to antineoplastic chemotherapy in outpatient cancer patients. INTRODUCTION This is a three-stage methodological study. The first relates to the construction of the instrument; the second, to the validation of its content and appearance by judges; and the third, the pilot test. In oncology, an ever increasing number of pharmacological and non-pharmacological strategies have been implemented to care for patients with cancer. In spite of this, both the disease and its therapy trigger many signs and symptoms – among them, fatigue. The first stage took place from December 2016 to February 2017 and was guided by the theoretical and methodological framework of Doak, Doak and Root(8), which presents some es- sential guidelines for the construction planning of educational materials. They are: a) defining the target audience – although it seems to be an obvious step, it is often neglected; b) limiting and defining the learning objectives, which must be compatible with the desired actions and behaviors from the educational in- tervention; c) during the construction itself, the active voice must be used in writing, since it makes reading easier and the reader more likely to practice the action; d) writing short sentences and avoiding technical terms that make comprehension difficult; e) including interactions that may make the guidelines simpler to understand and remember; and f) testing to ensure quality(8). Cancer-related fatigue is defined as “a subjective and persis- tent sensation of tiredness, physical, emotional and/or cognitive exhaustion, disproportionate to any recent activity, and that does not improve with rest and sleep, interfering in the activities of daily living”(1). Fatigue is also described in the Nursing Diagnostic Classification proposed by NANDA-I, described as “an overwhelm- ing sustained sense of exhaustion and decreased capacity for physical and mental work at the usual level”(2). This symptom is often experienced by cancer patients and affects about 75 to 95% of them, leading to compromises of daily living activities(3). In a study that compared adults with cancer to another group of adults without the disease, 56% of the cancer population experienced fatigue(4). g q y After this stage, content and appearance were evaluated by judges from March to May 2017. The next phase – the pilot study –, occurred in the outpatient chemotherapy clinic of a university hospital in the city of Fortaleza, Ceará, from July to August 2017. RESUMEN Obj i C Objetivo: Construir y validar una tecnología educativa (TE) sobre fatiga y estrategias no farmacológicas para el manejo del síntoma en personas con cáncer en tratamiento quimioterápico antineoplásico ambulatorio. Método: Estudio metodológico que consta de tres etapas: 1) elaboración de la TE utilizando el modelo teórico-metodológico de Doak, Doak y Root; 2) validación de contenido y apariencia por siete jueces enfermeros, por medio del índice de validez de contenido (IVC); y 3) realización de una prueba piloto con 10 pacientes. Resultados: La TE “Conociendo y lidiando con la fatiga” contempla la definición de fatiga, sus causas y las intervenciones con la práctica de ejercicios físicos, la higiene del sueño, la conservación de energía y la intervención comportamental. El IVC total obtenido con los jueces fue de 0,95. Conclusión: La TE presentó validez de contenido y apariencia para la educación en salud con relación a la fatiga relacionada a la quimioterapia antineoplásica en pacientes oncológicos ambulatorios. Descriptores:Paq etesdeAtenciónalPaciente EnfermeríaOncológica Fatiga Est diosde Corresponding Author: Marcela Maria de Melo Perdigão E-mail: marcelaperdigao@hotmail.com Submission: 06-14-2018 Approval: 04-10-2019 Descriptores: Paquetes de Atención al Paciente; Enfermería Oncológica; Fatiga; Estudios de Validación; Tecnología Educacional. http://dx.doi.org/10.1590/0034-7167-2018-0505 1519 Rev Bras Enferm. 2019;72(6):1519-25. Educational technology for fatigue management related to antineoplastic chemotherapy Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. INTRODUCTION Due to being a health problem, one of the obstacles related to its detection is that patients associate fatigue with the ineffec- tiveness of therapy – believing that it is necessary to stop it – or, believing that fatigue indicates the evolution of the disease. Thus, providing clarification about this symptom and its natural history to patients is fundamental due to causing such effect, especially patients who will undergo antineoplastic chemotherapy(5). Sample and inclusion and exclusion criteria In the selection of judges for validation of content and ap- pearance of the educational material, the criteria proposed by Jasper(9) were followed, which indicate that a judge must have a body of specialized knowledge or skill, experience in the field of practice, highly developed levels of recognition of standards and recognition by others. Following, Pasquali’s(10) proposal was also used, in which the number of judges must be at least six. To avoid a tie of opinions, this study chose to adopt an odd number of judges, establishing seven as the number of judges. Therefore, educational programs conducted by health pro- fessionals, including the use of technologies, are fundamental for the patient to adapt to and cope with fatigue. Counseling should be started from the first meeting, involving orientation on exercise practice, balancing activities and day-to-day rest, establishing priorities and delegating tasks, relaxation techniques, sleep hygiene measures, feeding and dietary supplementation(6). Given this context, the role of nurses stands out since non- pharmacological interventions can reduce patient fatigue, some- thing that has already been proven in a study about its benefit(7). Educational Technologies (ET) have contributed significantly to support the guidance provided. Therefore, educational programs conducted by health pro- fessionals, including the use of technologies, are fundamental for the patient to adapt to and cope with fatigue. Counseling should be started from the first meeting, involving orientation on exercise practice, balancing activities and day-to-day rest, establishing priorities and delegating tasks, relaxation techniques, sleep hygiene measures, feeding and dietary supplementation(6). Given this context, the role of nurses stands out since non- pharmacological interventions can reduce patient fatigue, some- thing that has already been proven in a study about its benefit(7). Educational Technologies (ET) have contributed significantly to support the guidance provided. Thus, the seven judges were selected according to their clinical and scientific experience with cancer patients on chemotherapeutic treatment through the Lattes platform of the CNPq Portal. The search was conducted using the simple search option for subject/ keyword (oncology, health education, printed educational materials). Sampling was conducted using the snowball method: when one participant was selected according to the established criteria, such participant recommended another with the same characteristics. OBJECTIVE To construct and validate an educational technology on fatigue and non-pharmacological strategies to cope with this symptom in people with cancer undergoing outpatient antineoplastic chemotherapy. During the pilot test stage, the sample of patients was de- lineated based on the hospital records, being composed of 73 individuals. Considering that the suggested sample for a pilot study to be effective is 10%(11), seven patients were calculated as an effective number and researchers chose to work with 10 to ensure greater efficacy. Sample selection occurred by convenience at the outpatient chemotherapy clinic on the days of collection, meeting the following inclusion criteria: being 18 years old or older, 15 score on the Glasgow scale and undergoing antineoplastic chemotherapy for gastric or colorectal cancer. This last criterion was based on a study that inferred that patients with gastric cancer presented more fatigue(12). The Glasgow scale was applied to ensure that the patient presented adequate level of temporal, personal and spatial orientation, as stressed in the item “verbal RESULTS The elaboration of the first version of the instrument was made based on 34 studies identified in the selected databases, which were organized in the following categories: presence of fatigue in cancer patients; health-related quality of life (HRQoL) in cancer patients undergoing antineoplastic chemotherapy; fatigue management by non-pharmacological methods in cancer patients undergoing antineoplastic therapy; and interpretation of family members of the factors that can cause fatigue. Of these, the categories “the presence of fatigue in cancer patients” and “fatigue management by non-pharmacological methods in cancer patients undergo- ing antineoplastic chemotherapy” were considered relevant in the preparation of the preliminary version of the instrument. The educational technology named “Knowing and coping with fatigue” (Conhecendo e lidando com a fadiga), was composed by three topics in its final version – the last topic has four subtopics. The folder’s image design, typography, choice of colors and layout mas made with the help of a visual arts professional. The researchers received updates on the process to provide their feedback and ap- proval. The art was done in the program Adobe Photoshop CC 2015. After finishing the preparation of the ET, an invitation letter was sent to the judges with a brief presentation of the research project, the objective to be evaluated, an explanation of the importance of its validation for later use in practice and what would be his/her function as a judge. After the accepting, the judges received an informed consent form, the ET and the instrument for content and appearance validation of the technology via e-mail. The content and appearance validation instrument was made using the Google Forms program. The validation questionnaire was adapted from Oliveira, Fernandes and Sawada(15). This instrument is divided into two parts: the first contains the characterization data on the judge, and the second presents the instructions for completion and the items to be evaluated (objectives, structure, presentation, relevance and content). The judges were asked to evaluate the ET regarding its content and appearance, with responses given by a Likert-type scale – 1 = inadequate; 2 = partially adequate; 3 = adequate; and 4 = totally adequate(15) –, as well as a space for comments and suggestions when options 1 and 2 were marked. On average, the reviews were returned to researchers after 30 days. Initially, the technology explains the definition of fatigue, its causes, and what can be done to improve the condition. Analysis of results and statistics Data were organized in a spreadsheet in the statistical soft- ware Microsoft Excel 2007. After tabulation, data were analyzed by descriptive statistics. To perform the agreement analysis of the experts, the Con- tent Validity Index (CVI) method was adopted, which measures the proportion or percentage of experts who agree on certain aspects of an instrument and its items. This study adopted < 0.80 CVI values, i.e., equivalent to 80% agreement among the judges, which is considered to be great for the items to be considered validated(16). The CVI was calculated by summing the number of responses marked as “3” or “4” by the judges and dividing the result by the total number of responses. Moreover, the written suggestions made by the judges were considered. Ethical aspects Following, they answered a validation questionnaire adapted from Oliveira, Fernandes and Sawada(15), containing instructions for completing the instru- ment and the items to be evaluated regarding the objectives, organization, writing style, appearance and motivation of the ET. Ethical aspects This study was approved by the Research Ethics Committee of the Walter Cantídio University Hospital/Universidade Federal do Ceará. Participants involved in the study signed an informed consent form. The ethical precepts of research with human beings, based on Resolution 466/2012 of the Brazilian National Health Council, were respected. 1520 Rev Bras Enferm. 2019;72(6):1519-25. 1520 Educational technology for fatigue management related to antineoplastic chemotherapy Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. Educational technology for fatigue management related to antineoplastic chemotherapy Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. response” of the scale, as well as an adequate motor response – another scale item – to comply some of the guidelines provided for fatigue control, such as performing physical activities. These items, coupled to eye opening, consistently indicate the highest degree of integration of the central nervous system. Regarding colorectal cancer, there are few studies that investigate the pres- ence of fatigue in patients with this neoplasm(13). Finally, also as an inclusion criterion, the patient should score at least 60% in the Karnofsky index, which indicates one’s capacity to take care of their personal needs, requiring only occasional help. Exclusion criteria were: illiteracy; chronic pain; use of megestrol acetate or antidepressants; and/or concomitant radiotherapy, which could have influence on fatigue(14). Megestrol acetate use was considered an exclusion criterion to ensure homogeneity in the sample, since this drug may be indicated for the pharmacological treatment of fatigue in cancer patients, improving the levels of this symptom and increasing the sensation of well-being(6). with the judges, the instrument was applied by three trained inter- viewers. They followed a standard operating procedure elaborated by the authors, containing conceptual and operational definitions. Patients were guided about their participation, having their anonymity and confidentiality of information ensured. All partici- pants signed an informed consent form. Following, they answered a validation questionnaire adapted from Oliveira, Fernandes and Sawada(15), containing instructions for completing the instru- ment and the items to be evaluated regarding the objectives, organization, writing style, appearance and motivation of the ET. with the judges, the instrument was applied by three trained inter- viewers. They followed a standard operating procedure elaborated by the authors, containing conceptual and operational definitions. Patients were guided about their participation, having their anonymity and confidentiality of information ensured. All partici- pants signed an informed consent form. Study protocol In the first stage of construction of the instrument, a search was made on the databases Medical Literature Analysis and Retrieval System Online (Medline), Latin American Literature in Health Sciences (Lilacs) and Nursing Database (Bdenf), using the Health Sciences Descriptors (DeCS/MeSH) “fatigue”, “cancer” and “chemotherapy”, with the Boolean term ‘and’. Studies published from 2011 to 2016 and that were available in full were considered for this study. In addition to searching the databases, materials published by Brazilian Consensus on Fatigue (Consenso Brasileiro de Fadiga)(6), Oncology Nurses Society (ONS), American Society of Clinical Oncology (Asco) and Brazilian Cancer Institute (Instituto Nacional de Câncer – Inca) were also used. RESULTS The last topic covers non-pharmacological interventions for fatigue management: “Practice physical exercises”, “Improve your sleep” and “Conserve your energy” and a subtopic with no specific title with information on behavioral intervention. Each of these subtopics presents an explanation of the concept of each intervention and how to apply each of them. Finally, part of the bibliography used is presented. After completing the elaboration of the text, the selection of images began by performing an electronic search on Google Im- ages; these images were sent to the visual arts professional so he could understand the idea that the illustrations were supposed to evoke, as they would be placed close to the texts to which they The third step refers to the pilot test performed with the patients from an outpatient chemotherapy clinic. After the validation process Rev Bras Enferm. 2019;72(6):1519-25. 1521 Educational technology for fatigue management related to antineoplastic chemotherapy Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. Educational technology for fatigue management related to antineoplastic chemotherapy Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. referred, to represent some information from the ET. The text was written in Garamond typeface, size 13 for the information, size 14 for the subheadings and size 28 for the title of the cover, and for subheadings and the title bold was also applied. Text boxes were used for pieces of information that required greater emphasis, using letter size 13 or 16 in bold or with a call for “at- tention”. A4-size coated paper with a light-colored background was used with black text and colored printing. rephrasing the sentence “Seek to know more about your fatigue” to “Seek to know more about the cause(s) of your fatigue” and to perform the necessary grammar corrections. Therefore, the material was sent to be revised by a specialized professional. As general comments, the judges stressed the excellent pro- posal of the ET to address a symptom that is so little known and valued and that nurses have difficulty to approach, arousing the need for greater knowledge of the professional. The CVI values of all items analyzed by the judges are de- scribed in Table 1. After finishing the ET, the content and appearance validation was performed by seven judges, all of whom were nurses and female. RESULTS Most judges had a master’s degree (57.1%), followed by Ph.D (28.5%); the training time of most was over 20 years (85.7%); and the professional practice time greater than 15 years (85.7%). Regarding professional practice, most were professors (57.1%) and others worked in care (42.8%), considering that, of these, 14.2% work in clinical oncology, 14.2% in palliative care and pain, and 14.2% quality in oncology. Regarding scientific publication, most were judges who published articles on cancer, ET, and instrument validation (71.4%). Table 1 – Content validity index of all items (objectives, structure and presentation, relevance and overall index), according to the analysis of the judges, Fortaleza, Ceará, Brazil, 2017 Items CVI Objectives 0,93 1) Does the folder cover the needs of cancer patients undergoing chemotherapy and facing fatigue? 1,00 2) Does the folder provide relevant information and guidance that contributes to the health education process? 0,86 3) Is the folder effective for the maintenance of self-care related to fatigue management? 1,00 4) Is the folder capable of promoting changes in behavior and attitude? 0,71 5) Can the folder circulate in the scientific field in the field of oncology? 1,00 6) Can this folder be implemented in the daily clinical practice of a nurse who works in an outpatient chemotherapy clinic? 1,00 Structure and presentation 0,94 1) Is the information presented clearly and objectively? 1,00 2) Is the information presented scientifically correct? 0,86 3) Does the instrument have a logical sequence? 1,00 4) Is the information well structured in terms of agreement and spelling? 1,00 5) Is the typeface adequate? 1,00 6) Is the font size adequate? 0,71 7) Is the spacing between the lines appropriate? 1,00 8) Is the instrument easy to read and to understand? 1,00 9) Are the images adequate? 0,86 10) Do the pictures depict what one actually wants to convey as information? 1,00 Relevance 1,00 1) Is the folder effective in suggesting to the patient he/she acquires knowledge on managing his/her fatigue at home? 1,00 2) Is the instrument relevant for guiding patients with fatigue who are undergoing chemotherapy? 1,00 3) Is the instrument relevant to the care provided by nurses to these patients? 1,00 4) Does this folder allow the transfer of relevant information about fatigue between the nurse professional and the patient undergoing chemotherapy? 1,00 Global CVI 0,95 Note: CVI = Content Validity Index Objectives The CVI result obtained for the item “objectives” was 0.93; 0.94 for structure and presentation; and 1.0 for relevance. The global IVC score was 0.95, thus assuring the validity of the content and appearance of the folder for use in the target population (Table 1). The CVI result obtained for the item “objectives” was 0.93; 0.94 for structure and presentation; and 1.0 for relevance. The global IVC score was 0.95, thus assuring the validity of the content and appearance of the folder for use in the target population (Table 1). One of the topics in “objectives”, represented by the question “Is this folder capable of promoting changes in behavior and attitude?”, obtained a 0.71 CVI. In the comments, the judges stated that behav- ioral change is something more complex, requiring a more specific indicator for evaluation, and also that the ET alone would not be able to promote changes without proper individual follow-up. One of the topics in “objectives”, represented by the question “Is this folder capable of promoting changes in behavior and attitude?”, obtained a 0.71 CVI. In the comments, the judges stated that behav- ioral change is something more complex, requiring a more specific indicator for evaluation, and also that the ET alone would not be able to promote changes without proper individual follow-up. Another item, represented by the question “Does the folder provide relevant information and guidance that contributes to the health education process?”, showed a 0.86 CVI. Two judges classified it as “partially adequate”. One of the judges advised that the suggestion for swimming should be removed as an interven- tion, which was justified by these patients being immunosup- pressed. Moreover, they stressed the importance having the medic responsible for the patient allowing them practice physical exercises. Another judge commented that the use of sunscreen should be included in the guidelines for physical exercises that are practiced outdoors. Both suggestions were followed. Regarding the “structure and presentation”, the item “Is the font size adequate?” totaled 0.71 CVI score. The judges suggested an increase in the font size. The judge’s suggestion was accepted. Given the small space available, font size was increased from 12 to 13. In the item: “Are the images adequate?”, 0.86 CVI, a judge considered it “partially adequate”, explaining that the cover should contain the image of an energetic person, conveying a positive message. Note: CVI = Content Validity Index Objectives This suggestion was accepted and the image of the ET cover was modified. Still considering “structure and presentation”, in the item “Is the typeface adequate?”, although it presented 1.0 CVI, a judge stated that the typeface used was tiring and suggested that it was changed to the Calibri typeface. However, the style used is in accordance with the guidelines proposed by the theoretical reference adopted: a serif typeface and size starting from 12. Therefore, the suggestion was not complied to. Regarding the “structure and presentation”, the item “Is the font size adequate?” totaled 0.71 CVI score. The judges suggested an increase in the font size. The judge’s suggestion was accepted. Given the small space available, font size was increased from 12 to 13. In the item: “Are the images adequate?”, 0.86 CVI, a judge considered it “partially adequate”, explaining that the cover should contain the image of an energetic person, conveying a positive message. This suggestion was accepted and the image of the ET cover was modified. Global CVI Note: CVI = Content Validity Index After applying the changes proposed by the judges and the folder was finished, the pilot test began. Of the 10 participants, six (60%) were female, five (50%) were aged between 51 and 70 years, four (40%) had incomplete primary education, five (50%) had colon cancer and four (40%) were undergoing the FLOX regimen (leucovorin, oxaliplatin and 5-fluorouracil). Still considering “structure and presentation”, in the item “Is the typeface adequate?”, although it presented 1.0 CVI, a judge stated that the typeface used was tiring and suggested that it was changed to the Calibri typeface. However, the style used is in accordance with the guidelines proposed by the theoretical reference adopted: a serif typeface and size starting from 12. Therefore, the suggestion was not complied to. Participants answered the evaluation instrument of ET, which comprised questions about the objectives (CVI = 0.90), organization (CVI = 1.00), writing style (CVI = 0.93), appearance (CVI = 1.00) and motivation (CVI = 0.98). CVI was also used in this phase to ensure There were other specific questions on items with CVI great- er than 0.80, such as changing the word “tumor” to “disease”, Rev Bras Enferm. 2019;72(6):1519-25. 1522 Educational technology for fatigue management related to antineoplastic chemotherapy Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. Educational technology for fatigue management related to antineoplastic chemotherapy Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. Energy conservation techniques refer to the deliberate and planned management of activities that expend energy, thus preventing its depletion. These strategies include planning, del- egation, setting priorities, and scheduling activities that require the use of high energy at peak energy times. These measures aim to reduce energy expenditure in the activities of daily living and are significantly effective in minimizing fatigue(6). the reliability of the results. The overall CVI was 0.95, and the validity of content and appearance was evidenced by the target popula- tion. A patient suggested the increase in the font size of the ET, due to the patient’s low visual acuity. After finishing the content and appearance validation process, the final version presents three topics, and the last one is composed of four subtopics. In the structure and presentation aspect, the item “Is the typeface adequate?” showed a 1.0 CVI. However, a judge suggested changing the typeface. This was the only unaccepted suggestion, since the theoretical reference adopted(14) points out that a serif typeface, from size 12, is considered easy to read, allowing greater fluidity. This typeface is un-stylized, of Roman origin, with perfect circles and balanced linear forms, making reading easier(22). Figure 1 – Final version of the educational technology for fatigue manage- ment in cancer patients undergoing antineoplastic chemotherapy, validated by judges and patients, Fortaleza, Ceará, Brazil, 2017 Note: CVI = Content Validity Index Figure 1 shows the final version of the ET – validated for con- tent and appearance by the specialized judges and participants of the pilot test – for fatigue management in cancer patients undergoing antineoplastic chemotherapy in outpatient clinics. Likewise, behavioral intervention and sleep hygiene presented favorable results in fatigue management, with evidence sup- porting its use(1,6,19). A very positive aspect in this study is the long experience in oncology of the judges, and in addition to their knowledge on the oncology area, ET and instrument validation, the fact that the judges are from different geographic regions of Brazil may reflect on different ways of dealing with symptoms. Figure 1 – Final version of the educational technology for fatigue manage- ment in cancer patients undergoing antineoplastic chemotherapy, validated by judges and patients, Fortaleza, Ceará, Brazil, 2017 The judges considered the non-pharmacological interventions proposed for fatigue to be relevant. One of them pointed out that, among the physical exercises suggested as intervention, swimming should be removed, considering that this patient population is often immunosuppressed due to antineoplastic agents have the adverse effect of myelosuppression, which carries the risk of a significant increase in infections. Due to being a natural reservoir for many pathogens, water could make the patient more susceptible to infections. The risk of disease or infection associated with swim- ming pools is mainly due to the fecal contamination of the water, which may be caused by feces released by swimmers or sources of contaminated water(20), which was confirmed in a study that identified Cryptosporidium and Giardia in swimming pools, leading to the occurrence of outbreaks among swimmers(21). Figure 1 – Final version of the educational technology for fatigue manage- ment in cancer patients undergoing antineoplastic chemotherapy, validated by judges and patients, Fortaleza, Ceará, Brazil, 2017 Still considering physical exercises, a judge stated that the guide- lines should include instructions for the patient to ingest water, and wear appropriate clothes and shoes when practicing exercises; the use of sunscreen during outdoors practice was also mentioned. These suggestions were followed. It must be considered that this study was based in the Northeast region of Brazil, with a predomi- nantly tropical climate during the whole year, and that secondary diseases, such as dehydration and skin cancer must be prevented. DISCUSSION The only items that did not reach CVI higher than 0.80 were “font size” (CVI = 0.71) and “Is the folder capable of promoting changes in behavior and attitude?” (CVI = 0.71). Regarding the font size, although the recommendation of the adopted theorists was followed, the judges’ suggestion was accepted, since in the pilot study with the patients they also suggested an increase in size. Given the reduced space available, font size was increased from 12 to 13. Although fatigue presents high prevalence and its crucial consequences in the life of cancer patients, this condition is not always valued by health professionals(5). The routine evaluation of the presence of fatigue is recommended to these professionals, from the initial diagnosis to the end of treatment(1). Regarding the item “to promote changes of behavior and at- titude”, two judges pointed out that the ET alone would not be capable of generating changes of behavior. We must emphasize that the study protocol foresees a quasi-experimental study, which corresponds to the second phase of this work. However, the judges recognized that the ET can contribute to the health Among the non-pharmacological interventions included in the ET as a strategy for the management of fatigue, we can highlight physical exercises, energy conservation measures, behavioral inter- vention and sleep hygiene. Performing physical exercises presents a strong level of evidence about its effectiveness in the maintenance of the symptom, with aerobics being the most suggested(6,17-18). Rev Bras Enferm. 2019;72(6):1519-25. 1523 Educational technology for fatigue management related to antineoplastic chemotherapy Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. CONCLUSION The process of constructing the instrument was based on the search for non-pharmacological interventions based on scientific evidence on how to manage fatigue. The items of the instru- ment were directed to physical exercises, energy conservation, behavioral interventions and sleep hygiene. The purpose of written educational material is to reinforce verbal information, act as a guideline for subsequent doubts, and assist in decision making(25). However, these instruments must be developed and validated to be used effectively(26). The validation process resulted in the adequacy of content and appearance of the educational technology to guide patients on chemotherapy-related fatigue, with a 0.95 global CVI, indicating an excellent level of agreement among judges. Furthermore, the target population considered the educational technology to be useful considering its objectives, organization, writing style, appearance and motivation, with a 95% global agreement rate. Therefore, clinical validation is foreseen in subsequent stud- ies to evaluate the efficiency of the instrument constructed and validated as a facilitator for obtaining data from patients seen at outpatient chemotherapy clinics. Study limitations The validation process resulted in the adequacy of content and appearance of the educational technology to guide patients on chemotherapy-related fatigue, with a 0.95 global CVI, indicating an excellent level of agreement among judges. Furthermore, the target population considered the educational technology to be useful considering its objectives, organization, writing style, appearance and motivation, with a 95% global agreement rate. As limitations of this study we can point that the results to be achieved via non-pharmacological interventions for fatigue cannot always be guaranteed, since cancer-related fatigue is multifactorial in most cases and may depend on some pharma- cological approaches. On the other hand, the definition of judges is not always easy to achieve. In this study, we chose to use the criteria proposed by Jasper(9), which considers aspects based on clinical experience, but it cannot be guaranteed, in fact, that all items will ensure clinical expertise. Therefore, clinical validation is foreseen in subsequent stud- ies to evaluate the efficiency of the instrument constructed and validated as a facilitator for obtaining data from patients seen at outpatient chemotherapy clinics. Contributions to the field of nursing education process (CVI = 0.86), which is effective for the main- tenance of self-care related to fatigue management (CVI = 1.0) and that can be implemented in the daily clinical practice of the nurse who works in an outpatient chemotherapy clinic (CVI = 1.0); thus, being a relevant instrument for the care provided by nursing professionals to these patients (CVI = 1.0). On the other hand, the patients who participated in the pilot study considered the folder to have a motivator effect (CVI = 0.98). We believe that the educational technology “Knowing and cop- ing with fatigue” will enable health professionals, especially nursing professionals, to provide care more in line with the needs of their patients, as well as to complement guidelines and clarifications provided to the patient, allowing him/her to better know and cope with fatigue. Furthermore, studies in the context of outpatient care are in line with international efforts to improve nurses’ activities in this specialty. In the Brazilian context, the specialty of outpatient oncology still lacks studies that seek to improve the practice of nurses, seeking care based on scientific evidence. We thus believe that the elaboration of an ET may better subsidize the practice of this professional in outpatient environments. Motivation is the first step for behavior change. A study aimed at the participation of middle-aged people in high-impact physical activity showed that the perception of clear and tangible benefits acts as a motivator for adherence to the practice of physical ac- tivities(23). Another study, conducted with patients submitted to stem cell transplantation, reported that being part of a physical activity motivation program reduced the hospitalization period, in addition to arousing a sense of commitment to physical activ- ity, even when the participants were tired(24). REFERENCES 1. Bower JE, Bak K, Berger A, Breitbart W, Escalante CP, Ganz PA, et al. Screening, assessment, and management of fatigue in adult survivors of cancer: an American Society of Clinical Oncology clinical practice guideline adaptation. J Clin Oncol. 2014;32(17):1840-50. doi: 10.1200/ JCO.2013.53.4495 1. Bower JE, Bak K, Berger A, Breitbart W, Escalante CP, Ganz PA, et al. Screening, assessment, and management of fatigue in adult survivors of cancer: an American Society of Clinical Oncology clinical practice guideline adaptation. J Clin Oncol. 2014;32(17):1840-50. doi: 10.1200/ JCO.2013.53.4495 2. Herdman TH, Kamitsuru S. 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Oncol Nurs Forum. 2015;42(4):E302-9. doi: 10.1188/15.ONF.E302-E309 5. Berger AN, Mooney K, Banerjee C, Breitbart WS, Carpenter KM, Chang Y, et al. Cancer-related fatigue – version 1.2018. J Natl Compr Canc Netw. 2018:1-62. 5. Berger AN, Mooney K, Banerjee C, Breitbart WS, Carpenter KM, Chang Y, et al. Cancer-related fatigue – version 1.2018. J Natl Compr Canc Netw. 2018:1-62. 6. Caponero R. Consenso brasileiro de fadiga. Rev Bras Cuidados Paliativos. 2010;3(2; Supl 1):1-32. 6. Caponero R. Consenso brasileiro de fadiga. Rev Bras Cuidados Paliativos. 2010;3(2; Supl 1):1-32. 7. Costa AIS, Reis PED. Complementary techniques to control cancer symptoms. Rev Dor. 2014;15(1):61-4. doi: 10.5935 7. Costa AIS, Reis PED. Complementary techniques to control cancer symptoms. Rev Dor. 2014;15(1):61-4. doi: 10.5935/1806-0013.20140014 8. Doak CC, Doak LG, Root JH. Teaching patients with low literacy skills. 2nd ed. Philadelphia: JB Lippincott; 1996. 8. Doak CC, Doak LG, Root JH. Teaching patients with low literacy skills. 2nd ed. Philadelphia: JB Lippincott; 1996. 9. Jasper MA. REFERENCES Expert: a discussion of the implications of the concept as used in nursing. J Adv Nurs. 1994; 20:769-76. doi: 10.1046/j.1365-2648.1994.20040769.x 9. Jasper MA. Expert: a discussion of the implications of the concept as used in nursing. J Adv Nurs. 1994; 20:769-76. doi: 10.1046/j.1365-2648.1994.20040769.x 10. Pasquali L. Instrumentos psicológicos: manual prático de elaboração. Brasília: LabPAM/IBAPP; 1999. 1524 Rev Bras Enferm. 2019;72(6):1519-25. Educational technology for fatigue management related to antineoplastic chemotherapy Perdigão MMM, Rodrigues AB, Magalhães TL, Freitas FMC, Bravo LG, Oliveira PP. 11. Canhota C. Qual a importância do estudo piloto. In: Silva EE, organizador. Investigação passo a passo: perguntas e respostas para investigação clínica. Lisboa: APMCG; 2008. p. 69-72. 12. Nicolussi AC, Sawada NO, Cardozo FMC, Andrade V, Paula JM. Health-related quality of life of cancer patients undergoing chemotherapy. Rev Rene. 2014;15(1):132-40. doi: 10.15253/2175-6783.2014000100017 12. Nicolussi AC, Sawada NO, Cardozo FMC, Andrade V, Paula JM. Health-related quality of life of cancer patients undergoing chemotherapy. Rev Rene. 2014;15(1):132-40. doi: 10.15253/2175-6783.2014000100017 13. Mota DDCF, Pimenta CAM, Caponero R. Fatigue in colorectal cancer patients: prevalence and associated factors. Rev Latino-Am Enfermagem. 2012;20(3):495-503. doi: 10.1590/S0104-11692012000300010 13. Mota DDCF, Pimenta CAM, Caponero R. Fatigue in colorectal cancer patients: prevalence and associated factors. Rev Latino-Am Enfermagem. 2012;20(3):495-503. doi: 10.1590/S0104-11692012000300010 14. Barsevick AM, Dudley W, Beck S, Sweeney C, Whitmer K, Nail L. A randomized clinical trial of energy conservation for patients with cancer- related fatigue. Cancer. 2004;100(6):1302-10. doi: 10.1002/cncr.20111 14. Barsevick AM, Dudley W, Beck S, Sweeney C, Whitmer K, Nail L. A randomized clinical trial of energy conservation for patients with cancer- related fatigue. Cancer. 2004;100(6):1302-10. doi: 10.1002/cncr.20111 15. Oliveira MS, Fernandes AFC, Sawada NO. Manual educativo para o autocuidado da mulher mastectomizada: um estudo de validação. Texto Contexto Enferm. 2008;17(1):115-23. doi: 10.1590/S0104-07072008000100013 15. Oliveira MS, Fernandes AFC, Sawada NO. Manual educativo para o autocuidado da mulher mastectomizada: um estudo de validação. Texto Contexto Enferm. 2008;17(1):115-23. doi: 10.1590/S0104-07072008000100013 16. Souza Neto VL, Silva RAR, Silva CC, Negreiros RV, Rocha CCT, Nóbrega MML. Proposal of nursing care plan in people hospitalized with AIDS. Rev Esc Enferm USP. 2017;51:e03204. doi: 10.1590/s1980-220x2016027203204 16. Souza Neto VL, Silva RAR, Silva CC, Negreiros RV, Rocha CCT, Nóbrega MML. Proposal of nursing care plan in people hospitalized with AIDS. Rev Esc Enferm USP. 2017;51:e03204. doi: 10.1590/s1980-220x2016027203204 17. Al-Majid S, Wilson LD, Rakovski C, Coburn JW. Effects of exercise on biobehavioral outcomes of fatigue during cancer treatment: results of a feasibility study. REFERENCES Biol Res Nurs. 2015;17(1):40-8. doi: 10.1177/1099800414523489 18. Jensen W, Baumamm FT, Stein A, Bloch W, Bokemeyer C, de Wit M, et al. Exercise training in patients with advanced gastrointestinal cancer undergoing palliative chemotherapy: a pilot study. Support Care Cancer. 2014;22(7):1797-806. doi: 10.1007/s00520-014-2139-x 19. Casault L, Savard J, Ivers H, Savard MH. A randomized-controlled trial of an early minimal cognitive-behavioural therapy for insomnia comorbid with cancer. Behav Res Ther. 2015;67:45-54. doi: 10.1016/j.brat.2015.02.003 20. World Health Organization (WHO). Guidelines for safe recreational water environments. Volume 2: swimming pools and similar environments [Internet]. Geneva: WHO; 2006 [cited 2018 Jan 24]. Available from: https://www.who.int/water_sanitation_health/bathing/ srwe2full.pdf 21. Xiao S, Yin P, Zhang Y, Hu S. Occurrence of Cryptosporidium and Giard relationship between protozoa and wate indicators in swimming pools. Korean J Parasitol. 2017;55(2):129-35. doi: 10.3347/kjp.2017.55.2.129 22. Passamai MPB, Sampaio HAC, Sabry MOD, Sá MLB, Cabral LA. Letramento funcional em saúde e nutrição. Fortaleza: EdUECE; 2011. 23. Simmonds BAJ, Hannam KJ, Fox KR, Tobias JH. An exploration of barriers and facilitators to older adults participation in higher impact physical activity and bone health: a qualitative study. Osteoporos Int. 2016;27(3):979-87. doi: 10.1007/s00198-015-3376-7 24. Brassil KJ, Szewczyk N, Fellman B, Neumann J, Burgess J, Urbauer D, et al. Impact of an incentive-based mobility program, “Motivated and Moving,” on physiologic and quality of life outcomes in a stem cell transplant population. Cancer Nurs. 2014;37(5):345-54. doi: 10.1097/ NCC.0b013e3182a40db2 25. Moreira MF, Nóbrega MML, Silva MIT. Comunicação escrita: contribuição para elaboração de material educativo em saúde. Rev Bras Enferm. 2003;56(2):184-8. doi: 10.1590/S0034-71672003000200015 25. Moreira MF, Nóbrega MML, Silva MIT. Comunicação escrita: contribuição para elaboração de material educativo em saúde. Rev Bras Enferm. 2003;56(2):184-8. doi: 10.1590/S0034-71672003000200015 26. Benevides JL, Coutinho JFV, Pascoal LC, Joventino ES, Martins MC, Gubert FA, et al. Development and validation of educational technology for venous ulcer care. Rev Esc Enferm USP. 2016;50(2):306-12. doi: 10.1590/S0080-623420160000200018 26. Benevides JL, Coutinho JFV, Pascoal LC, Joventino ES, Martins MC, Gubert FA, et al. Development and validation of educational technology for venous ulcer care. Rev Esc Enferm USP. 2016;50(2):306-12. doi: 10.1590/S0080-623420160000200018 1525 Rev Bras Enferm. 2019;72(6):1519-25.
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Effect of Hydroxychloroquine in Hospitalized Patients with Covid-19
New England journal of medicine/˜The œNew England journal of medicine
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The University of Manchester Research The University of Manchester Research The University of Manchester Research Link to publication record in Manchester Research Explorer Link to publication record in Manchester Research Explorer Citation for published version (APA): RECOVERY Collaborative Group, & Evans, D. G. (2020). Effect of Hydroxychloroquine in Hospitalized Patients with Covid-19. The New England Journal of Medicine, 383(21), 2030-2040. https://doi.org/10.1056/NEJMoa2022926, https://doi.org/10.1056/nejmoa2022926 Citing this paper Citing this paper Please note that where the full-text provided on Manchester Research Explorer is the Author Accepted Manuscript or Proof version this may differ from the final Published version. If citing, it is advised that you check and use the publisher's definitive version. Published in: Published in: The New England Journal of Medicine Effect of Hydroxychloroquine in Hospitalized Patients with Covid-19 DOI: 10.1056/NEJMoa2022926 10.1056/nejmoa2022926 Document Version Final published version General rights General rights Copyright and moral rights for the publications made accessible in the Research Explorer are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Takedown policy If you believe that this document breaches copyright please refer to the University of Manchester’s Takedown Procedures [http://man.ac.uk/04Y6Bo] or contact uml.scholarlycommunications@manchester.ac.uk providing relevant details, so we can investigate your claim. Download date:24. Oct. 2024 Takedown policy If you believe that this document breaches copyright please refer to the University of Manchester’s Takedown Procedures [http://man.ac.uk/04Y6Bo] or contact uml.scholarlycommunications@manchester.ac.uk providing relevant details, so we can investigate your claim. Citation for published version (APA): Citation for published version (APA): RECOVERY Collaborative Group, & Evans, D. G. (2020). Effect of Hydroxychloroquine in Hospitalized Patients with Covid-19. The New England Journal of Medicine, 383(21), 2030-2040. https://doi.org/10.1056/NEJMoa2022926, https://doi.org/10.1056/nejmoa2022926 BACKGROUND Hydroxychloroquine and chloroquine have been proposed as treatments for coro- navirus disease 2019 (Covid-19) on the basis of in vitro activity and data from uncontrolled studies and small, randomized trials. The members of the writing committee (Peter Horby, F.R.C.P., Marion Mafham, M.D., Louise Linsell, D.Phil., Jennifer L. Bell, M.Sc., Natalie Staplin, Ph.D., Jona- than R. Emberson, Ph.D., Martin Wiselka, Ph.D., Andrew Ustianowski, Ph.D., Einas Elmahi, M.Phil., Benjamin Prudon, F.R.C.P., Tony Whitehouse, F.R.C.A., Timothy Fel- ton, Ph.D., John Williams, M.R.C.P., Jakki Faccenda, M.D., Jonathan Underwood, Ph.D., J. Kenneth Baillie, M.D., Ph.D., Lucy C. Chappell, Ph.D., Saul N. Faust, F.R.C.P.C.H., Thomas Jaki, Ph.D., Katie Jeffery, Ph.D., Wei  Shen Lim, F.R.C.P., Alan Montgomery, Ph.D., Kathryn Rowan, Ph.D., Joel Tarning, Ph.D., James A. Wat- son, D.Phil., Nicholas J. White, F.R.S., Ed- mund Juszczak, M.Sc., Richard Haynes, D.M., and Martin J. Landray, Ph.D.) as- sume responsibility for the overall con- tent and integrity of this article. Effect of Hydroxychloroquine in Hospitalized Patients with Covid-19 The RECOVERY Collaborative Group*​ ABSTR ACT RESULTS The enrollment of patients in the hydroxychloroquine group was closed on June 5, 2020, after an interim analysis determined that there was a lack of efficacy. Death within 28 days occurred in 421 patients (27.0%) in the hydroxychloroquine group and in 790 (25.0%) in the usual-care group (rate ratio, 1.09; 95% confidence inter- val [CI], 0.97 to 1.23; P = 0.15). Consistent results were seen in all prespecified subgroups of patients. The results suggest that patients in the hydroxychloroquine group were less likely to be discharged from the hospital alive within 28 days than those in the usual-care group (59.6% vs. 62.9%; rate ratio, 0.90; 95% CI, 0.83 to 0.98). Among the patients who were not undergoing mechanical ventilation at baseline, those in the hydroxychloroquine group had a higher frequency of invasive mechanical ventilation or death (30.7% vs. 26.9%; risk ratio, 1.14; 95% CI, 1.03 to 1.27). There was a small numerical excess of cardiac deaths (0.4 percentage points) but no difference in the incidence of new major cardiac arrhythmia among the patients who received hydroxychloroquine. The affiliations of the members of the writing committee are listed in the Ap- pendix. Address reprint requests to Dr. Horby or Dr. Landray at the RECOVERY Central Coordinating Office, Richard Doll Bldg., Old Road Campus, Roosevelt Dr., Oxford OX3 7LF, United Kingdom, or at ­recoverytrial@​­ndph​.­ox​.­ac​.­uk. *A complete list of collaborators in the RECOVERY trial is provided in the Supple- mentary Appendix, available at NEJM.org. Drs. Horby, Mafham, and Linsell and Prof. Juszczak, Dr. Haynes, and Dr. Landray contributed equally to this article. METHODS In this randomized, controlled, open-label platform trial comparing a range of possible treatments with usual care in patients hospitalized with Covid-19, we randomly assigned 1561 patients to receive hydroxychloroquine and 3155 to receive usual care. The primary outcome was 28-day mortality. Takedown policy Download date:24. Oct. 2024 The new engl and jour nal of medicine CONCLUSIONS Among patients hospitalized with Covid-19, those who received hydroxychloro- quine did not have a lower incidence of death at 28 days than those who received usual care. (Funded by UK Research and Innovation and National Institute for Health Research and others; RECOVERY ISRCTN number, ISRCTN50189673; ClinicalTrials.gov number, NCT04381936.) j ; j , The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. N Engl J Med 2020;383:2030-40. DOI: 10.1056/NEJMoa2022926 Copyright © 2020 Massachusetts Medical Society. This article was published on October 8, 2020, at NEJM.org. This article was published on October 8, 2020, at NEJM.org. This is the New England Journal of Medicine version of record, which includes all Journal editing and enhancements. The Author Fi- nal Manuscript, which is the author’s ver- sion after external peer review and before publication in the Journal, is available un- der a CC BY license at PMC7556338. N Engl J Med 2020;383:2030-40. DOI: 10.1056/NEJMoa2022926 Copyright © 2020 Massachusetts Medical Society. N Engl J Med 2020;383:2030-40. DOI: 10.1056/NEJMoa2022926 Copyright © 2020 Massachusetts Medical Society. 2030 n engl j med 383;21  nejm.org  November 19, 2020 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. n engl j med 383;21  nejm.org  November 19, 2020 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Hydroxychloroquine in Patients with Covid-19 S hospitalized with mild-to-moderate Covid-19 showed that hydroxychloroquine (at a dose of 400 mg twice daily, with or without azithromy- cin) did not improve clinical status at day 15, as compared with usual care.25-29 Here, as part of the controlled, open-label Randomized Evalua- tion of Covid-19 Therapy (RECOVERY) trial, we report the results of a comparison between hy- droxychloroquine and usual care involving pa- tients hospitalized with Covid-19. S evere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (Covid-19), emerged in China in late 2019 from a zoonotic source.1 The majority of Covid-19 infections are either asymptomatic or result in only mild disease. However, in a substantial proportion of infected persons, the infection leads to a respiratory ill- ness requiring hospital care,2 which can progress to critical illness with hypoxemic respiratory fail- ure and lead to prolonged ventilatory support.3-6 Among the patients with Covid-19 who have been admitted to hospitals in the United Kingdom, the case fatality rate is approximately 30%.7 Trial Design and Oversight The RECOVERY trial is an investigator-initiated platform trial to evaluate the effects of potential treatments in patients hospitalized with Covid-19. The trial is being conducted at 176 hospitals in the United Kingdom. (Details are provided in the Supplementary Appendix, available with the full text of this article at NEJM.org.) The investigators were assisted by the National Institute for Health Research Clinical Research Network, and the trial is coordinated by the Nuffield Department of Population Health at the University of Oxford, the trial sponsor. Although patients are no lon- ger being enrolled in the hydroxychloroquine, dexamethasone, and lopinavir–ritonavir groups, the trial continues to study the effects of azithro- mycin, tocilizumab, convalescent plasma, and REGN-COV2 (a combination of two monoclonal antibodies directed against the SARS-CoV-2 spike protein). Other treatments may be studied in the future. The hydroxychloroquine that was used in this phase of the trial was supplied by the U.K. National Health Service (NHS). Trial Design and Oversight Hydroxychloroquine and chloroquine, two 4-aminoquinoline drugs that were developed more than 70 years ago and have been used to treat malaria and rheumatologic conditions, have been proposed as treatments for Covid-19. Chloro- quine has been shown to have in vitro activity against a variety of viruses, including SARS-CoV-2 and the related SARS-CoV-1.8-13 The exact mecha- nism of antiviral action is uncertain, but these drugs increase the pH of endosomes that the virus uses for cell entry and also interfere with the glycosylation of angiotensin-converting– enzyme 2 (ACE2), which is the cellular receptor of SARS-CoV, and of associated gangliosides.10,14 The 4-aminoquinoline levels that are required to inhibit SARS-CoV-2 replication in vitro are higher than the free plasma levels that have been ob- served in the prevention and treatment of ma- laria.15 These drugs generally have an acceptable side-effect profile and are inexpensive and wide- ly available. After oral administration, they are rapidly absorbed, even in severely ill patients. Therapeutic hydroxychloroquine levels could be expected to be reached in human lung tissue shortly after an initial loading dose. Hospitalized patients were eligible for the trial if they had clinically-suspected or laboratory- confirmed SARS-CoV-2 infection and no medical history that might, in the opinion of the attend- ing clinician, put patients at substantial risk if they were to participate in the trial. Initially, recruitment was limited to patients who were at least 18 years of age, but the age limit was re- moved as of May 9, 2020. In small preclinical studies of SARS-CoV-2 infection in animals, prophylaxis or treatment with hydroxychloroquine had no beneficial ef- fect on clinical disease or viral replication.16 A clinical benefit and an antiviral effect from the administration of these drugs alone or in com- bination with azithromycin in patients with Covid-19 have been reported in some observa- tional studies17-21 but not in others.22-24 The re- sults of a few small trials of hydroxychloroquine or chloroquine for the treatment of Covid-19 have been inconclusive, whereas one larger random- ized, controlled trial involving patients who were Written informed consent was obtained from all the patients or from a legal representative if they were too unwell or unable to provide con- sent. The trial was conducted in accordance with Good Clinical Practice guidelines of the Interna- tional Conference on Harmonisation and was approved by the U.K. The new engl and jour nal of medicine Products Regulatory Agency (MHRA) and the Cambridge East Research Ethics Committee. The protocol with its statistical analysis plan are available at NEJM.org, with additional informa- tion in the Supplementary Appendix and on the trial website at www​.­recoverytrial​.­net. In the hydroxychloroquine group, patients re- ceived hydroxychloroquine sulfate (in the form of a 200-mg tablet containing a 155-mg base equivalent) in a loading dose of four tablets (total dose, 800 mg) at baseline and at 6 hours, which was followed by two tablets (total dose, 400 mg) starting at 12 hours after the initial dose and then every 12 hours for the next 9 days or until discharge, whichever occurred earlier (see the Supplementary Appendix).15 The assigned treat- ment was prescribed by the attending clinician. The patients and local trial staff members were aware of the assigned trial groups. The initial version of the manuscript was drafted by the first and last authors, developed by the writing committee, and approved by all members of the trial steering committee. The funders had no role in the analysis of the data, in the preparation or approval of the manuscript, or in the decision to submit the manuscript for publication. The first and last members of the writing committee vouch for the completeness and accuracy of the data and for the fidelity of the trial to the protocol and statistical analysis plan. Procedures A single online follow-up form was to be com- pleted by the local trial staff members when each trial patient was discharged, at 28 days af- ter randomization, or at the time of death, which- ever occurred first. Information was recorded regarding the adherence to the assigned treat- ment, receipt of other treatments for Covid-19, duration of admission, receipt of respiratory support (with duration and type), receipt of renal dialysis or hemofiltration, and vital status (in- cluding cause of death). Starting on May 12, 2020, extra information was recorded on the occur- rence of new major cardiac arrhythmia. In addi- tion, we obtained routine health care and regis- try data that included information on vital status (with date and cause of death) and discharge from the hospital. Trial Design and Oversight Medicines and Healthcare 2031 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Randomization and Treatment We collected baseline data using a Web-based case-report form that included demographic data, level of respiratory support, major coexist- ing illnesses, the suitability of the trial treat- ment for a particular patient, and treatment availability at the trial site. Using a Web-based unstratified randomization method with the con- cealment of trial group, we assigned patients to receive either the usual standard of care or the usual standard of care plus hydroxychloroquine or one of the other available treatments that were being evaluated. The number of patients who were assigned to receive usual care was twice the number who were assigned to any of the active treatments for which the patient was eligible (e.g., 2:1 ratio in favor of usual care if the patient was eligible for only one active treatment group, 2:1:1 if the patient was eligible for two active treatments, etc.). n engl j med 383;21  nejm.org  November 19, 2020 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. n engl j med 383;21  nejm.org  November 19, 2020 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Hydroxychloroquine in Patients with Covid-19 data cutoff of September 21, 2020. Information regarding the primary outcome is complete for all the trial patients. a range of uncertainty around the results that was narrow enough) to affect national and global treatment strategies. In such a circumstance, the committee would inform the members of the trial steering committee, who would make the results available to the public and amend the trial ac- cordingly. Unless that happened, the steering committee, investigators, and all others involved in the trial would remain unaware of the interim results until 28 days after the last patient had been randomly assigned to a particular treatment group. Outcome Measures The primary outcome was all-cause mortality within 28 days after randomization; further analyses were specified at 6 months. Secondary outcomes were the time until discharge from the hospital and a composite of the initiation of in- vasive mechanical ventilation including extracor- poreal membrane oxygenation or death among patients who were not receiving invasive mechani- cal ventilation at the time of randomization. Decisions to initiate invasive mechanical ventila- tion were made by the attending clinicians, who were informed by guidance from NHS England and the National Institute for Health and Care Excellence. Subsidiary clinical outcomes included cause-specific mortality (which was recorded in all patients) and major cardiac arrhythmia (which was recorded in a subgroup of patients). All in- formation presented in this report is based on a For some patients, hydroxychloroquine was unavailable at the hospital at the time of enroll- ment or was considered by the managing physi- cian to be either definitely indicated or definitely contraindicated. Patients with a known prolonged corrected QT interval on electrocardiography were ineligible to receive hydroxychloroquine. (Coadministration with medications that prolong the QT interval was not an absolute contraindi- cation, but attending clinicians were advised to check the QT interval by performing electrocar- diography.) These patients were excluded from entry in the randomized comparison between hydroxychloroquine and usual care. 2032 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Patients From March 25 to June 5, 2020, a total of 11,197 patients underwent randomization; of these pa- tients, 7513 (67%) were eligible to receive hy- droxychloroquine (i.e., the patient had no known indication for or contraindication to hydroxy- chloroquine, and the drug was available in the hospital at the time) (Fig. 1). Of the eligible pa- tients, 1561 were assigned to receive hydroxy- chloroquine and 3155 were assigned to receive usual care; the remainder of the patients were randomly assigned to one of the other treatment groups. v ded t e Supp e e ta y ppe d .) Estimates of rate and risk ratios are shown with 95% confidence intervals without adjust- ment for multiple testing. The P value for the assessment of the primary outcome is two-sided. The full database is held by the trial team, which collected the data from the trial sites and per- formed the analyses, at the Nuffield Department of Population Health at the University of Oxford. The independent data monitoring committee was asked to review unblinded analyses of the trial data and any other information that was considered to be relevant at intervals of approxi- mately 2 weeks. The committee was then charged with determining whether the randomized com- parisons in the trial provided evidence with re- spect to mortality that was strong enough (with Estimates of rate and risk ratios are shown with 95% confidence intervals without adjust- ment for multiple testing. The P value for the assessment of the primary outcome is two-sided. The full database is held by the trial team, which collected the data from the trial sites and per- formed the analyses, at the Nuffield Department of Population Health at the University of Oxford. The mean (±SD) age of the patients in this trial was 65.4±15.3 years (Table 1 and Table S1 in the Supplementary Appendix). A total of 38% of the patients were female; 18% were Black or Asian or had a minority ethnic background. No children were enrolled. A history of diabetes was present in 27% of patients, heart disease in 26%, and chronic lung disease in 22%, with 57% hav- The independent data monitoring committee was asked to review unblinded analyses of the trial data and any other information that was considered to be relevant at intervals of approxi- mately 2 weeks. Statistical Analysis For the primary outcome of 28-day mortality, we used the log-rank observed-minus-expected sta- tistic and its variance both to test the null hy- pothesis of equal survival curves and to calculate the one-step estimate of the average mortality rate ratio in the comparison between the hydroxy- chloroquine group and the usual-care group. Kaplan–Meier survival curves were constructed to show cumulative mortality over the 28-day period. The same methods were used to analyze the time until hospital discharge, with censor- ing of data on day 29 for patients who had died in the hospital. We used the Kaplan–Meier esti- mates to calculate the median time until hospi- tal discharge. For the prespecified composite secondary outcome of invasive mechanical venti- lation or death within 28 days (among patients who had not been receiving invasive mechanical ventilation at randomization), the precise date of the initiation of invasive mechanical ventilation was not available, so the risk ratio was estimated instead. Estimates of the between-group differ- ence in absolute risk were also calculated. On June 4, 2020, in response to a request from the MHRA, the independent data monitor- ing committee conducted a review of the data and recommended that the chief investigators review the unblinded data for the hydroxychloro- quine group. The chief investigators and steer- ing committee members concluded that the data showed no beneficial effect of hydroxychloro- quine in patients hospitalized with Covid-19. Therefore, the enrollment of patients in the hy- droxychloroquine group was closed on June 5, 2020, and the preliminary result for the primary outcome was made public. Investigators were advised that any patients who were receiving hydroxychloroquine as part of the trial should discontinue the treatment. All the analyses were performed according to the intention-to-treat principle. Prespecified analy- ses of the primary outcome were performed in six subgroups, as defined by characteristics at randomization: age, sex, race, level of respira- tory support, days since symptom onset, and predicted 28-day risk of death. (Details are pro- vided in the Supplementary Appendix.) Primary Outcome Death at 28 days occurred in 421 of 1561 pa- tients (27.0%) in the hydroxychloroquine group and in 790 of 3155 patients (25.0%) in the usual- care group (rate ratio, 1.09; 95% confidence in- terval [CI], 0.97 to 1.23; P = 0.15) (Fig. 2). Similar results were seen across all six prespecified sub- groups (Fig. 3). In a post hoc exploratory analysis that was restricted to the 4266 patients (90.5%) with a positive SARS-CoV-2 test result, the result was similar to the overall result (rate ratio, 1.09; 95% CI, 0.96 to 1.23). ing at least one major coexisting illness that was recorded. In this analysis, 90% of the patients had laboratory-confirmed SARS-CoV-2 infection, with the result not known for less than 1%. At randomization, 17% were receiving invasive me- chanical ventilation including extracorporeal membrane oxygenation, 60% were receiving oxy- gen only (with or without noninvasive ventila- tion), and 24% were receiving neither. Figure 1. Enrollment and Outcomes in the RECOVERY Trial. The enrollment number that is shown is the total num- ber of patients in the RECOVERY platform trial during the period in which adult patients could be recruited for the comparison between hydroxychloroquine and usual care. Patients could have more than one reason for not participating in the hydroxychloroquine trial. At the time of this analysis, data from the trial follow-up form were available for 1553 of 1561 patients (99.5%) in the hydroxychloroquine group and for 3140 of 3155 patients (99.5%) in the usual-care group. The subgroup of patients who later underwent a second randomiza- tion to tocilizumab versus usual care in the RECOVERY trial included 37 of 1561 patients (2.4%) in the hydroxy- chloroquine group and 89 of 3155 patients (2.8%) in the usual care group. In addition, 6 patients were ran- domly assigned to receive either convalescent plasma or usual care alone (1 patient [0.1%] in the hydroxy- chloroquine group and 5 patients [0.2%] in the usual- care group) in accordance with protocol version 6.0. Among the 167 sites at which at least 1 patient was ­assigned to receive hydroxychloroquine, the median number of patients who underwent randomization was 20 (interquartile range, 11 to 41). 7513 (67%) Underwent randomization to receive hydroxychloroquine or other treatments 2797 Were assigned to another active treatment 1010 Were assigned to lopinavir– ritonavir 1170 Were assigned to dexameth- asone 617 Were assigned to azithro- mycin 4716 (42%) Underwent randomization to receive hydroxychloroquine or usual care alone group received hydroxychloroquine. The frequen- cy of use of azithromycin or other macrolide drug during the follow-up period was similar in the hydroxychloroquine group and the usual- care group (18.6% vs. 20.3%), as was the use of dexamethasone (9.1% vs. 9.2%). Remdesivir was administered to less than 0.1% of the patients in each group. Patients The committee was then charged with determining whether the randomized com- parisons in the trial provided evidence with re- spect to mortality that was strong enough (with 2033 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. The new engl and jour nal of medicine 7513 (67%) Underwent randomization to receive hydroxychloroquine or other treatments 11,197 Patients were recruited 639 (6%) Did not have access to hydroxychloroquine at their hospital 3199 (29%) Were considered unsuitable for receiving hydroxychloroquine 4716 (42%) Underwent randomization to receive hydroxychloroquine or usual care alone 2797 Were assigned to another active treatment 1010 Were assigned to lopinavir– ritonavir 1170 Were assigned to dexameth- asone 617 Were assigned to azithro- mycin 1561 (100%) Were assigned to receive hydroxychloroquine 1430 of 1553 (92%) Received hydroxychloroquine 3155 (100%) Were assigned to receive usual care 12 of 3140 (0.4%) Received hydroxychloroquine 3 (0.2%) Withdrew consent 5 (0.2%) Withdrew consent 75 (4.8%) Proceeded to second randomization 178 (5.6%) Proceeded to second randomization 1561 (100%) Were included in the 28-day intention-to-treat analysis 3155 (100%) Were included in the 28-day intention-to-treat analysis Figure 1. Enrollment and Outcomes in the RECOVERY Trial. n engl j med 383;21  nejm.org  November 19, 2020 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Secondary Outcomes Patients in the hydroxychloroquine group had a longer duration of hospitalization than those in the usual-care group (median, 16 days vs. 13 days) and a lower probability of discharge alive within 28 days (59.6% vs. 62.9%; rate ratio, 0.90; 95% CI, 0.83 to 0.98) (Table 2). Among the patients A total of 1430 patients in the hydroxychloro- quine group (92%) received at least one dose (Table S2). The median duration of treatment was 6 days (interquartile range, 3 to 10 days). In addition, 12 patients (0.4%) in the usual-care 2034 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Hydroxychloroquine in Patients with Covid-19 Table 1. Characteristics of the Patients at Baseline.* Characteristic Hydroxychloroquine (N = 1561) Usual Care (N = 3155) Age Mean ±SD 65.2±15.2 65.4±15.4 Distribution — no. (%) <70 yr 925 (59.3) 1873 (59.4) ≥70 to <80 yr 342 (21.9) 630 (20.0) ≥80 yr 294 (18.8) 652 (20.7) Sex — no. (%) Male 960 (61.5) 1974 (62.6) Female† 601 (38.5) 1181 (37.4) Race or ethnic group — no. (%)‡ White 1181 (75.7) 2298 (72.8) Black, Asian, or minority ethnic group 264 (16.9) 593 (18.8) Unknown 116 (7.4) 264 (8.4) Median no. of days since symptom onset (IQR)§ 9 (5–14) 9 (5–13) Median no. of days since hospitalization (IQR) 3 (1–6) 3 (1–5) Respiratory support — no. (%) No oxygen received 362 (23.2) 750 (23.8) Oxygen only 938 (60.1) 1873 (59.4) Invasive mechanical ventilation 261 (16.7) 532 (16.9) Previous disease — no. (%) Any of the listed conditions 882 (56.5) 1807 (57.3) Diabetes 427 (27.4) 856 (27.1) Heart disease 422 (27.0) 789 (25.0) Chronic lung disease 334 (21.4) 712 (22.6) Tuberculosis 4 (0.3) 9 (0.3) HIV infection 8 (0.5) 13 (0.4) Severe liver disease¶ 18 (1.2) 46 (1.5) Severe kidney impairment‖ 111 (7.1) 261 (8.3) SARS-CoV-2 test result — no. (%) Positive 1399 (89.6) 2867 (90.9) Negative 156 (10.0) 275 (8.7) Unknown 6 (0.4) 13 (0.4) * Percentages may not total 100 because of rounding. HIV denotes human immunodeficiency virus, IQR interquartile range, and SD standard deviation. * Percentages may not total 100 because of rounding. HIV denotes human immunodeficiency virus, IQR interquartile range, and SD standard deviation. * Percentages may not total 100 because of rounding. * Percentages may not total 100 because of rounding. HIV denotes human immunodeficiency virus, IQR interquartile range, and SD standard deviation. † Among the women, 2 in the hydroxychloroquine group and 4 in the usual-care group were pregnant. ‡ Race or ethnic group is reported as it was recorded in the patient’s electronic health record. § Data regarding the number of days since symptom onset were missing for 9 patients in the hydroxychloroquine group and 9 patients in the usual-care group. ¶ Severe liver disease was defined as a diagnosis that resulted in ongoing specialist care. ‖ Severe kidney impairment was defined as an estimated glomerular filtration rate of less than 30 ml per minute per 1.73 m2 of body-surface area. Secondary Outcomes HIV denotes human immunodeficiency virus, IQR interquartile range, and SD standard deviation. † Among the women, 2 in the hydroxychloroquine group and 4 in the usual-care group were pregnant. ‡ Race or ethnic group is reported as it was recorded in the patient’s electronic health record. § Data regarding the number of days since symptom onset were missing for 9 patients in the hydroxychloroquine group and 9 patients in the usual-care group. ¶ Severe liver disease was defined as a diagnosis that resulted in ongoing specialist care. ‖ Severe kidney impairment was defined as an estimated glomerular filtration rate of less than 30 ml per minute per 1.73 m2 of body-surface area. who were not undergoing invasive mechanical ventilation at baseline, the number of patients who had progression to the prespecified com- posite secondary outcome of invasive mechani- cal ventilation or death was higher among those in the hydroxychloroquine group than among posite secondary outcome of invasive mechani- cal ventilation or death was higher among those in the hydroxychloroquine group than among who were not undergoing invasive mechanical ventilation at baseline, the number of patients who had progression to the prespecified com- 2035 n engl j med 383;21  nejm.org  November 19, 2020 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. The new engl and jour nal of medicine Figure 2. Mortality at 28 Days. Death at 28 days (the primary outcome) occurred in 421 patients (27.0%) in the hydroxychloroquine group and in 790 (25.0%) in the usual-care group. The inset shows the same data on an expanded y axis. Mortality (%) 100 80 90 70 60 40 30 10 50 20 0 0 7 14 21 28 Days since Randomization 30 10 20 0 15 25 5 0 7 14 21 28 Rate ratio, 1.09 (95% CI, 0.97–1.23) P=0.15 by log-rank test No. at Risk Hydroxychloroquine Usual care 1561 3155 1337 2750 1227 2525 1169 2414 1137 2360 Hydroxychloroquine Usual care atrioventricular block requiring intervention (0.1% vs. 0.1%) (Table S4). Discussion In this analysis of the RECOVERY trial, we de- termined that hydroxychloroquine was not an effective treatment for patients hospitalized with Covid-19. The lower boundary of the confidence limit for the primary outcome ruled out any reasonable possibility of a meaningful mortality benefit. The results were consistent across sub- groups according to age, sex, race, time since illness onset, level of respiratory support, and baseline-predicted risk. In addition, the results suggest that the patients who received hydroxy- chloroquine had a longer duration of hospital- ization and, among those who were not under- going mechanical ventilation at baseline, a higher risk of invasive mechanical ventilation or death than those who received usual care. Figure 2. Mortality at 28 Days. Death at 28 days (the primary outcome) occurred in 421 patients (27.0%) in the hydroxychloroquine group and in 790 (25.0%) in the usual-care group. The inset shows the same data on an expanded y axis. Death at 28 days (the primary outcome) occurred in 421 patients (27.0%) in the hydroxychloroquine group and in 790 (25.0%) in the usual-care group. The inset shows the same data on an expanded y axis. those in the usual-care group (risk ratio, 1.14; 95% CI, 1.03 to 1.27). Secondary Outcomes There was one report of a serious adverse reaction that was deemed by investigators to be related to hydroxychloro- quine: a case of torsades de pointes, from which the patient recovered without undergoing inter- vention. Among the patients who were not re- ceiving renal dialysis or hemofiltration at ran- domization, the percentage who went on to receive such treatment during the follow-up period was the same in the hydroxychloroquine group and the usual-care group (7.9% vs. 7.9%) (Table S5). Mortality (%) The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Other Prespecified Outcomes 0.75 1.0 2.0 1.5 Usual Care Better Hydroxychloroquine Better Age <70 yr ≥70 to <80 yr ≥80 yr Sex Male Female Race or ethnic group White Black, Asian, or minority ethnic group Days since symptom onset ≤7 >7 Respiratory support at randomization No oxygen received Oxygen only Invasive mechanical ventilation Baseline risk <30% ≥30% to <45% ≥45% All Participants Hydroxychloroquine Rate Ratio (95% CI) Usual Care Subgroup 0.50 no. of events/total no. (%) 160/925 (17.3) 314/1873 (16.8) 1.03 (0.85−1.25) 128/342 (37.4) 207/630 (32.9) 1.17 (0.93–1.47) 133/294 (45.2) 269/652 (41.3) 1.14 (0.92−1.42) 276/960 (28.8) 543/1974 (27.5) 1.05 (0.91−1.22) 145/601 (24.1) 247/1181 (20.9) 1.19 (0.96−1.47) 335/1181 (28.4) 610/2298 (26.5) 1.09 (0.95–1.25) 65/264 (24.6) 115/593 (19.4) 1.32 (0.96–1.81) 177/622 (28.5) 339/1275 (26.6) 1.10 (0.91−1.32) 242/930 (26.0) 445/1871 (23.8) 1.11 (0.94−1.30) 58/362 (16.0) 99/750 (13.2) 1.24 (0.89−1.73) 253/938 (27.0) 475/1873 (25.4) 1.08 (0.93−1.26) 110/261 (42.1) 216/532 (40.6) 1.03 (0.81−1.30) 146/994 (14.7) 274/1990 (13.8) 1.07 (0.88−1.32) 135/317 (42.6) 246/635 (38.7) 1.12 (0.90−1.40) 140/250 (56.0) 270/530 (50.9) 1.17 (0.95−1.45) 421/1561 (27.0) 790/3155 (25.0) P=0.15 1.09 (0.97−1.23) Figure 3. Mortality at 28 Days, According to Subgroup. The size of the squares representing rate ratios is proportional to the amount of statistical information that was available for each comparison. The method that was used for calculating the baseline-predicted risk in each sub- group is described in the Supplementary Appendix. Race or ethnic group was recorded in the patient’s electronic health record. 0.75 1.0 2.0 1.5 Usual Care Better Hydroxychloroquine Better Age <70 yr ≥70 to <80 yr ≥80 yr Sex Male Female Race or ethnic group White Black, Asian, or minority ethnic group Days since symptom onset ≤7 >7 Respiratory support at randomization No oxygen received Oxygen only Invasive mechanical ventilation Baseline risk <30% ≥30% to <45% ≥45% All Participants Hydroxychloroquine Rate Ratio (95% CI) Usual Care Subgroup 0.50 no. of events/total no. Other Prespecified Outcomes There was no difference between the hydroxy- chloroquine group and the usual-care group in 28-day mortality that was ascribed to Covid-19 (24.0% vs. 23.5%). However, patients in the hy- droxychloroquine group had a greater risk of death from cardiac causes (mean [±SE] excess, 0.4±0.2 percentage points) and from non–SARS- CoV-2 infection (mean excess, 0.4±0.2 percent- age points) (Table S3). Data regarding the occur- rence of new major cardiac arrhythmia were collected for 735 of 1561 patients (47.1%) in the hydroxychloroquine group and 1421 of 3155 pa- tients (45.0%) in the usual-care group, after col- lection of this information was added to the follow-up form on May 12, 2020. Among these patients, there were no significant differences between the hydroxychloroquine group and the usual-care group in the frequency of supraven- tricular tachycardia (7.6% vs. 6.0%), ventricular tachycardia or fibrillation (0.7% vs. 0.4%), or The RECOVERY trial is a large, pragmatic, randomized, controlled platform trial designed to assess the effect of potential treatments for Covid-19 on 28-day mortality. Approximately 15% of the patients who were hospitalized with Covid-19 in the United Kingdom during the trial period were enrolled, and the percentage of pa- tients in the usual-care group who died was consistent with the hospitalized case fatality rate among hospitalized patients in the United King- dom and elsewhere.7,30,31 Only essential data were collected at hospital sites, with additional infor- mation (including long-term mortality) ascer- tained through linkage with routine data sources. We did not collect information on physiologic, electrocardiographic, laboratory, or virologic measurements. Hydroxychloroquine has been proposed as a treatment for Covid-19 largely on the basis of its 2036 n engl j med 383;21  nejm.org  November 19, 2020 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Hydroxychloroquine in Patients with Covid-19 Figure 3. Mortality at 28 Days, According to Subgroup. The size of the squares representing rate ratios is proportional to the amount of statistical information that was available for each comparison. The method that was used for calculating the baseline-predicted risk in each sub- group is described in the Supplementary Appendix. Race or ethnic group was recorded in the patient’s electronic health record. Other Prespecified Outcomes However, the 4-amino- quinoline drugs are relatively weak antiviral agents.15 The demonstration of therapeutic effi- cacy of hydroxychloroquine in severe Covid-19 would require rapid attainment of efficacious levels of free drug in the blood and respiratory epithelium.32 Thus, to provide the greatest chance of providing benefit in life-threatening Covid-19, the dose regimen in our trial was designed to result in rapid attainment and maintenance of plasma levels that were as high as safely possi- ble.15 These levels were predicted to be at the upper end of those observed during steady-state treatment of rheumatoid arthritis with hydroxy- chloroquine.33 Our dosing schedule was based on pharmacokinetic modeling of hydroxychloro- quine that referenced a SARS-CoV-2 50% effec- tive concentration of 0.72 μM, as scaled to whole-blood levels and on the assumption that cytosolic levels in the respiratory epithelium are in dynamic equilibrium with blood levels.8,15,34 of very few events, but we did not observe ex- cess mortality in the first 2 days of treatment with hydroxychloroquine, the time when early effects of dose-dependent toxicity might be ex- pected. Furthermore, the data presented here did not show any excess in ventricular tachycardia or ventricular fibrillation in the hydroxychloro- quine group. g These findings indicate that hydroxychloro- quine is not an effective treatment for hospital- ized patients with Covid-19 but do not address its use as prophylaxis or in patients with less severe SARS-CoV-2 infection managed in the com- munity. A review of Covid-19 treatment guide- lines that was produced early in the pandemic showed that chloroquine or hydroxychloroquine was recommended in China, France, Italy, the Netherlands, and South Korea.37 In the United States, the use of chloroquine and hydroxychlo- roquine was permitted in certain hospitalized pa- tients under an Emergency Use Authorization (EUA) of the Food and Drug Administration (FDA). A retrospective cohort study involving 1376 pa- tients with Covid-19 who were admitted to the hospital in New York City in March and April 2020 showed that 59% of the patients received hydroxychloroquine.22,38 Since our preliminary re- sults were made public on June 5, 2020, the FDA has revoked the EUA for chloroquine and hydroxy- chloroquine,39 and the World Health Organiza- tion (WHO) and the National Institutes of Health have ceased trials of its use in hospitalized pa- tients on the grounds of a lack of benefit. Other Prespecified Outcomes (%) 160/925 (17.3) 314/1873 (16.8) 1.03 (0.85−1.25) 128/342 (37.4) 207/630 (32.9) 1.17 (0.93–1.47) 133/294 (45.2) 269/652 (41.3) 1.14 (0.92−1.42) 276/960 (28.8) 543/1974 (27.5) 1.05 (0.91−1.22) 145/601 (24.1) 247/1181 (20.9) 1.19 (0.96−1.47) 335/1181 (28.4) 610/2298 (26.5) 1.09 (0.95–1.25) 65/264 (24.6) 115/593 (19.4) 1.32 (0.96–1.81) 177/622 (28.5) 339/1275 (26.6) 1.10 (0.91−1.32) 242/930 (26.0) 445/1871 (23.8) 1.11 (0.94−1.30) 58/362 (16.0) 99/750 (13.2) 1.24 (0.89−1.73) 253/938 (27.0) 475/1873 (25.4) 1.08 (0.93−1.26) 110/261 (42.1) 216/532 (40.6) 1.03 (0.81−1.30) 146/994 (14.7) 274/1990 (13.8) 1.07 (0.88−1.32) 135/317 (42.6) 246/635 (38.7) 1.12 (0.90−1.40) 140/250 (56.0) 270/530 (50.9) 1.17 (0.95−1.45) 421/1561 (27.0) 790/3155 (25.0) P=0.15 1.09 (0.97−1.23) Figure 3. Mortality at 28 Days, According to Subgroup. The size of the squares representing rate ratios is proportional to the amount of statistical information that was available for each comparison. The method that was used for calculating the baseline-predicted risk in each sub- group is described in the Supplementary Appendix. Race or ethnic group was recorded in the patient’s electronic health record. he size of the squares representing rate ratios is proportional to the amount of statistical information that was vailable for each comparison. The method that was used for calculating the baseline-predicted risk in each sub- oup is described in the Supplementary Appendix. Race or ethnic group was recorded in the patient’s electronic ealth record. Table 2. Primary and Secondary Outcomes. Outcome Hydroxychloroquine (N = 1561) Usual Care (N = 3155) Rate or Risk Ratio (95% CI) no./total no. (%) Primary outcome: 28-day mortality 421/1561 (27.0) 790/3155 (25.0) 1.09 (0.97–1.23)* Secondary outcomes Discharge from hospital in ≤28 days 931/1561 (59.6) 1983/3155 (62.9) 0.90 (0.83–0.98)* Invasive mechanical ventilation or death† 399/1300 (30.7) 705/2623 (26.9) 1.14 (1.03–1.27)‡ Invasive mechanical ventilation 128/1300 (9.8) 225/2623 (8.6) 1.15 (0.93–1.41) Death 311/1300 (23.9) 574/2623 (21.9) 1.09 (0.97–1.23) * The between-group difference was calculated as a rate ratio. † Patients who were receiving invasive mechanical ventilation at randomization were excluded from this analysis. ‡ The between-group difference was calculated as a risk ratio. 2037 n engl j med 383;21  nejm.org  November 19, 2020 The new engl and jour nal of medicine in vitro SARS-CoV-2 antiviral activity and on data from observational studies reporting effective reduction in viral loads. The views expressed in this article are those of the authors and not necessarily those of the National Health Service (NHS), the National Institute for Health Research (NIHR), or the De- partment of Health and Social Care. n engl j med 383;21  nejm.org  November 19, 2020 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Other Prespecified Outcomes The WHO has released preliminary results from the SOLIDARITY trial on the effectiveness of hy- droxychloroquine in hospitalized patients with Covid-19 that are consistent with the results from the RECOVERY trial.40 The primary concern with short-term, high- dose 4-aminoquinoline regimens is cardiovas- cular toxicity. Hydroxychloroquine causes pre- dictable prolongation of the corrected QT interval on electrocardiography, which is exacerbated by coadministration with azithromycin, as widely prescribed in Covid-19 treatment.16-18 Although torsades de pointes has been described, serious cardiovascular toxicity has been infrequently re- ported, despite the high prevalence of cardio- vascular disease in hospitalized patients, the common occurrence of myocarditis in Covid-19, and the extensive use of hydroxychloroquine and azithromycin together. The exception is a Brazilian study that was stopped early because of cardiotoxicity. However, in that study, chloro- quine was administered at a base dose of 600 mg twice daily for 10 days, a higher total dose than those that were used in other trials, including the RECOVERY trial.35,36 Pharmacokinetic mod- eling in combination with information regarding blood levels and mortality from a case series involving 302 patients with chloroquine over- dose predicts that a chloroquine regimen that was equivalent to the hydroxychloroquine regi- men used in our trial should have an acceptable safety profile.36 There was a small absolute ex- cess of cardiac mortality of 0.4 percentage points in the hydroxychloroquine group on the basis The views expressed in this article are those of the authors and not necessarily those of the National Health Service (NHS), the National Institute for Health Research (NIHR), or the De- partment of Health and Social Care. Supported by a grant (MC_PC_19056) to the University of Oxford from UK Research and Innovation and the NIHR and by core funding provided by NIHR Oxford Biomedical Research Centre, Wellcome, the Bill and Melinda Gates Foun- dation, the Department for International Development, Health Data Research UK, the Medical Research Council Population Health Research Unit, the NIHR Health Protection Unit in Emerging and Zoonotic Infections, and NIHR Clinical Trials Unit Support Funding. Tocilizumab was provided free of charge for this study by Roche. AbbVie contributed some supplies of lopinavir–ritonavir for use in the trial. The hydroxychloroquine that was used in the trial was supplied by the NHS. Disclosure forms provided by the authors are available with the full text of this article at NEJM.org. Appendix The authors’ full names and academic degrees are as follows: The RECOVERY Collaborative GroupPeter Horby, F.R.C.P., Marion Mafham, M.D., Louise Linsell, D.Phil., Jennifer L. Bell, M.Sc., Natalie Staplin, Ph.D., Jonathan R. Emberson, Ph.D., Martin Wiselka, Ph.D., Andrew Ustianowski, Ph.D., Einas Elmahi, M.Phil., Benjamin Prudon, F.R.C.P., Tony Whitehouse, F.R.C.A., Timothy Felton, Ph.D., John Wil- liams, M.R.C.P., Jakki Faccenda, M.D., Jonathan Underwood, Ph.D., J. Kenneth Baillie, M.D., Ph.D., Lucy C. Chappell, Ph.D., Saul N. Faust, F.R.C.P.C.H., Thomas Jaki, Ph.D., Katie Jeffery, Ph.D., Wei Shen Lim, F.R.C.P., Alan Montgomery, Ph.D., Kathryn Rowan, Ph.D., Joel Tarning, Ph.D., James A. Watson, D.Phil., Nicholas J. White, F.R.S., Edmund Juszczak, M.Sc., Richard Haynes, D.M., and Martin J. Landray, Ph.D. The authors’ full names and academic degrees are as follows: The RECOVERY Collaborative GroupPeter Horby, F.R.C.P., Marion Mafham, M.D., Louise Linsell, D.Phil., Jennifer L. Bell, M.Sc., Natalie Staplin, Ph.D., Jonathan R. Emberson, Ph.D., Martin Wiselka, Ph.D., Andrew Ustianowski, Ph.D., Einas Elmahi, M.Phil., Benjamin Prudon, F.R.C.P., Tony Whitehouse, F.R.C.A., Timothy Felton, Ph.D., John Wil- liams, M.R.C.P., Jakki Faccenda, M.D., Jonathan Underwood, Ph.D., J. Kenneth Baillie, M.D., Ph.D., Lucy C. Chappell, Ph.D., Saul N. Faust, F.R.C.P.C.H., Thomas Jaki, Ph.D., Katie Jeffery, Ph.D., Wei Shen Lim, F.R.C.P., Alan Montgomery, Ph.D., Kathryn Rowan, Ph.D., Joel Tarning, Ph.D., James A. Watson, D.Phil., Nicholas J. White, F.R.S., Edmund Juszczak, M.Sc., Richard Haynes, D.M., and Martin J. Landray, Ph.D. Hydroxychloroquine in Patients with Covid-19 A data sharing statement provided by the authors is available with the full text of this article at NEJM.org. of Health and Social Care, the Intensive Care National Audit and Research Centre, Public Health Scotland, National Records Ser- vice of Scotland, the Secure Anonymised Information Linkage at University of Swansea, and the NHS in England, Scotland, Wales, and Northern Ireland; and the members of the independent data monitoring committee: Peter Sandercock, Janet Darbyshire, David DeMets, Robert Fowler, David Lalloo, Ian Roberts, and Janet Wittes. We thank the thousands of patients who participated in this trial; the doctors, nurses, pharmacists, other allied health profession- als, and research administrators at 176 NHS hospitals across the United Kingdom who were assisted by the NIHR Clinical Research Network, NHS DigiTrials, Public Health England, the Department Appendix y, The affiliations of the members of the writing committee are as follows: the Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine (P.H., J.T., J.A.W., N.J.W.), Nuffield Department of Population Health (M.M., L.L., J.L.B., N.S., J.R.E., E.J., R.H., M.J.L.), the Medical Research Council (MRC) Population Health Research Unit (N.S., J.R.E., R.H., M.J.L.), University of Oxford, the Oxford University Hospitals NHS Foundation Trust (K.J., M.J.L.), and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (M.J.L.), Oxford, University Hospitals of Leicester NHS Trust and University of Leicester, Leicester (M.W.), the Regional Infectious Diseases Unit, North Manchester General Hospital (A.U.), University of Manchester (A.U., T.F.), and Manches- ter University NHS Foundation Trust (T.F.), Manchester, the Research and Development Department, Northampton General Hospital, Northampton (E.E.), the Department of Respiratory Medicine, North Tees and Hartlepool NHS Foundation Trust, Stockton-on-Tees (B.P.), University Hospitals Birmingham NHS Foundation Trust and Institute of Microbiology and Infection, University of Birmingham, Birmingham (T.W.), James Cook University Hospital, Middlesbrough (J.W.), North West Anglia NHS Foundation Trust, Peterborough (J.F.), the Department of Infectious Diseases, Cardiff and Vale University Health Board, and the Division of Infection and Immunity, Cardiff University, Cardiff (J.U.), Roslin Institute, University of Edinburgh, Edinburgh (J.K.B.), the School of Life Course Sciences, King’s College London (L.C.C.), and the Intensive Care National Audit and Research Centre (K.R.), London, the NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, Southampton (S.N.F.), the Department of Mathematics and Statistics, Lancaster University, Lancaster (T.J.), the MRC Biostatistics Unit, University of Cambridge, Cambridge (T.J.), and the Respiratory Medicine Department, Nottingham University Hos- pitals NHS Trust (W.S.L.), and the School of Medicine, University of Nottingham (A.M., E.J.), Nottingham — all in the United King- dom; and the Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand (J.T., J.A.W., N.J.W.). Other Prespecified Outcomes 2038 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. References stratification of patients admitted to hos- pital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: devel- opment and validation of the 4C Mortality Score. BMJ 2020;​370:​m3339. stratification of patients admitted to hos- pital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: devel- opment and validation of the 4C Mortality Score. BMJ 2020;​370:​m3339. Clinical evidence for repurposing chloro- quine and hydroxychloroquine as anti- viral agents: a systematic review. Clin Microbiol Infect 2020;​26:​979-87. stratification of patients admitted to hos- pital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: devel- opment and validation of the 4C Mortality Score. 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Hydroxychloroquine proves ineffec- tive in hamsters and macaques infected with SARS-CoV-2. Hydroxychloroquine in Patients with Covid-19 Hydroxychloroquine in Patients with Covid-19 Clinical and microbiological effect of a combination of hydroxychloroquine and azithromycin in 80 COVID-19 patients with at least a six-day follow up: a pilot observational study. Travel Med Infect Dis 2020;​34:​101663. 34. Yao X, Ye F, Zhang M, et al. In vitro antiviral activity and projection of opti- mized dosing design of hydroxychloro- quine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2). Clin Infect Dis 2020;​71:​732-9. to moderate coronavirus disease 2019: open label, randomised controlled trial. BMJ 2020;​369:​m1849. to moderate coronavirus disease 2019: open label, randomised controlled trial. BMJ 2020;​369:​m1849. 26. Huang M, Tang T, Pang P, et al. Treat- ing COVID-19 with chloroquine. J Mol Cell Biol 2020;​12:​322-5. 35. Borba MGS, Val FFA, Sampaio VS, et al. 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Chen Z, Hu J, Zhang Z, et al. Efficacy of hydroxychloroquine in patients with COVID-19: results of a randomized clinical trial. April 10, 2020 (https://www​.­medrxiv​ .­org/​­content/​­10​.­1101/​­2020​.­03​.­22​ 20. Gao J, Tian Z, Yang X. Breakthrough: chloroquine phosphate has shown appar- ent efficacy in treatment of COVID-19 associated pneumonia in clinical studies. Biosci Trends 2020;​14:​72-3. .­20040758v3). preprint. .­20040758v3). preprint. 21. Yu B, Li C, Chen P, et al. Low dose of hydroxychloroquine reduces fatality of criti- cally ill patients with COVID-19. Sci China Life Sci 2020 May 15 (Epub ahead of print). 22. Geleris J, Sun Y, Platt J, et al. Observa- tional study of hydroxychloroquine in hos- pitalized patients with Covid-19. N Engl J Med 2020;​382:​2411-8. 37. Hydroxychloroquine in Patients with Covid-19 Dagens A, Sigfrid L, Cai E, et al. Scope, quality, and inclusivity of clinical guidelines produced early in the covid-19 pandemic: rapid review. 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Letter from the U.S. Food and Drug Administration re:​ revocation of the Emer- gency Use Authorization (EUA) letter of March 20, 2020. June 15, 2020 (https:// www​.­fda​.­gov/​­media/​­138945/​­download). 40. World Health Organization. WHO dis- continues hydroxychloroquine and lopina- vir/ritonavir treatment arms for COVID-19. July 4, 2020 (https://www​.­who​.­int/​­news​ -­room/​­detail/​­04​-­07​-­2020​-­who​-­discontinues​ -­hydroxychloroquine​-­and​-­lopinavir​ -­ritonavir​-­treatment​-­arms​-­for​-­covid​-­19). Copyright © 2020 Massachusetts Medical Society. 31. Armstrong RA, Kane AD, Cook TM. Outcomes from intensive care in patients with COVID-19: a systematic review and meta-analysis of observational studies. Anaesthesia 2020;​75:​1340-9. 24. Molina JM, Delaugerre C, Le Goff J, et al. No evidence of rapid antiviral clear- ance or clinical benefit with the combina- tion of hydroxychloroquine and azithro- mycin in patients with severe COVID-19 infection. Med Mal Infect 2020;​50:​384. 32. Austin D, Okour M. Evaluation of po- tential therapeutic options for COVID-19. J Clin Pharmacol 2020;​60:​976-7. 33. Carmichael SJ, Charles B, Tett SE. Population pharmacokinetics of hydroxy- chloroquine in patients with rheumatoid arthritis. Ther Drug Monit 2003;​25:​671-81. 25. Tang W, Cao Z, Han M, et al. Hydroxy- chloroquine in patients with mainly mild 25. Tang W, Cao Z, Han M, et al. Hydroxy- chloroquine in patients with mainly mild 2040 n engl j med 383;21  nejm.org  November 19, 2020 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. References June 11, 2020 (https:// www​.­biorxiv​.­org/​­content/​­10​.­1101/​­2020​.­06​ .­10​.­145144v1). preprint. 5. Cao J, Tu W-J, Cheng W, et al. Clinical features and short-term outcomes of 102 patients with coronavirus disease 2019 in Wuhan, China. Clin Infect Dis 2020;​71:​ 748-55. 11. Zhou P, Yang X-L, Wang X-G, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 2020;​579:​270-3. 12. Keyaerts E, Vijgen L, Maes P, Neyts J, Van Ranst M. In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine. Biochem Biophys Res Commun 2004;​323:​264-8. 17. Gautret P, Lagier J-C, Parola P, et al. Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial. Int J Antimicrob Agents 2020;​56:​105949. 18. Gautret P, Lagier J-C, Parola P, et al. 6. Ruan Q, Yang K, Wang W, Jiang L, Song J. Clinical predictors of mortality due to COVID-19 based on an analysis of data of 150 patients from Wuhan, China. Intensive Care Med 2020;​46:​846-8. 13. Rodrigo C, Fernando SD, Rajapakse S. 13. Rodrigo C, Fernando SD, Rajapakse S. 7. Knight SR, Ho A, Pius R, et al. Risk 2039 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved. Hydroxychloroquine in Patients with Covid-19 The New England Journal of Medicine Downloaded from nejm.org on February 21, 2021. For personal use only. No other uses without permission. Copyright © 2020 Massachusetts Medical Society. All rights reserved.
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Fear of falling and postural reactivity in patients with glaucoma
PloS one
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RESEARCH ARTICLE Fa´bio B. Daga1,2,3, Alberto Diniz-Filho3, Erwin R. Boer3, Carolina P. B. Gracitelli2,3, Ricardo Y. Abe3, Felipe A. Medeiros1,3* Fa´bio B. Daga1,2,3, Alberto Diniz-Filho3, Erwin R. Boer3, Carolina P. B. Gracitelli2,3, Ricardo Y. Abe3, Felipe A. Medeiros1,3* Fa´bio B. Daga1,2,3, Alberto Diniz-Filho3, Erwin R. Boer3, Carolina P. B. Gracitelli2,3, Ricardo Y. Abe3, Felipe A. Medeiros1,3* 1 Duke Eye Center and Department of Ophthalmology, Duke University, Durham, North Carolina, United States of America, 2 Department of Ophthalmology and Vision Science, Federal University of São Paulo, São Paulo, Brazil, 3 Department of Ophthalmology, University of California, San Diego, La Jolla, California, United States of America * felipe.medeiros@duke.edu a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: National Institutes of Health/National Eye Institute grant EY021818 (F.A.M), fellowship grant from Brazilian National Council for Scientific and Technological Development (CNPq) 233829/2014- 8 (A.D.F.). Financial support FAM: Alcon Laboratories (Fort Worth, TX), Bausch & Lomb (Garden City, NY), Carl Zeiss Meditec (Jena, Germany), Heidelberg Engineering (Heidelberg, Germany), Merck (White House Station, NJ), Editor: Manabu Sakakibara, Tokai University, JAPAN Editor: Manabu Sakakibara, Tokai University, JAPAN Received: August 4, 2017 Accepted: October 16, 2017 Published: December 6, 2017 Abstract Purpose To investigate the relationship between postural metrics obtained by dynamic visual stimula- tion in a virtual reality environment and the presence of fear of falling in glaucoma patients. Results Copyright: © 2017 Daga et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Subjects with glaucoma reported greater fear of falling compared to controls (-0.21 vs. 0.27; P = 0.039). In glaucoma patients, postural metrics during dynamic visual stimulus were more associated with fear of falling (R2 = 18.8%; P = 0.001) than static (R2 = 3.0%; P = 0.005) and dark field (R2 = 5.7%; P = 0.007) conditions. In the univariable model, fear of fall- ing was not significantly associated with binocular standard perimetry mean sensitivity (P = 0.855). In the multivariable model, each 1 Nm larger SDTM in anteroposterior direction dur- ing dynamic stimulus was associated with a worsening of 0.42 units in the fear of falling questionnaire score (P = 0.001). Methods Citation: Daga FB, Diniz-Filho A, Boer ER, Gracitelli CPB, Abe RY, Medeiros FA (2017) Fear of falling and postural reactivity in patients with glaucoma. PLoS ONE 12(12): e0187220. https://doi.org/ 10.1371/journal.pone.0187220 This cross-sectional study included 35 glaucoma patients and 26 controls that underwent evaluation of postural balance by a force platform during presentation of static and dynamic visual stimuli with head-mounted goggles (Oculus Rift). In dynamic condition, a peripheral translational stimulus was used to induce vection and assess postural reactivity. Standard deviations of torque moments (SDTM) were calculated as indicative of postural stability. Fear of falling was assessed by a standardized questionnaire. The relationship between a summary score of fear of falling and postural metrics was investigated using linear regres- sion models, adjusting for potentially confounding factors. Editor: Manabu Sakakibara, Tokai University, JAPAN Introduction Allergan (Irvine, CA), Sensimed (Lausanne, Switzerland), Topcon (Livermore, CA), Reichert (Dewey, NY), National Eye Institute (Bethesda, MD); Research support – Alcon Laboratories (Fort Worth, TX), Allergan (Irvine, CA), Carl Zeiss Meditec (Jena, Germany), Reichert (Dewey, NY); Consultant – Allergan (Irvine, CA), Carl-Zeiss Meditec, (Jena, Germany), Novartis (Basel, Switzerland), nGoggle (San Diego, CA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Falls are one of the most common and potentially disabling issues among elderly people, jeop- ardizing their health and independence.[1–7] Vision has an important role in balance control and environment navigation, with previous studies demonstrating that conditions leading to visual impairment are associated to higher risk of falling.[8–11] Glaucoma is a progressive optic neuropathy characterized by degeneration of retinal ganglion cells and their axons and previous studies have reported a higher risk of falling in patients with glaucoma compared to normal subjects.[12–14] Glaucoma has also been related to greater fear of falling.[15–19] Fear of falling may have major impact in older adults, since it leads to restriction of daily activities,[20] causing reduc- tion in social interaction and mobility,[21,22] loss of confidence,[2,20,21] and depression.[23] In addition, by restricting physical activity, fear of falling may result in further increase in risk of falling. As actual falls may then lead to increased fear of falling, the process can become a vicious circle.[24] Therefore, an assessment of fear of falling is important in order to under- stand factors associated with fall risk and for development of assistive strategies. Competing interests: The authors have declared that no competing interests exist Competing interests: The authors have declared that no competing interests exist Although standard automatic perimetry (SAP) has been the gold standard test for assessing visual function loss in glaucoma, the association with measures of fear of falling has been inconsistent in the literature.[24] In SAP visual function is measured by assessing sensitivity to detect a static white stimulus against a white background. Due to its simplicity, it is likely that SAP testing does not fully capture certain dynamic aspects of vision that may be important in performing daily activities, such as maintaining balance. Fear of falling and postural reactivity Introduction In a previous study, we developed a virtual reality paradigm to evaluate postural control of glaucoma patients in response to dynamic visual stimulation.[11] Postural reactivity was induced by presenting peripheral dynamic visual stimuli in an immersive virtual environment using stereoscopic goggles, while assessing balance through a balance platform. Metrics obtained under this testing paradigm performed significantly better to predict history of falls in patients with glaucoma compared to SAP. However, the relationship between postural reactivity metrics and fear of falling has not yet been investigated. Such relationship could be important in understanding factors that are associated with increased fear of falling in glaucoma. The purpose of this study was to quantify fear of falling in a cohort of patients with glau- coma and control subjects and investigate the relationship between fear of falling and metrics of postural reactivity obtained using a virtual reality environment. Conclusion In glaucoma patients, postural reactivity to a dynamic visual stimulus using a virtual reality environment was more strongly associated with fear of falling than visual field testing and traditional balance assessment. 1 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 Methods This was a cross-sectional study. Written informed consent was obtained from all participants (including controls and glaucoma patients). Institutional review board approval was obtained and the study was conducted in adherence with the Declaration of Helsinki and to the Health Insurance Portability and Accountability Act. Participants in this study underwent a comprehensive ophthalmologic examination, and each visited included clinical examination, slit lamp biomicroscopy, visual acuity testing, gonioscopy, dilated fundus examination, intraocular pressure measurement and stereophotog- raphy. In addition, participants underwent visual field testing using the Swedish Interactive Thresholding Algorithm Standard 24–2 strategy on a Humphrey Field Analyzer II-i (Carl Zeiss Meditec, Dublin, CA), and they were required to have reliable visual field tests, which was defined as having  33% fixation losses or false negative errors, or  15% of false positive errors. Visual acuity was measured using Early Treatment Diabetic Retinopathy Study chart and letter acuity was expressed as the logarithm of minimum angle of resolution. We included only subjects with open angles on gonioscopy. We also investigated about previous systemic PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 2 / 13 Fear of falling and postural reactivity diseases (diabetes and hypertension), and also about the systemic use of β-blockers or α-ago- nists. Subjects were excluded if they presented any other ocular or systemic disease that could affect optic nerve or visual field. Subjects were also excluded if they presented with history of systemic conditions affecting lower limbs, such as arthritis, gout, history of knee or hip replacement, or any other pathology affecting the vestibular system. Glaucoma was defined by the presence of repeatable abnormal SAP tests (pattern standard deviation with P < 0.05 and/or a Glaucoma Hemifield Test outside normal limits) and corre- sponding optic nerve damage in at least one eye. Healthy control participants in this study were recruited from the general population through advertisements and were required to be normal on ophthalmological examination and normal appearance of the optic disc on masked grading of stereophotographs. Severity of visual field defect was represented by the integrated binocular mean sensitivity (MS) obtained from monocular SAP 24–2 tests. The integrated bin- ocular MS was calculated as the average of sensitivities of the integrated binocular visual fields obtained according to the binocular summation model described by Nelson-Quigg et al.[25] All subjects had measurements of weight and height obtained at the time of testing. Fear of falling evaluation Fear of falling was evaluated using the previously validated 16-item University of Illinois at Chicago fear of falling scoring questionnaire (Fig 1).[28] Questionnaires were administered orally to subjects during an in-person interview. Patients were asked about how much fear they would have if they were to perform any of 16 different tasks, regardless of whether these tasks had been performed recently. Three possible responses were accepted: not at all worried (score 3), moderately worried (score 2), or very worried (score 1).[28] A partial credit item response theory (IRT) model was used to summarize data from the questionnaires and a final score of fear of falling was obtained. By taking into account item difficulty and discrimination, summary scores of fear of falling were obtained for each subject. Scores ranged from -3 to +1, with lower values associated with greater fear of falling. Methods These were used to calculate body mass index (BMI) for each subject, as the quotient of mass (in kilo- grams) divided by the square of height (in meters). Level of physical activity was investigated using the Physical Activity Scale for the Elderly (PASE) questionnaire.[26] The scale ranges from 0 to 400, with higher scores indicating greater level of physical activity.[26] History of falls was acquired using the Elderly Fall Screening Test and the Multi-factor Falls Question- naire.[27] Virtual reality environment for assessing postural reactivity Postural reactivity to visual information was assessed using an immersive virtual environment with head-mounted stereoscopic goggles (Oculus Rift, Oculus VR, LLC, Irvine, CA) (Fig 2). Details of the testing procedure have been described previously.[11] The Oculus Rift was used to present a stereoscopic 3D image on a binocular field of view of approximately 100 degrees diagonal. Postural stability was evaluated using a force platform (AMTI Optima Human Per- formance System, Advanced Mechanical Technology, Inc., Watertown, MA). Subjects were supported by a harness system to prevent falling (Handrail and Harness Safety Structure, Ber- tec Corp., Columbus, OH) (Fig 2). Subjects were required to remove their shoes and stand upright on the center of the force platform with arms by their side and feet close together. Subjects underwent postural assessment under three conditions: 1. No Oculus Rift (static condition); 2. Oculus Rift in a dark field, without any visual stimulation; PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 3 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 Fear of falling and postural reactivity Fig 1. The 16-item University of Illinois at Chicago fear of falling measure scoring questionnaire. https://doi.org/10.1371/journal.pone.0187220.g001 3. Oculus Rift with translational stimulus (dynamic condition). 3. Oculus Rift with translational stimulus (dynamic condition). 3. Oculus Rift with translational stimulus (dynamic condition). 3. Oculus Rift with translational stimulus (dynamic condition). Postural stability was initially examined without the Oculus Rift. Subjects had both eyes open and were instructed to fixate at a red dot on the wall. Patients were then instructed to put on the Oculus Rift and keep their eyes always opened. Postural stability was then tested with the Oculus Rift showing a completely dark field, i.e., a black screen without any visual stimula- tion. As no visual input was present, this condition assessed the somatosensory and vestibular contributions to postural control. In the dynamic condition, postural reactivity was assessed by presenting dynamic visual sti- muli in order to induce the sensation of self-motion. This was done by presenting an ecolog- ically valid peripheral background perturbation through the Oculus Rift, a peripheral translational stimulus (tunnel) while the patient fixated down the tunnel. Ecological validity refers to the fact that the visual scene moved as expected when the patients moved his/her head and that the stimulus was what one would visually experience if moving through a tunnel. The peripheral stimulus was presented only in the region outside the central 10 degrees of view, while the patient was instructed to keep fixation on a central red dot. The translational stimulus was comprised of a sum of four sinusoids with frequencies of 0.1167, 0.2833, 0.5167 and 0.9833 hertz. The amplitude of each sinusoid was inversely related PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 4 / 13 Fig 2. Patient performing the test on the virtual reality environment, while standing on th platform and wearing the head-mounted goggles. https://doi.org/10.1371/journal.pone.0187220.g002 Fear of falling and po one 0187220 December 6 2017 Fear of falling and postural reactivity Fig 2. Patient performing the test on the virtual reality environment, while standing on the force platform and wearing the head-mounted goggles. https://doi.org/10.1371/journal.pone.0187220.g002 Fig 2. Patient performing the test on the virtual reality environment, while standing on the force platform and wearing the head-mounted goggles. Fig 2. Patient performing the test on the virtual reality environment, while standing on the force platform and wearing the head-mounted goggles. https://doi.org/10.1371/journal.pone.0187220.g002 https://doi.org/10.1371/journal.pone.0187220.g002 5 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 Fear of falling and postural reactivity to its frequency to prevent that the highest frequency would dominate. The phases were selected to minimize the difference between maximum magnitude of the combined signal and its root mean square (RMS) magnitude; this process is called cresting and is used to avoid salient signal characteristics caused by an excessively high signal magnitude or an excessively long period of a low signal magnitude. The resulting signal was scaled to yield an amplitude RMS of 0.4 meters and a velocity RMS of 0.5 meters/second for the tunnel stimulus. The bene- fit of using sums-of-sinusoid stimuli is that the perturbation is unpredictable by the patient unlike the single stimulus. Each test consisted of 15 seconds with a stationary peripheral stimu- lus followed by 120 seconds of peripheral stimulation. The analysis was performed on the 120 seconds during which the peripheral stimulus was in motion. For each one of three test conditions described above, torque moments produced in the mediolateral and anteroposterior directions around the center of the force plate were mea- sured. The torque moments are generated when patient’s center of gravity moves causing a change in the center of pressure on the force plate.[29] The standard deviations of the torque moments (SDTM) were calculated as metrics indicative of postural stability and reported in Newton meters (Nm). Standard deviations of the mediolateral and anteroposterior torque moments were computed separately as well as the sum of them. Larger values of SDTM were indicative of worse postural stability. Statistical analysis Descriptive statistics included mean and standard deviation of the variables. Normality assumption was assessed by inspection of histograms and using Shapiro-Wilk test. Fisher’s exact test was used for group comparison for categorical variables. Student t test was used for group comparison for normally distributed variables and Wilcoxon rank-sum (Mann-Whit- ney) test was used for group comparison for continuous non-normally distributed variables. The association between postural metrics and fear of falling was investigated using linear regression models, where the summary score of fear of falling was used as the dependent vari- able and the different postural metrics as independent variables. We initially ran univariable models evaluating the association of each variable with the outcome. Subsequently, multivari- able models were used adjusting for the potential confounding factors that had a P value < 0.2 in the univariable model. We also investigate the association between severity of visual field defect on SAP and fear of falling. All statistical analyses were performed using commercially available software Stata, version 14 (StataCorp LP, College Station, TX). The alpha level (type I error) was set at 0.05. PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 Fear of falling and postural reactivity Table 1. Demographic and clinical characteristics of glaucoma and control subjects included in the study evaluating the relationship between fear of falling and postural reactivity.*. Glaucoma (n = 35) Control (n = 26) P-value Age, years 70.0 ± 11.2 67.2 ± 11.2 0.262a Gender, n (%) female 15 (43) 17 (65) 0.120b Race, n (%) White 18 (51) 15 (58) 0.499b African American 11 (31) 10 (39) Asian 3 (9) 1 (3) Other 3 (9) 0 (0) Hypertension, n (%) 22 (68) 15 (68) 0.965b Diabetes, n (%) 10 (31) 7 (31) 0.965b Systemic β-blockers use, n (%) 18 (50) 7 (25) Systemic α-agonists use, n (%) 16 (45) 0 Score of fear of falling -0.21 ± 1.0 0.27 ± 0.7 0.039a BMI, kg/m2 25.0 ± 4.0 25.1 ± 4.8 0.897c Number of falls in past 12 months 0.94 ± 1.3 0.4 ± 0.6 0.013d Summary score of PASE 156.6 ± 98.5 174.2 ± 96.7 0.526a MD SAP 24–2 (worse eye), dB -5.9 ± 7.8 -0.9 ± 1.9 <0.001a MD SAP 24–2 (better eye), dB -1.95 ± 4.4 0.3 ± 2.3 <0.001a Binocular MS SAP 24–2, dB 28.5 ± 3.9 31.3 ± 1.6 <0.001a Binocular visual acuity, logMAR -0.02 ± 0.12 -0.07 ± 0.10 0.074c of glaucoma and control subjects included in the study evaluating the relationship between https://doi.org/10.1371/journal.pone.0187220.t001 the anteroposterior direction during dynamic condition was associated with a worsening of 0.32 units in the fear of falling questionnaire score (P = 0.009; R2 = 18.8%) (Table 2). SDTM in the anteroposterior direction had a higher association with fear of falling than SDTM in the mediolateral direction (P<0.001). When torque moments in the anteroposterior direction were considered, postural metrics obtained during dynamic visual stimulation were signifi- cantly more predictive of fear of falling than those obtained during static (R2 = 3.0%; P = 0.005) and dark field conditions (R2 = 5.7%; P = 0.007). Fear of falling was not significantly associated with integrated binocular MS (R2 = 0.1%; P = 0.855) (Table 2). For glaucoma patients, number of falls in the past 12 months was significantly associated with fear of falling (P = 0.035) (Table 2), with a 0.26 worse fear of falling score for each addi- tional fall. Female gender was also associated with 0.82 units worsening in the fear of falling score (P = 0.010) (Table 2). Results The study included 35 glaucoma patients and 26 control subjects. Table 1 presents demographic and clinical characteristics of the studied population. There was no significant difference in mean age between the glaucoma and control groups (70.0±11.2 vs. 67.2±11.2 years, respectively; P = 0.262). There were also no statistically significant differences in gender, race, average BMI, PASE scores, binocular visual acuity, and prevalence of hypertension or diabetes between the two groups. As expected, the integrated binocular MS of SAP 24–2 showed worse values in glau- coma patients compared with controls (28.5±3.9 vs. 31.3±1.6 dB, respectively; P<0.001). Sub- jects with glaucoma reported worse mean scores of fear of falling compared to controls (-0.21 vs. 0.27, respectively; P = 0.039). Diagnosis of glaucoma was also associated with a 2.45 times higher rate of falls in the past 12 months (rate ratio = 2.45; 95% CI: 1.20–4.97; P = 0.013). Postural metrics during dynamic visual stimulus presentation were significantly associated with fear of falling in glaucoma patients. In the univariable model, each 1 Nm larger SDTM in PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 6 / 13 BMI = body mass index; kg/m2 = kilograms per square meter; PASE: Physical Activity Scale for the Elderly; MD = mean deviation; SAP = standard 2 = kilograms per square meter; PASE: Physical Activity Scale for the Elderly; MD = mean deviation; SAP = standar dB = decibels; MS = mean sensitivity; logMAR = logarithm of the minimum angle of resolution. https://doi.org/10.1371/journal.pone.0187220.t001 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 automated perimetry; dB = decibels; MS = mean sensitivity; logMAR = logarithm of the minimum angle of resolution *Values are presented as mean ± standard deviation, unless otherwise noted. as mean ± standard deviation, unless otherwise noted. rd deviation, unless otherwise noted. *Values are presented as mean ± standard deviation, unless otherwise noted. Fear of falling and postural reactivity Table 2. Results of the univariable and multivariable linear regression models for explaining fear of falling in glaucoma patients*. Characteristic Univariable Model Multivariable Model Coefficient (95% CI) P-value Coefficient (95% CI) P-value Anteroposterior SDTM in Dynamic, per 1 Nm increase -0.32 (-0.55 to -0.08) 0.009 -0.56 (-0.96 to -0.17) 0.007 Anteroposterior SDTM in Dark Field, per 1 Nm increase -0.20 (-0.50 to 0.09) 0.007 0.20 (-0.23 to 0.64) 0.354 Age, per decade older -0.03 (-0.06 to 0.00) 0.059 -0.16 (-0.38 to 0.06) 0.157 Gender, female -0.82 (-1.43 to -0.21) 0.010 -1.04 (-1.61 to -0.47) 0.001 Race, African American 0.40 (-0.31 to 1.11) 0.258 Hypertension 0.19 (-0.49 to 0.86) 0.576 Diabetes -0.19 (-0.86 to 0.49) 0.576 BMI, per 1 kg/m2 higher Number of Falls in past 12 months PASE score, per 100 points lower -0.03 (-0.12 to 0.05) -0.26 (-0.51 to -0.02) 0.31 (-0.01 to 0.64) 0.454 0.035 0.059 0.03 (-0.19 to 0.24) -0.06 (0.20 to -0.32) 0.818 0.644 Binocular MS, per 1 dB lower 0.01 (-0.12 to 0.10) 0.855 Binocular visual acuity, per 0.1 logMAR higher 0.86 (-2.67 to 4.38) 0.621 CI = confidence interval; SDTM = standard deviations of the torque moments; Nm = Newton meter; BMI = body mass index; kg/m2 = kilogram per square meter; PASE = Physical Activity Scale for the Elderly; MS = mean sensitivity; dB = decibel; logMAR = logarithm of the minimum angle of resolution. *Multivariable model was adjusted for age, gender, number of falls in the past 12 months and PASE score. https://doi org/10 1371/journal pone 0187220 t002 riable and multivariable linear regression models for explaining fear of falling in glaucoma patients*. CI = confidence interval; SDTM = standard deviations of the torque moments; Nm = Newton meter; BMI = body mass index; kg/m2 = kilogram per square meter; PASE = Physical Activity Scale for the Elderly; MS = mean sensitivity; dB = decibel; logMAR = logarithm of the minimum angle of resolution. *Multivariable model was adjusted for age, gender, number of falls in the past 12 months and PASE score. For healthy subjects none of the postural metrics obtained during dynamic condition were sig- nificantly associated with fear of falling. For healthy subjects none of the postural metrics obtained during dynamic condition were sig- nificantly associated with fear of falling. PASE scores were associated with 0.31 units worsening in the fear of falling questionnaire, but results did not reach statistical significance (P = 0.059). In a multi- variable model that included age, gender, SDTM in the anteroposterior direction during dark field condition, number of falls in past 12 months, and PASE score, each 1 Nm larger SDTM in the anteroposterior direction during dynamic stimulus was associated with a worsening of 0.56 units in the fear of falling questionnaire score (P = 0.001). The multivariable model had an adjusted R2 of 48.8% for predicting fear of falling in glaucoma subjects. (Table 2) (Fig 3). PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 7 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 Discussion In the present study, we found that metrics of postural reactivity in response to dynamic visual stimulation presented in a virtual reality environment were significantly associated with fear of falling in patients with glaucoma. The postural reactivity metrics showed stronger relationship with fear of falling compared to traditional visual field assessment by SAP. To the best of our knowledge, this is the first study to investigate the relationship between postural reactivity and fear of falling in glaucoma patients. Our findings may help improve the understanding of fac- tors associated with fear of falling in glaucoma and may also potentially assist in the develop- ment of management strategies to decrease fear of falling and improve quality of life. In agreement with previous studies, patients with glaucoma had worse scores on the fear of falling questionnaire compared to control subjects.[15,17] However, lower scores (i.e., worse fear) reported by glaucoma patients were not significantly associated with visual field loss on standard perimetry. Our results contrast to those of Ramulu and colleagues who found a sig- nificant association between fear of falling and degree of visual field loss.[15] This could be related to differences in the populations studied. The study by Ramulu and colleagues included mostly patients with moderate and severe visual field loss, with median MD in the better eye of -8dB. In contrast, our study included mostly patients with mild to moderate disease, with median MD in the better eye of only approximately -2dB, although with a wide range from -14.69dB to 2.97dB. Our results indicate that fear of falling in glaucoma patients with relatively mild to moderate disease does not seem to be mediated only by their knowledge of the pres- ence of disease, or by the degree of visual field loss, as indicated by the weak association with SAP results. The parameter most strongly associated with fear of falling in our study was the SDTM in the anteroposterior direction during dynamic visual stimulus presentation, with each 1 Nm larger SDTM associated with a worsening of 0.32 units in the fear of falling questionnaire score (P = 0.001). SDTM in response to dynamic visual stimuli was more associated with fear PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 8 / 13 Fig 3. Predicted fear of falling with 95% confidence interval for different values of standard deviation of torque moments (SDTM) in the anteroposterior direction during dynamic visual stimulus presentation. PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 Discussion Predicted values were derived from the multivariable model adjusting for confounding factors. Fear of falling and postural reactivity Fear of falling and postural reactivity Fi 3 P di t d f f f lli ith 95% fid i t l f diff t l f t d d d i ti f t t (SDTM) i th Fig 3. Predicted fear of falling with 95% confidence interval for different values of standard deviation of torque moments (SDTM) in the anteroposterior direction during dynamic visual stimulus presentation. Predicted values were derived from the multivariable model adjusting for confounding factors. Fig 3. Predicted fear of falling with 95% confidence interval for different values of standard deviation of torque moments (SDTM) in the anteroposterior direction during dynamic visual stimulus presentation. Predicted values were derived from the multivariable model adjusting for confounding factors. ith 95% confidence interval for different values of standard deviation of torque moments (SDTM) in the g dynamic visual stimulus presentation. Predicted values were derived from the multivariable model adjusting for https://doi.org/10.1371/journal.pone.0187220.g003 https://doi.org/10.1371/journal.pone.0187220.g003 of falling than SDTM in the static condition. Previous studies have shown that under static con- ditions central and peripheral visual fields appear to have equal importance in the control of stance.[30] However, in the presence of dynamic information, peripheral vision plays a crucial role in the control of stance by processing visual information on location and velocity and allow- ing an adapted postural response to perceived perturbation.[31,32] As glaucoma has a relatively larger effect on peripheral compared to central vision, this may help explain the better perfor- mance of postural metrics obtained in dynamic versus static visual stimuli conditions in our study. In fact, previous studies have suggested that differences in postural control may only be detectable when the inducing environment is dynamic, rather than static.[33–35] Our results also indicate that fear of falling in our sample of glaucoma patients does not seem to be mediated by perceived weaknesses in somatosensory and vestibular systems, as indicated by the weaker relationship to SDTM in the dark field condition, i.e., in the absence of any visual stimulation. We used a virtual reality environment to present dynamic visual stimuli that simulated a tunnel moving in anteroposterior direction (translational stimuli). Discussion It is well known that the PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 9 / 13 Fear of falling and postural reactivity motion of the environment creates an illusion of self-motion (vection), which in turn induces compensatory postural responses.[36] In a previous study, we have demonstrated that these postural responses are significantly different in glaucoma compared to healthy subjects, with glaucoma patients showing larger SDTM, i.e. greater postural instability in response to the visual stimuli.[11] This increased instability in glaucoma patients may have several explana- tions. The visual stimuli in our virtual reality paradigm are composed of a sum of sinusoids of different spatial frequencies. In normal subjects, the high spatial frequencies may mask the ability of lower spatial frequencies in effectively inducing vection and, therefore, postural responses would be diminished. For glaucoma patients, it has been shown that retinal ganglion cell loss may result in impaired motion detection, especially for higher spatial frequencies. [37,38] This would then “unmask” the vection-inducing low spatial frequencies, resulting in greater vection and larger postural compensatory responses. Of note, if visual information pro- cessing is slow as may happen in glaucoma patients,[39] these compensatory responses may be deficient or inappropriate, leading to postural instability. It is interesting to note that postural perturbations in the anteroposterior direction (i.e., same direction as of the visual stimuli) were more strongly associated with fear of falling than those in the mediolateral direction. This is in contrast to our previous study investigating the relationship between postural reactivity and risk of falls using the same virtual reality para- digm.[11] In our previous study, we showed that the SDTM in the mediolateral direction was more strongly associated with history of falls than the SDTM in the anteroposterior direction, for the same translational visual stimuli.[11] The higher association with history of falls for the mediolateral SDTM is probably explained by the fact that increased postural perturbations in the direction orthogonal to the visual stimuli may actually be a more important indicator of overall destabilization of the subject and indicate greater risk of falls. However, fear of falling is a subjective perception and, as such, may be more related to the greater sway of the patient that is felt in the anteroposterior direction in response to translational stimuli. PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 S2 Fig. Back page of patient from Fig 2 license to publish under the creative commons attribution license. (ZIP) S2 Fig. Back page of patient from Fig 2 license to publish under the creative commons attribution license. (ZIP) S3 Fig. Signed PLOS consent form for publication of Fig 2 in a PLOS journal. (TIF) S1 Appendix. Dataset underlying the findings in the manuscript. (XLSX) Fear of falling and postural reactivity different instruments to assess fear of falling. As another limitation, it is possible that other unmeasured variables, such as gait abnormalities, use of medications or other systemic condi- tions, could also be associated with fear of falling in glaucoma and this issue requires further investigations. In conclusion, evaluation of postural reactivity to a dynamic visual stimulus using a virtual reality environment was more strongly associated with fear of falling in glaucoma patients than visual field testing and traditional balance assessment. These results may contribute to the knowledge of risk factors for fear of falling in glaucoma and may assist in the development of strategies to reduce fear of falling and improve quality of life in patients affected by this condi- tion. In addition, they suggest a promising role for virtual reality in replicating dynamic visual conditions that might be superior to standard perimetry in assessing how vision impacts daily activities in patients with glaucoma. S2 Fig. Back page of patient from Fig 2 license to publish under the creative commons attribution license. S2 Fig. Back page of patient from Fig 2 license to publish under the creative commons attribution license. S2 Fig. Back page of patient from Fig 2 license to publish under the creative commons attribution license. (ZIP) Supporting information S1 Fig. Front page of patient from Fig 2 license to publish under the creative commons attribution license. Conceptualization: Felipe A. Medeiros. Data curation: Fa´bio B. Daga, Alberto Diniz-Filho, Carolina P. B. Gracitelli, Ricardo Y. Abe, Felipe A. Medeiros. Formal analysis: Fa´bio B. Daga, Erwin R. Boer, Felipe A. Medeiros. Funding acquisition: Felipe A. Medeiros. Funding acquisition: Felipe A. Medeiros. Investigation: Felipe A. Medeiros. Investigation: Felipe A. Medeiros. Methodology: Fa´bio B. Daga, Felipe A. Medeiros. Project administration: Felipe A. Medeiros. Discussion The significant association between fear of falling and our proposed postural metrics could indicate that these metrics might be useful tools to assess the efficacy of interventions designed to reduce fear of falling and risk of falls in glaucoma patients, such as exercise-based interven- tions. It should be noted, however, that fear of falling in an individual patient may have multi- ple origins.[40,41] In fact, even the best postural reactivity metric in our study was able to explain only approximately 20% of the variability in fear of falling scores in our sample of glau- coma patients. Other factors were also associated with fear of falling in our study, such as pre- vious history of falls and female gender, whereas age and physical activity were of borderline statistical significance. Importantly, metrics of postural reactivity to dynamic visual stimula- tion still had significant predictive value even in multivariable models, indicating an indepen- dent contribution in explaining fear of falling. The multivariable model was able to explain more than 50% of the variability of fear of falling scores, which could be considered a relatively good predictive ability for such multifactorial and subjective outcome. Our study had limitations. Due to the cross-sectional design, we were not able to clearly determine the temporal relationship between the proposed postural reactivity metrics and development of fear of falling. In addition, we were not able to investigate the longitudinal relationship between history of falls and fear of falling. However, such relationships are com- plex and it is likely that simple causal effects cannot be demonstrated. Future longitudinal studies should be able to clarify the role of postural reactivity metrics as proposed in our study and risk of falls and fear of falling in glaucoma. As another limitation of our study, we used only a single questionnaire to investigate and quantify the presence of fear of falling. Although the questionnaire has been previously validated for this purpose, other scales and instruments have also been developed. Future studies should attempt to validate our findings using PLOS ONE | https://doi.org/10.1371/journal.pone.0187220 December 6, 2017 10 / 13 References 1. Nevitt MC, Cummings SR, Kidd S, Black D (1989) Risk factors for recurrent nonsyncopal falls. A pro- spective study. JAMA 261: 2663–2668. PMID: 2709546 2. Tinetti ME, Speechley M, Ginter SF (1988) Risk factors for falls among elderly persons living in the com- munity. N Engl J Med 319: 1701–1707. https://doi.org/10.1056/NEJM198812293192604 PMID: 3205267 3. 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Boer ER, Diniz A, Gracitelli C, Abe RY, Van Driel N, Yang ZY, et al. (2015) A Computational Visual-Ves- tibular Balance Control Model with Peripheral Visual Input. Investigative Ophthalmology & Visual Sci- ence 56. 40. Lach HW (2005) Incidence and risk factors for developing fear of falling in older adults. Public Health Nurs 22: 45–52. https://doi.org/10.1111/j.0737-1209.2005.22107.x PMID: 15670324 41. Scheffer AC, Schuurmans MJ, van Dijk N, van der Hooft T, de Rooij SE (2008) Fear of falling: measure- ment strategy, prevalence, risk factors and consequences among older persons. Age Ageing 37: 19– 24. https://doi.org/10.1093/ageing/afm169 PMID: 18194967 13 / 13
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Persistence of infectivity in elderly individuals diagnosed with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection 10 days after onset of symptoms: A cross-sectional study
Infection control and hospital epidemiology
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Population and setting In this prospective cross-sectional study, we included a conven- ience sample of unvaccinated individuals aged >79 years with COVID-19 confirmed by RT-PCR from 3 long-term care facili- ties and 1 acute-care institution in Montreal, Canada, between November 8, 2020, and January 25, 2021. Participants were identified using institutional infection control databases. Following verbal consent, a nasopharyngeal sample was col- lected on day 10 after symptom onset using a flocked swab Infection Control & Hospital Epidemiology (2023), 44, 659–662 Infection Control & Hospital Epidemiology (2023), 44, 659–662 doi:10.1017/ice.2021.502 Infection Control & Hospital Epidemiology (2023), 44, 659–662 doi:10.1017/ice.2021.502 Infection Control & Hospital Epidemiology (2023), 44, 659–662 doi:10.1017/ice.2021.502 Abstract We performed viral culture of nasopharyngeal specimens in individuals aged 79 and older, infected with severe acute respiratory coronavirus virus 2 (SARS-CoV-2), 10 days after symptom onset. A positive viral culture was obtained in 10 (45%) of 22 participants, including 4 (33%) of 12 individuals with improving symptoms. The results of this small study suggest that infectivity may be prolonged among older individuals. (Received 28 July 2021; accepted 22 November 2021; electronically published 6 December 2021) (Received 28 July 2021; accepted 22 November 2021; electronically published 6 December 2021) Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).1 Infected indi- viduals must be placed under isolation precautions until infectivity is resolved.1 The current recommendation is based on studies that used viral culture as an indicator of infectivity and requires isolation for 10 days for nonsevere infections in immunocompetent individ- uals, provided that symptoms are improving.1,2 However, these studies enrolled relatively young individuals and may not be general- izable to older patients.1,3,4 Furthermore, some studies have reported a longer duration of SARS-CoV-2 RNA shedding by reverse tran- scription polymerase chain reaction (RT-PCR) among older patients.5 We assessed the presence of infectious SARS-CoV-2 virus in elderly individuals with COVID-19, 10 days after symptom onset, using viral culture as a surrogate for infectivity. (FLOQSwabs, Copan Italia, Brescia, Italy) and placed in 3 mL universal viral transport media (Copan Italia). The samples were kept at −80°C until RT-PCR and viral culture. Clinical data (ie, immunosupression, date of symptom onset, symp- tomatology, clinical outcomes) and the cycle threshold (Ct) value of the first positive RT-PCR were extracted from patient charts. (FLOQSwabs, Copan Italia, Brescia, Italy) and placed in 3 mL universal viral transport media (Copan Italia). The samples were kept at −80°C until RT-PCR and viral culture. Clinical data (ie, immunosupression, date of symptom onset, symp- tomatology, clinical outcomes) and the cycle threshold (Ct) value of the first positive RT-PCR were extracted from patient charts. Laboratory methods Viral cultures were performed on Vero E6 cells in 4-mL shell vials as previously described using a 0.1-mL aliquot of specimen as inoc- ulum.6 Cultures were kept for 15 days and monitored for a cyto- pathic effect (CPE) every other day. On initial (day 0) samples, viral RNA was extracted using the MagMAX Viral/Pathogen II Nucleic Acid Isolation Kit (Thermo Scientific, Waltham MA). RT-PCR was performed on a LightCycler LC480 (Roche) using TaqPath RT-qPCR Master Mix (Thermo Scientific) and primers and probe targeting the E gene as described previously.7 Samples collected on day 10 and culture super- natants were processed with an in-house RT-PCR targeting the N gene as previously described.6 We used the following forward, reverse and probe sequences: AACCAGAATGGAGAACGCAGTG, CGGTGAACCAAGACGCAGTATTAT and CGATCAAAACAA CGTCGGCCCCAAGGTTTAC.6 Persistence of infectivity in elderly individuals diagnosed with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection 10 days after onset of symptoms: A cross-sectional study Persistence of infectivity in elderly individuals diagnosed with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection 10 days after onset of symptoms: A cross-sectional study Yves Longtin MD1,2 , Leighanne O. Parkes MD1 , Hugues Charest PhD3,4,5, Stacy Rajarison RN, BScN1, Gerasimos J. Zaharatos MD1,2, Judith Fafard MD3, Michel Roger MD, PhD3 and Gaston De Serres MD, PhD4 1Jewish General Hospital Sir Mortimer B. Davis, Montreal, Canada, 2Lady Davis Research Institute, Montreal, Canada, 3Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada, 4Institut National de Santé Publique du Québec, Quebec City, Canada and 5Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, Canada © The Author(s), 2021. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America. This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited. https://doi.org/10.1017/ice.2021.502 Published online by Cambridge University Press mbridge University Press on behalf of The Society for Healthcare Epidemiology of America. This is an Open Access article, distributed under the on licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original Author for correspondence: Dr Yves Longtin, E-mail: yves.longtin@mcgill.ca Statistical analyses The primary outcome was culture positivity, defined as the detec- tion of a CPE combined with a RT-PCR Ct value on the superna- tant that is lower than the Ct value of the original specimen. To investigate factors associated with culture positivity, the Fisher Author for correspondence: Dr Yves Longtin, E-mail: yves.longtin@mcgill.ca Cite this article: Longtin Y, et al. (2023). Persistence of infectivity in elderly individuals diagnosed with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection 10 days after onset of symptoms: A cross-sectional study. Infection Control & Hospital Epidemiology, 44: 659–662, https://doi.org/10.1017/ice.2021.502 © The Author(s), 2021. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America. This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited. © The Author(s), 2021. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America. This is an terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distributi article is properly cited. https://doi.org/10.1017/ice.2021.502 Published online by Cambridge University Press 2 Published online by Cambridge University Press 660 Yves Longtin et al Table 1. Comparison of Patients With Positive or Negative Culture for SARS-CoV-2 on Day 10 of Infection Table 1. Comparison of Patients With Positive or Negative Culture for SARS-CoV-2 on Day 10 of Infection Characteristic Total (N=22), No. (%) Culture Positive (N=10), No. (%) Culture Negative (N=12), No. Statistical analyses (%) P Value Sex, female 12 (55) 5 (50) 7 (58) 1.00 Age, median y (IQR) 90 (86–96) 90 (86–98) 90 (84–96) .69 Immunosuppression 4 (18) 2 (20) 2 (17) 1.00 Reception of steroids 13 (59) 8 (80) 5 (42) .10 Outcome Hospitalized 8 (36) 5 (50) 3 (25) .38 Death 7 (32) 3 (30) 4 (33) 1.00 Duration of isolation precautions, d (IQR) 13 (11–16) 14 (11–22) 12 (11–16) .38 Symptoms1 Cough 16 (73) 8 (80) 8 (67) .65 Fever 11 (50) 6 (60) 5 (42) .67 Respiratory distress 7 (32) 4 (40) 3 (25) .65 Other COVID-19–compatible symptoms2 16 (73) 7 (70) 9 (75) 1.00 Absence of risk factors for prolonged shedding3 4 (18) 2 (20) 2 (17) 1.00 Symptomatology on day 10 of infection Resolved symptoms 8 (36) 3 (30) 5 (42) .68 Persistent but improving symptoms 4 (18) 1 (10) 3 (25) .59 Persistent and not improving symptoms 10 (45) 6 (60) 4 (33) .39 Persistent fever4 4 (18) 2 (20) 2 (17) 1.00 Laboratory Ct value on RT-PCR on day of diagnosis5 (IQR) 21 (16–27) 24 (15–27) 21 (18–29) .73 Ct value on RT-PCR on day 10 of infection (IQR)6 21 (16–24) 17 (15–19) 23 (21–26) .002 Specimens on day 10 had a median Ct of 21 (IQR, 16–24). A pos- itive viral culture was obtained in 10 (45%) of 22 samples. Detection of a CPE occurred early; 6 (60%) of 10 samples demon- strated a CPE by incubation day 3, and 9 (90%) of 10 by incubation day 8. exact test and the Mann-Whitney U test were performed as appro- priate. To investigate the capacity of Ct value on day 10 to predict culture positivity, a receiver operating characteristics (ROC) curve was plotted to determine the probability of a true positive result as a function of the probability of a false positive result for all possible Ct values. A P <.05 was considered significant. The study was approved by the local research ethics committees. y A positive culture was obtained for 6 (60%) of 10 individuals whose symptoms were not improving on day 10 and for 4 (33%) of 12 of those with improving or resolved symptoms. Individuals with positive cultures tended to be more frequently hospitalized than culture-negative individuals: 5 (50%) of 10 versus 3 (25%) of 12, respectively. Statistical analyses They were also more likely to have received steroids than those with negative cultures: 8 (80%) of 10 versus 5 (42%) of 12. However, individuals with positive cul- tures were less likely to die than those with negative cultures: 3 (30%) of 10 versus 4 (33%) of 12, respectively. Notably, these differences were not statistically significant. Among patients with- out a recognized risk factor for prolonged shedding, half (2 of 4) had a positive culture on day 10. https://doi.org/10.1017/ice.2021.502 Published online by Cambridge University Press Results Note. RT-PCR, detection of SARS-CoV-2 by reverse-transcription polymerase chain reaction. Fig. 1. Box plot showing the cycle threshold value of SARS-CoV-2 RT-PCR of nasopharyngeal swabs taken on the day of diagnosis and on day 10 after onset of symptoms from elderly patients infected with COVID-19, stratified by persistence of infectivity on day 10 after onset of symptoms. The horizontal line in each box indicates the median, whereas the top and bottom lines represent the 75th and 25th percentiles, respectively. Error bars represent 95% confidence intervals, and the dot represents an outlier. Note. RT-PCR, detection of SARS-CoV-2 by reverse-transcription polymerase chain reaction. culture on day 10, 24 vs 21; P = .73) (Fig. 1). In contrast, the Ct value of the sample collected on day 10 predicted culture positivity (median Ct of positive vs negative cultures, 17 (IQR, 15–19) vs 23 (IQR, 21–26), respectively; P = .003). The performance of the day- 10 Ct value in predicting culture positivity is shown through the receiver operating characteristics (ROC) curve (Supplementary Fig. 1 online). The area under the ROC curve was 0.90 (95% CI, 0.74–1.00). Using a cutoff Ct of 20.7 had 90% sensitivity (9 of 10 patients) and 90% specificity (9 of 10 patients) to predict culture positivity. other predictors of prolonged infectivity. Cultures were performed after a freeze–thaw cycle that may affect the integrity of the virus. We did not perform epidemiological investigations to correlate culture positivity and transmissibility to other individuals. Most individuals had risk factors for prolonged viral shedding. Still, per- sistent infectivity in our elderly population was much more fre- quent than previously reported among severe cases in younger individuals in which ∼5% remain infectious by day 10.8 y y In conclusion, this investigation suggests that infectivity may be longer than recognized among older individuals and appear to be predicted by low Ct values on day 10 of infection. Further studies are required to determine whether isolation precaution recom- mendations should be modified among the older individuals. Discussion The belief that patients with COVID-19 remain infectious for <10 days stems from studies conducted among younger populations, with an average or median age ranging from 33 to 57.3,4 This notion may not be generalizable to patients over the age of 79; ∼50% of individuals in our study were still shedding infectious viral par- ticles 10 days after symptom onset. Furthermore, clinical improve- ment was not predictive of loss of infectivity; ∼33% those with resolved or improving symptoms remained infective. In contrast, a lower cycle threshold (indicating a greater quantity of viral RNA in the sample) was a predictor of culture positivity on day 10 of COVID-19, as reported elsewhere.2,3,8 Supplementary material. To view supplementary material for this article, please visit https://doi.org/10.1017/ice.2021.502 Acknowledgments. We thank the microbiology technicians of the virology laboratory at the Laboratoire de Santé Publique du Québec for their assistance in conducting the viral cultures. Financial support. Laboratoire de Santé Publique du Québec. Dr Yves Longtin’s research is supported by the Fonds de Recherche du Québec en Santé. Financial support. Laboratoire de Santé Publique du Québec. Dr Yves Longtin’s research is supported by the Fonds de Recherche du Québec en Santé. Conflicts of interest. Yves Longtin declares research grants outside of the sub- mitted work from Merck, Gojo and Becton Dickinson. All other authors declare no competing interests. Few studies have investigated infectivity specifically among older individuals. In British long-term care homes, infectious virus could be recovered for up to 13 days among residents (median age, 85) compared to up to 7 days among staff (median age, 47).9 Among nursing home residents in Washington, 4 of 8 samples col- lected between days 7 and 13 after symptom onset were positive by viral culture.2 By contrast, recovery of replication-competent SARS-CoV-2 was 8 days or less after diagnosis in 8 of 9 nursing home residents in Arkansas, although infectivity persisted for 19 days in 1 immunocompromised individual.10 https://doi.org/10.1017/ice.2021.502 Published online by Cambridge University Press Results Overall, 22 participants were recruited. The median age was 90 years old (interquartile range [IQR], 86–96) and 12 (55%) were female (Table 1). Also, 4 patients (18%) were immunosuppressed, 13 (59%) received steroids to treat their infection, 8 (36%) were hospi- talized, and 7 (32%) died. The initial sample to confirm the diagnosis was taken within 1 day of symptom onset in 21 (95%) of 22 and had a median RT-PCR Ct value of 21 (IQR, 16–27). By day 10 after symptom onset, 8 (36%) of 22 had no residual symptom, 4 (18%) of 22 were still symptomatic but improving, whereas 10 (45%) of 22 had no symptom improvement. The Ct value of the initial sample did not predict culture pos- itivity (median Ct of participants with and without a positive 661 Infection Control & Hospital Epidemiology Fig. 1. Box plot showing the cycle threshold value of SARS-CoV-2 RT-PCR of nasopharyngeal swabs taken on the day of diagnosis and on day 10 after onset of symptoms from elderly patients infected with COVID-19, stratified by persistence of infectivity on day 10 after onset of symptoms. The horizontal line in each box indicates the median, whereas the top and bottom lines represent the 75th and 25th percentiles, respectively. Error bars represent 95% confidence intervals, and the dot represents an outlier. Note. RT-PCR, detection of SARS-CoV-2 by reverse-transcription polymerase chain reaction. Fig. 1. Box plot showing the cycle threshold value of SARS-CoV-2 RT-PCR of nasopharyngeal swabs taken on the day of diagnosis and on day 10 after onset of symptoms from elderly patients infected with COVID-19, stratified by persistence of infectivity on day 10 after onset of symptoms. The horizontal line in each box indicates the median, whereas the top and bottom lines represent the 75th and 25th percentiles, respectively. Error bars represent 95% confidence intervals, and the dot represents an outlier. Note. RT-PCR, detection of SARS-CoV-2 by reverse-transcription polymerase chain reaction. Fig. 1. Box plot showing the cycle threshold value of SARS-CoV-2 RT-PCR of nasopharyngeal swabs taken on the day of diagnosis and on day 10 after onset of symptoms from elderly patients infected with COVID-19, stratified by persistence of infectivity on day 10 after onset of symptoms. The horizontal line in each box indicates the median, whereas the top and bottom lines represent the 75th and 25th percentiles, respectively. Error bars represent 95% confidence intervals, and the dot represents an outlier. 02 Published online by Cambridge University Press 5. Owusu D, Pomeroy MA, Lewis NM, et al. Persistent SARS-CoV-2 RNA shedding without evidence of infectiousness: a cohort study of individuals with COVID-19. J Infect Dis 2021;224:1362–1371. 6. Longtin Y, Charest H, Quach C, et al. Infectivity of healthcare workers diag- nosed with coronavirus disease 2019 (COVID-19) approximately 2 weeks after onset of symptoms: a cross-sectional study. Infect Control Hosp Epidemiol 2021. doi: 10.1017/ice.2020.1420. 4. Basile K, McPhie K, Carter I, et al. Cell-based culture of SARS-CoV-2 informs infectivity and safe de-isolation assessments during COVID-19. Clin Infect Dis 2021;73:e2952–e2959. 4. Basile K, McPhie K, Carter I, et al. Cell-based culture of SARS-CoV-2 informs infectivity and safe de-isolation assessments during COVID-19. Clin Infect Dis 2021;73:e2952–e2959. 5. Owusu D, Pomeroy MA, Lewis NM, et al. Persistent SARS-CoV-2 RNA shedding without evidence of infectiousness: a cohort study of individuals with COVID-19. J Infect Dis 2021;224:1362–1371. 6. Longtin Y, Charest H, Quach C, et al. Infectivity of healthcare workers diag- nosed with coronavirus disease 2019 (COVID-19) approximately 2 weeks after onset of symptoms: a cross-sectional study. Infect Control Hosp Epidemiol 2021. doi: 10.1017/ice.2020.1420. https://doi.org/10.1017/ice.2021.502 Published online by Cambridge University Press References 1. Kadire SR, Fabre V, Wenzel RP. Doctor, how long should I isolate? N Engl J Med 2021;384:e47. 2. Arons MM, Hatfield KM, Reddy SC, et al. Presymptomatic SARS-CoV-2 infections and transmission in a skilled nursing facility. N Engl J Med 2020;382:2081–2090. 2. Arons MM, Hatfield KM, Reddy SC, et al. Presymptomatic SARS-CoV-2 infections and transmission in a skilled nursing facility. N Engl J Med 2020;382:2081–2090. 3. Gniazdowski V, Morris CP, Wohl S, et al. Repeat COVID-19 molecular test- ing: correlation of SARS-CoV-2 culture with molecular assays and cycle thresholds. Clin Infect Dis 2021;73:e860–e869. 3. Gniazdowski V, Morris CP, Wohl S, et al. Repeat COVID-19 molecular test- ing: correlation of SARS-CoV-2 culture with molecular assays and cycle thresholds. Clin Infect Dis 2021;73:e860–e869. Our study has several limitations. The small sample size limits its generalizability. We did not collect data on comorbidities and 662 Yves Longtin et al Yves Longtin et al 4. Basile K, McPhie K, Carter I, et al. Cell-based culture of SARS-CoV-2 informs infectivity and safe de-isolation assessments during COVID-19. Clin Infect Dis 2021;73:e2952–e2959. 7. Corman VM, Landt O, Kaiser M, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill 2020;25:2000045. 8. Kim MC, Cui C, Shin KR, et al. Duration of culturable SARS-CoV-2 in hospitalized patients with COVID-19. N Engl J Med 2021;384: 671–673. 9. Ladhani SN, Chow JY, Janarthanan R, et al. Investigation of SARS-CoV-2 outbreaks in six care homes in London, April 2020. EClinicalMedicine 2020;26:100533. f 6. Longtin Y, Charest H, Quach C, et al. Infectivity of healthcare workers diag- nosed with coronavirus disease 2019 (COVID-19) approximately 2 weeks after onset of symptoms: a cross-sectional study. Infect Control Hosp Epidemiol 2021. doi: 10.1017/ice.2020.1420. f 6. Longtin Y, Charest H, Quach C, et al. Infectivity of healthcare workers diag- nosed with coronavirus disease 2019 (COVID-19) approximately 2 weeks after onset of symptoms: a cross-sectional study. Infect Control Hosp Epidemiol 2021. doi: 10.1017/ice.2020.1420. 10. Surie D, Huang JY, Brown AC, et al. Infectious period of severe acute res- piratory syndrome coronavirus 2 in 17 nursing home residents—Arkansas, June–August 2020. Open Forum Infect Dis 2021;8:ofab048.
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Extensively Drug-Resistant Klebsiella pneumoniae Causing Nosocomial Bloodstream Infections in China: Molecular Investigation of Antibiotic Resistance Determinants, Informing Therapy, and Clinical Outcomes
Frontiers in microbiology
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ORIGINAL RESEARCH published: 30 June 2017 doi: 10.3389/fmicb.2017.01230 Extensively Drug-Resistant Klebsiella pneumoniae Causing Nosocomial Bloodstream Infections in China: Molecular Investigation of Antibiotic Resistance Determinants, Informing Therapy, and Clinical Outcomes Wenzi Bi 1, 2, Haiyang Liu 1, Rhys A. Dunstan 3, Bin Li 1, Von Vergel L. Torres 3, Jianming Cao 2, Lijiang Chen 1, Jonathan J. Wilksch 3, Richard A. Strugnell 4, Trevor Lithgow 3* and Tieli Zhou 1* Keywords: antimicrobial resistance determinants, bacteraemia, clinical outcomes, Klebsiella pneumoniae, XDR 1 Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China, 2 School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China, 3 Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia, 4 Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Parkville, VIC, Australia Edited by: Miklos Fuzi, Semmelweis University, Hungary Reviewed by: Xiaoting Hua, Zhejiang University, China Marcelo Tolmasky, California State University, Fullerton, United States Reviewed by: Xiaoting Hua, Zhejiang University, China Marcelo Tolmasky, California State University, Fullerton, United States The rise in diversity of antimicrobial resistance phenotypes seen in Klebsiella pneumoniae is becoming a serious antibiotic management problem. We sought to investigate the molecular characteristics and clinical implications of extensively drug-resistant (XDR) K. pneumoniae isolated from different nosocomial bloodstream infections (BSIs) patients from July 2013 to November 2015. Even in combination treatment, meropenem did not protect against mortality of BSIs patients (P = 0.015). In contrast, tigecycline in combination with other antimicrobial agents significantly protected against mortality (P = 0.016). Antimicrobial susceptibility tests, molecular detection of antibiotic resistance determinants, conjugation experiments, multilocus sequence typing (MLST), S1-PFGE, Southern blot, SDS-PAGE, immunoblot analysis, and pulsed-field gel electrophoresis (PFGE) were used to characterize these isolates. These XDR K. pneumoniae strains were resistant to conventional antimicrobials except tigecycline and polymyxin B and co-harbored diverse resistance determinants. rmtB, blaKPC−2 as well as blaCTX−M−9 were located on a transferable plasmid of ∼54.2 kb and the most predominant replicon type was IncF. 23 of the 35 isolates belonging the predominant clone were found to incorporate the globally-disseminated sequence type ST11, but others including a unique, previously undiscovered lineage ST2281 (allelic profile: 4-1-1-22-7-4-35) were also found and characterized. The porins OmpK35 and OmpK36 were deficient in two carbapenemase-negative carbapenem-resistant strains, suggesting decreased drug uptake as a mechanism for carbapenem resistance. This study highlights the importance of tracking hospital acquired infections, monitoring modes of antibiotic resistance to improve health outcomes of BSIs patients and to highlight the problems of XDR K. pneumoniae dissemination in healthcare settings. *Correspondence: Trevor Lithgow trevor.lithgow@monash.edu Tieli Zhou wyztli@163.com *Correspondence: Trevor Lithgow trevor.lithgow@monash.edu Tieli Zhou wyztli@163.com Specialty section: This article was submitted to Antimicrobials, Resistance and Chemotherapy, a section of the journal Frontiers in Microbiology Received: 24 April 2017 Accepted: 19 June 2017 Published: 30 June 2017 Specialty section: This article was submitted to Antimicrobials, Resistance and Chemotherapy, a section of the journal Frontiers in Microbiology Specialty section: This article was submitted to Antimicrobials, Resistance and Chemotherapy, a section of the journal Frontiers in Microbiology Received: 24 April 2017 Accepted: 19 June 2017 Published: 30 June 2017 Clinical Data Collection The Gram-negative bacterium Klebsiella pneumoniae is widely distributed in the environment and increasingly reported as a cause of invasive infections in healthcare settings, particulary in immunocompromised patients (Bagley, 1985; Lee et al., 2016; Paczosa and Mecsas, 2016; Wyres and Holt, 2016). Antimicrobial resistance in K. pneumoniae is increasing, particularly beta-lactamases and carbapenemases having been well-characterized as increasing the infection threat (Mathers et al., 2015; Campos et al., 2016; Lee et al., 2016). This seriously antibiotic management problem is now frequently seeing both nosocomial and community associated infections. Infections caused by extensively drug-resistant (XDR) K. pneumoniae, such as pneumonia, urinary tract infections, and bloodstream infections (BSIs) (Bagley, 1985; Girometti et al., 2014; Paczosa and Mecsas, 2016), have been closely related to increased morbidity, mortality, long hospital stay, and high healthcare costs (Giske et al., 2008; Bush et al., 2011). From July 2013 to November 2015, a total of 131 BSIs patients hospitalized in the First Affiliated Hospital of Wenzhou Medical University were shown to carry K. pneumoniae. Among these, 35 patients were defined as XDR K. pneumoniae BSIs patients if their blood cultures were positive for XDR K. pneumoniae and with clinical signs of systemic inflammatory response syndrome. BSIs patients were further divided into two groups based on clinical outcome of antimicrobial treatment: death group (n = 14) and survivor group (n = 21). Medical records and clinical data (patient age, gender, ICU length of stay, reasons for ICU admission, intensive care procedures, comorbidities, medical care measures before BSIs, antibiotic administration, microbiological data, and outcomes) were collected and analyzed and are presented in Table 1. All of the investigation protocols in this study were approved by The Ethics Committee of The First Affiliated Hospital of Wenzhou Medical University. Informed consent was waived because this retrospective study with retrospective observational nature mainly focused on bacteria and did no interventions to patients. Antimicrobial resistance is a global problem, and K. pneumoniae is recognized as a major pathogen of hospital- acquired infections. In the past several years, Chinese clinicians have witnessed a remarkable increase in the drug resistance rate of K. pneumoniae strains isolated from clinical settings. For example, carbapenemase-producing K. pneumoniae was first identified in China in 2007 and by 2013 a carbapenemase- resistance cassette was carried by 13.4% of K. pneumoniae isolated from hospital patients (Qi et al., 2011; Hu et al., 2016). Citation: Citation: Bi W, Liu H, Dunstan RA, Li B, Torres VVL, Cao J, Chen L, Wilksch JJ, Strugnell RA, Lithgow T and Zhou T (2017) Extensively Drug-Resistant Klebsiella pneumoniae Causing Nosocomial Bloodstream Infections in China: Molecular Investigation of Antibiotic Resistance Determinants, Informing Therapy, and Clinical Outcomes. Front. Microbiol. 8:1230. doi: 10.3389/fmicb.2017.01230 June 2017 | Volume 8 | Article 1230 Frontiers in Microbiology | www.frontiersin.org 1 Bi et al. XDR K. Pneumoniae Causing BSIs Clinical Data Collection Now, a substantial portion of hospitalized patients are colonized by these pathogens, causing outbreaks of nosocomial infections in various regions across the country (Paczosa and Mecsas, 2016). K. pneumoniae is now seen as one of the major pathogenic bacteria of BSIs, accounting for 11.3% between 2011 and 2012 in China (Lv et al., 2014). The dissemination of XDR K. pneumoniae is now causing difficult- to-treat infections worldwide, bringing with its tremendous challenges to the clinical therapeutic options (Lim et al., 2015). Although carbapenems possess good antibacterial activity to Gram-negative bacteria, the rates of carbapenem resistance among K. pneumoniae escalated from 0.7% in 2006 to 10% in 2013 (Hu et al., 2016). The availability of alternative, effective antimicrobial agents is limited (Tang et al., 2016). Bacterial Isolates Identification and Antimicrobial Susceptibility Profiling p y g This retrospective study was conducted at the First Affiliated Hospital of Wenzhou Medical University, China. Based on the standardized international definition for XDR described by Li et al. (2012), 35 non-repetitive K. pneumoniae strains, isolated from nosocomial BSIs patients that were found to be susceptible to two or fewer antimicrobial categories, were collected. Initially, bacterial identification and antimicrobial susceptibility tests were conducted by the Vitek2 system (BioMèrieux, France). Then, the isolates were stored in frozen condition at −80◦C with 30% glycerol. Subsequently, minimum inhibitory concentrations (MICs) of tigecycline and polymyxin B were determined by broth dilution method and interpreted by the recommendation of the European Committee on Antimicrobial Susceptibility Testing (EUCAST, 2015). Escherichia coli ATCC 25922 served as the control strain for susceptibility testing. Frontiers in Microbiology | www.frontiersin.org Molecular Detection of Antibiotic Resistance Determinants The presence of resistant mechanisms, including ESBLs genes (blaCTX−M−1, blaCTX−M−9, blaTEM, blaSHV, blaVEB, and blaPER), AmpC genes (blaCMY, blaFOX, blaMOX, blaDHA), carbapenemase genes (blaKPC, blaSPM, blaIMP, blaVIM, blaGES, blaNDM, blaOXA−23, blaOXA−48), PMQR genes [qnrA, qnrB, qnrC, qnrD, qnrS, qepA, aac(6′)-Ib-cr, oqxA, oqxB, gyrA, parC], AMEs [AAC(6′)-Ib, APH(3′)-Ia, AAC(3)-IV, ANT(2′′)-Ia], and 16S-RMTase genes (armA, rmtA, rmtB, rmtC, rmtD, rmtE) were investigated by PCR and sequencing. For each isolate, DNA was extracted from fresh bacterial colonies using an AxyPrep Bacterial Genomic DNA Miniprep kit (Axygen Scientific, Union city, CA, USA). PCR assays were performed on a Veriti Several mechanisms are known to mediate antibiotic resistance to commonly used antimicrobial agents, including extended-spectrum β-lactamases (ESBLs) and carbapenemases, as well as plasmid-mediated quinolone resistance (PMQR) genes, aminoglycoside-modifying enzymes (AMEs), and 16S rRNA methyltransferase (16S-RMTase) (Hu et al., 2014; Findlay et al., 2015; Buruk et al., 2016). The current study focused on pinpointing the antibiotic resistance determinants of XDR K. pneumoniae isolated from nosocomial BSIs patients and factors closely related to clinical outcome, with emphasis on determining appropriate antimicrobial drug therapy. June 2017 | Volume 8 | Article 1230 Frontiers in Microbiology | www.frontiersin.org 2 Bi et al. Bi et al. XDR K. Pneumoniae Causing BSIs TABLE 1 | Clinical characteristics of nosocomial BSIs patients. Molecular Detection of Antibiotic Resistance Determinants Characteristics of BSIs patients variable All patients (n = 35) BSIs patients P Death group Survivor group (n = 14 ) (n = 21) Age (years), median (IOR) 60 (14–90) 65 (14–90) 59 (16–83) Male 28 (80.0) 11 (31.4) 17 (48.6) 1 Type of ICU admission Direct 13 (37.1) 6 (17.1) 7 (20.0) 0.724 Transfer 8 (22.9) 5 (14.3) 3 (8.6) 0.221 Reason for ICU admission Respiratory failure 6 (17.1) 1 (2.8) 5 (14.3) 0.366 Shock 4 (11.4) 3 (8.6) 1 (2.8) 0.279 Coma 6 (17.1) 5 (14.3) 1 (2.8) 0.028 ICU intensive care procedures Invasive mechanical ventilation 16 (45.8) 8 (22.9) 8 (22.9) 0.317 Central venous catheter 18 (51.4) 8 (22.9) 10 (28.5) 0.733 Urinary catheter 12 (34.3) 8 (22.9) 4 (11.4) 0.031 Pre-infection health care interventions Surgery 8 (22.9) 5 (14.3) 3 (8.6) 0.221 Dialysis 6 (17.1) 2 (5.7) 4 (11.4) 1 Mechanical ventilation 17 (48.6) 8 (22.9) 9 (25.7) 0.5 Indwelling invasive devices Central venous catheter 28 (80.0) 13 (37.1) 15 (42.9) 0.203 Urinary catheter 20 (57.2) 12 (34.3) 8 (22.9) 0.007 Treatments administered Corticosteroids 11 (31.4) 4 (11.4) 7 (20.0) 1 Chemotherapy, radiotherapy 6 (17.1) 1 (2.8) 5 (14.3) 0.366 Comorbidities Intracranial disease 7 (20.0) 6 (17.1) 1 (2.8) 0.01 Respiratory disease 27 (77.2) 10 (28.6) 17 (48.6) 0.685 Cardiovascular disease 11 (31.4) 4 (11.4) 7 (20.0) 1 Tumor, leukemia, and lymphoma 5 (14.2) 1 (2.8) 4 (11.4) 0.627 Diabetes 8 (22.9) 3 (8.6) 5 (14.3) 1 Trauma 4 (11.4) 2 (5.7) 2 (5.7) 1 Kidney disease 11 (31.4) 4 (11.4) 7 (20.0) 1 Combination drug therapy Combination including tigecycline (50 mg/12 h) 14 (40.0) 2 (5.7) 12 (34.3) 0.016 Combination including meropenem (1 g/8 h) 9 (25.7) 7 (20.0) 2 (5.7) 0.015 Length of stay ICU length of stay, days 16 (1–58) 15 (1–58) 17 (3–57) Hospital length of stay, days 30 (1–86) 40 (1–60) 16 (6–86) Data are presented as number (%) or median [IQR]. TABLE 1 | Clinical characteristics of nosocomial BSIs patients. available on request. BLAST was utilized to align drug-resistance gene nucleotide sequences (http://blast.ncbi.nlm.nih.gov/Blast. cgi). Outer Membrane Proteins Analysis Outer Membrane Proteins Analysis A crude outer membrane protein (OMP) fraction was isolated by sonication, and OMPs were separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (12% SDS-PAGE), and OmpK35 and OmpK36 were detected by immunoblotting (serum dilution 1:20,000). K. pneumoniae ATCC 13883 served as a control strain for OMP profiling (Webb et al., 2012; Zhou et al., 2015). For outer membrane purification, crude membranes were isolated from K. pneumoniae ATCC 13883 and subjected to sucrose density fractionation. Membrane fractions were then subject to analysis by SDS-PAGE and Coomassie blue staining. Alternatively, fractions were analyzed by immunoblotting to determine the localization of inner (F1β) and outer (BamB) membrane proteins markers (Clements et al., 2009; Zhou et al., 2015). Data are presented as number (%) or median [IQR]. Plasmid Analysis and Southern Blot Plasmid Analysis and Southern Blot Major plasmid incompatibility groups: F, FIA, FIB, FIC, HI1, HI2, I1, L/M, N, P, W, T, X, Y, K, A/C, B/O, FII, FrepB, were detected by a PCR-based replicon typing (PBRT) scheme (Carattoli et al., 2005). S1 nuclease converted supercoiled plasmids into full-length linear molecules, and S1-PFGE can be used to screen for megaplasmids simultaneously (Barton et al., 1995). Total DNA from the K. pneumoniae donor strains and E. coli transconjugants were isolated using an Axyprep Bacterial Genomic DNA Miniprep kit, digested with S1 nuclease (Takara Bio, Inc.) and analyzed in a CHEF-Mapper XA PFGE system (Bio-Rad). The gel was then subject to Southern blot analysis, after transfer to a positively charged nylon membrane (Roche Diagnostics, Branford, USA) by the capillary method. The membrane was subject to hybridization with labeled blaKPC−2, rmtB, blaCTX−M−9 probes according to the instructions of Detection Starter Kit II (Roche, Sant Cugat del Vallès, Spain). The plasmids of Salmonella H9812 served as size markers (Zhou et al., 2015). Conjugation Experiments To determine the transferability of resistance determinants, Luria-Bertani (LB) mating experiments were implemented. Sodium azide-resistant E. coli J53 served as the recipient strain (Yi et al., 2012). Transconjugants were selected on Mueller-Hinton agar plates containing sodium azide (100 mg/L) and ertapenem (0.5 mg/L). The resistance genes successfully transferred from the donor strains were verified by PCR. MICs of antibiotics for the transconjugants were compared to donors and E. coli J53 to further confirm the transferable resistance genes. Distribution of Resistance Determinants Diverse resistance determinants were detected among the 35 XDR K. pneumoniae strains (Table 2). Of these, 33 strains (94.3%) were detected as co-harboring three or more resistance determinants. There is a global spread of KPC-2 carbapenemase (Naas et al., 2008; Nordmann et al., 2009) that usually explains such findings. However, two strains (FK688 and FK1934) did not express KPC-2 carbapenemase (highlighted in Figure 1). Other β-lactamases were also prevalent, including CTX-M-type ESBLs (31 isolates), SHV (28 isolates), and TEM (11 isolates). In addition, several strains harbored the β-lactamases CMY and DHA-1. Additional genes conferring drug resistance were sequenced, including the DNA gyrase encoding gyrA and the DNA topoisomerase IV encoding parC. Amino acid substitutions detected in 31 (88.6%) of the strains were gyrA (S83I, D87G) and parC (S80I). In addition, mutations were detected in quinolone resistance-determining regions (QRDRs). Intriguingly, 29 of the 30 major ST strains (ST11, ST656) among the fluoroquinolone- resistant strains carried the favorable “double serine” mutations in the gyrA and parC genes plus an additional-energetically less favorable gyrA mutation. A single ST11 strain (2048/15) carried just one favorable serine mutation without any less favorable Bacterial Clonal Relatedness the predominant clone (Table 2, Figure 1). This finding is consistent with the epidemic dissemination of K. pneumoniae carbapenemase (KPC)-producing K. pneumoniae in China described in another study (Zhou et al., 2015). Another six STs were also identified: ST1525 (FK688/13), ST290 (FK782/13), ST2281 (FK1468/14), ST268 (FK2152/15), ST14 (FK2203/15), ST656 (FK2180/15). The novel ST2281 (allelic profile: 4-1-1-22- 7-4-35) which was a multiple locus variant, has not previously been documented and has been submitted to the MLST database. the predominant clone (Table 2, Figure 1). This finding is consistent with the epidemic dissemination of K. pneumoniae carbapenemase (KPC)-producing K. pneumoniae in China described in another study (Zhou et al., 2015). Another six STs were also identified: ST1525 (FK688/13), ST290 (FK782/13), ST2281 (FK1468/14), ST268 (FK2152/15), ST14 (FK2203/15), ST656 (FK2180/15). The novel ST2281 (allelic profile: 4-1-1-22- 7-4-35) which was a multiple locus variant, has not previously been documented and has been submitted to the MLST database. been documented and has been submitted to the MLST database. The PFGE patterns of the 35 XDR K. pneumoniae isolates show a major cluster of 23 closely related isolates that exhibited >80% similarity: these are all KPC-2-producing resistant strains and are all ST11 clones (Figure 1). The rest 12 isolates which exhibited <80% similarity were assigned to seven STs (ST11, ST1525, ST290, ST2281, ST268, ST14, and ST656). Eighteen XDR K. pneumoniae isolated from ICU patients (directly admitted and transferred) belong to the predominant cluster, and the other five isolates belonging to the predominant cluster were separated from other departments. A worrying finding is that the close relatedness among the 23 XDR K. pneumoniae isolates suggests a phenomenon of clone dissemination within the clinic and the transfer of patients in different medical departments may accelerate clonal spread of pathogens. Statistical Analysis Categorical variables were compared with the chi-square test using SPSS software (version 17.0). Calculated p-values of < 0.05 were considered to be statistically significant. Susceptibilities of XDR K. pneumoniae Susceptibilities of XDR K. pneumoniae MIC assays of the patient isolates revealed that each of the XDR K. pneumoniae strains were highly resistant to at least one of the β-lactams, carbapenems, aminoglycosides, quinolones, β- lactam/inhibitor combinations, and other clinical antimicrobial agents (Table 3). Consistent with the treatment success is the observation that tigecycline exhibited superior bacteriostasis activity in vitro. In addition, 33 isolates were susceptible to polymyxin B (Table 3). Clinical Characteristics of BSIs Patients There is a growing trend of mortality in hospital patients caused by infections with K. pneumoniae (Paczosa and Mecsas, 2016). A total of 35 nosocomial BSIs patients (age 14–90 years; male: female 4:1) were included in the present study (Table 1). These patients had been admitted in the intensive care unit (60.0%), hematology department (28.6%), and neurosurgery department (11.4%), data not shown. The BSIs patients were primarily elderly, suffered severe comorbidities and had been submitted to invasive procedures, such as central venous catheterization and urinary catheterization. As documented in Table 1, the BSIs resulted in lengthy ICU stays (1–58 days; median 16 days), within long overall hospital length of stay (1–86 days; median 30 days). The mortality rate attributed to BSIs caused by XDR K. pneumoniae was 40.0%, i.e., 14 of the 35 patients died from the BSI. Two groups of BSI patients had an increased risk of death, those that received urinary catheterization (34.3% died vs. 22.9% survived, P = 0.007), and patients with intracranial disease (17.1% died vs. 2.8% survived, P = 0.01). In terms of their treatment, combination therapy including meropenem proved to be ineffective against mortality of BSIs patients caused by XDR K. pneumoniae (P = 0.015), but tigecycline in combination with other antimicrobial agents was significantly effective and reduced the risk of death (P = 0.016). Furthermore, nine patients of the survivor group were treated with fosfomycin combined with more than three other antibiotics. Bacterial Clonal Relatedness Clonal relatedness for the 35 K. pneumoniae strains was analyzed by pulsed-field gel electrophoresis (PFGE). Genomic DNA was extracted using an AxyPrep Bacterial Genomic DNA Miniprep kit, subjected to complete digestion with the restriction endonuclease XbaI (Takara Bio, Dalian, China), and 96-well Thermal Cycler (Bio-Rad, USA) using specific primers, corresponding to related studies (Jacoby, 2009; Yu et al., 2009; Li et al., 2012; Ramirez and Tolmasky, 2013). Primer sequences are June 2017 | Volume 8 | Article 1230 Frontiers in Microbiology | www.frontiersin.org Frontiers in Microbiology | www.frontiersin.org 3 XDR K. Pneumoniae Causing BSIs Bi et al. Bi et al. the diagnostic DNA fragments then separated in a PFGE CHEF- Mapper XA system (Bio-Rad) using 0.5 × Tris-borate-EDTA buffer at 120 V for 19 h, with pulse times ranging from 5 to 35 s. DNA fragments were stained with Gel Red (Biotium, USA) and analyzed using Quality one software (Bio-Rad). The DNA fingerprint patterns were analyzed according to the criteria proposed by Tenover et al. (Hu et al., 2013) and strains with more than 80% similarity were regarded as the same clone. Molecular typing of XDR K. pneumoniae strains was performed according to the protocol described on the Institut Pasteur K. pneumoniae MLST website (http://bigsdb.web.pasteur.fr/klebsiella/klebsiella. html). The sequences of seven housekeeping genes (i.e., gapA, infB, mdh, pgi, phoE, rpoB, and tonB) were amplified and sequence types (STs) were assigned by the MLST database according to Diancourt et al. (2005). The novel STs were submitted to the MLST database. the diagnostic DNA fragments then separated in a PFGE CHEF- Mapper XA system (Bio-Rad) using 0.5 × Tris-borate-EDTA buffer at 120 V for 19 h, with pulse times ranging from 5 to 35 s. DNA fragments were stained with Gel Red (Biotium, USA) and analyzed using Quality one software (Bio-Rad). The DNA fingerprint patterns were analyzed according to the criteria proposed by Tenover et al. (Hu et al., 2013) and strains with more than 80% similarity were regarded as the same clone. Molecular typing of XDR K. pneumoniae strains was performed according to the protocol described on the Institut Pasteur K. pneumoniae MLST website (http://bigsdb.web.pasteur.fr/klebsiella/klebsiella. html). The sequences of seven housekeeping genes (i.e., gapA, infB, mdh, pgi, phoE, rpoB, and tonB) were amplified and sequence types (STs) were assigned by the MLST database according to Diancourt et al. (2005). The novel STs were submitted to the MLST database. Genotypes and Clonal Relatedness of XDR K. pneumoniae Molecular typing enables detection of nosocomial transmission of bacterial pathogens, and can assist in identifying the routes of transmission in hospital settings. Multilocus sequence typing (MLST) identified seven different STs with ST11 being Frontiers in Microbiology | www.frontiersin.org June 2017 | Volume 8 | Article 1230 4 Bi et al. XDR K. Pneumoniae Causing BSIs ABLE 2 | Molecular characteristics and epidemiological analysis of XDR K. pneumoniae clinical isolates in Wenzhou, 2013–2015 (n = 35). Genotypes and Clonal Relatedness of XDR K. pneumoniae olate/year Resistance determinants Epidemiological analysis Carbape- nemases Other β-lactamases genes Quinolone resistance genes Aminoglycoside resistance determinants Size of blaKPC-2 plasmid (kb) Transcon- jugant Replicon types STs K 688/13 — blaCMY, blaDHA−1 — AAC(6′)-Ib, APH(3′)-Ia — — 1,525 K 729/13 KPC-2 blaCTX−M−14, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, rmtB — — IncFrepB 11 K 782/13 KPC-2 blaCTX−M−65, blaSHV−11 qnrS AAC(6′)-Ib — — — 290 K 1186/14a KPC-2 blaCTX−M−65, blaSHV−11 qnrS, gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, rmtB 54.7 J1186 IncFrepB 11 K 1271/14 KPC-2 — gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, rmtB — — IncFrepB 11 K 1425/14 KPC-2 blaCTX−M−14, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, — — IncFrepB 11 K 1468/14a KPC-2 blaCTX−M−14, blaSHV−11 qnrB, gyrA (S83I, D87G) AAC(6′)-Ib, AAC(3)-IV 54.7 J1468 — 2,281 K 1668/14 KPC-2 blaCTX−M−14, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, rmtB — — IncFrepB 11 K 1743/14a KPC-2 blaCTX−M−65, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, rmtB 167.1 J1743 IncFrepB 11 K 1855/14 KPC-2 blaCTX−M−14, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, rmtB — — IncFrepB 11 K 1869/14 KPC-2 blaCTX−M−65, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, rmtB — — IncFrepB 11 K 1919/15 KPC-2 blaCTX−M−14, blaSHV−11 aac(6′)-Ib-cr, gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, rmtB — — IncFrepB 11 K 2048/15 KPC-2 blaCTX−M−65, blaSHV−11 qnrS, parC (S80I) AAC(6′)-Ib — — IncFrepB 11 K 2104/15 KPC-2 blaCTX−M−65, blaSHV−11 aac(6′)-Ib-cr, gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, rmtB — — IncFrepB 11 K 2152/15a KPC-2 blaCTX−M−15, blaSHV−11 qnrS AAC(6′)-Ib 54.7 J2152 — 268 K 2200/15 KPC-2 blaCTX−M−65, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, rmtB — — IncFrepB 11 K 2203/15 KPC-2 blaCTX−M−15 — AAC(6′)-Ib — — — 14 K 2206/15 KPC-2 blaTEM−1, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, rmtB — — IncFrepB 11 K 2219/15 KPC-2 blaCTX−M−14 qnrB, gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, rmtB — — IncFrepB 11 K 2267/15 KPC-2 blaCTX−M−65, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, rmtB — — IncFrepB 11 K 2302/15a KPC-2 blaCTX−M−15, blaCTX−M−65, blaTEM−1, blaSHV−11 qnrS, gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, rmtB 54.7 J2302 IncFrepB 11 K 2322/15a KPC-2 blaCTX−M−14 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, rmtB 54.7 J2322 — 11 K 2346/15a KPC-2 blaCTX−M−65, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, rmtB 54.7 J2346 IncFrepB 11 K 2348/15 KPC-2 blaCTX−M−65, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, rmtB — — IncFrepB 11 K 2578/15 KPC-2 blaCTX−M−14, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, rmtB — — IncFrepB 11 K 1881/15a KPC-2 blaCTX−M−65, blaTEM−1, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, rmtB 54.7 J1881 IncFrepB 11 K 1905/15 KPC-2 blaCTX−M−14, blaTEM−1, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, AAC(3)-IV, rmtB — — IncFrepB 11 K 1934/15 — blaSHV−11, blaDHA−1 aac(6′)-Ib-cr, gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, AAC(3)-IV, rmtB — — — 11 K 1944/15 KPC-2 blaCTX−M−65, blaTEM−1, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, rmtB — — IncFrepB 11 K 2076/15a KPC-2 blaCTX−M−65, blaTEM−1 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, rmtB 54.7 J2076 — 11 K 2016/15 KPC-2 blaCTX−M−14, blaTEM−1, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, rmtB — — IncFrepB 11 K 2047/15a KPC-2 blaCTX−M−65, blaTEM−1, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6’)-Ib, APH(3′)-Ia, AAC(3)-IV, rmtB 54.7 J2047 IncFrepB 11 K 2078/15 KPC-2 blaCTX−M−65, blaTEM−1 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, rmtB — — — 11 K 2142/15a KPC-2 blaCTX−M−65, blaTEM−1, blaSHV−11 gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, rmtB 54.7 J2142 IncFrepB 11 K 2180/15a KPC-2 blaCTX−M−14, blaTEM−1, blaSHV−11 qnrB, aac(6′)-Ib-cr, gyrA (S83I, D87G), parC (S80I) AAC(6′)-Ib, APH(3′)-Ia, rmtB 54.7 J2180 — 656 Strains that have successfully transferred carbapenem resistance genes blaKPC to E. June 2017 | Volume 8 | Article 1230 Genotypes and Clonal Relatedness of XDR K. pneumoniae DNA fingerprints were revealed by Gel Red staining. For MLST-based categorization of the strains, the sequences of seven housekeeping genes (i.e., gapA, infB, mdh, pgi, phoE, rpoB, and tonB) were analyzed, and the PFGE patterns have been organized according to a dendogram of 35 XDR K. pneumoniae isolates based on MLST analysis. In red text are those isolates with no detectable carbapenemase genes. The gray box highlights the prevalence of the ST11 sequence type. but no transconjugants were recovered for the other 23 donor strains, despite repeated attempts, may due to the lack of sex factor F or conjugative plasmids which are key vehicles and contain simultaneously important elements, including an origin of transfer, DNA-processing factors (a relaxase and accessory proteins), and mating pair formation proteins (Achtman et al., 1971; Goessweiner-Mohr et al., 2014) (Table 2). The MIC values for the transconjugants determined for β-lactam antibiotics were consistent with the transfer of carbapenemase expression. Southern blot analysis revealed the presence of the blaKPC−2 in the transconjugants and in 11 cases corresponded to a plasmid of ∼50 kb (Figure 3), while strain J1743 carried the blaKPC−2 gene on a plasmid of ∼160 kb (Figure 3). These results are in accordance with the S1-PFGE analysis of the isolates (Figure 2). Some of these strains were found to be FrepB-positive by PBRT, showing that these plasmids belong to an IncF-type. mutations. In contrast, fluoroquinolone-resistant minor clone strains either failed to harbor any gyrA or parC mutations (ST1525, ST290, ST268, ST14) or harbored one favorable serine mutation together with a less favorable mutation (ST2281) (Table 2). The 16S-rRNA methylase encoding gene rmtB was present in 28 (80%) of the strains, a gene that confers resistance to most clinically relevant aminoglycosides. The plasmid-mediated quinolone resistance genes qnrB, qnrS, and aac(6′)-Ib-cr were also determined as present in 11 (31.4%) of the strains. 35 (100%) of the strains possessed AMEs, including AAC(6′)- Ib (100%), APH(3′)-Ia (48.6%), AAC(3)-IV (11.4%), ANT(2′′)- Ia (0%). Taken together, these results demonstrate carriage of multiple genetic determinants for drug resistance in the BSI strains. Genotypes and Clonal Relatedness of XDR K. pneumoniae coli J53; “—” means undetected. June 2017 | Volume 8 | Article 1230 5 XDR K. Pneumoniae Causing BSIs Bi et al. FIGURE 1 | PFGE analysis of XDR K. pneumoniae isolates. In order to generate diagnostic genomic DNA fragmentation fingerprints, genomic DNA from each of the XDR K. pneumoniae isolates was digested using XbaI and subjected to pulsed-field gel electrophoresis. DNA fingerprints were revealed by Gel Red staining. For MLST-based categorization of the strains, the sequences of seven housekeeping genes (i.e., gapA, infB, mdh, pgi, phoE, rpoB, and tonB) were analyzed, and the PFGE patterns have been organized according to a dendogram of 35 XDR K. pneumoniae isolates based on MLST analysis. In red text are those isolates with no detectable carbapenemase genes. The gray box highlights the prevalence of the ST11 sequence type. FIGURE 1 | PFGE analysis of XDR K. pneumoniae isolates. In order to generate diagnostic genomic DNA fragmentation fingerprints, genomic DNA from each of the XDR K. pneumoniae isolates was digested using XbaI and subjected to pulsed-field gel electrophoresis. DNA fingerprints were revealed by Gel Red staining. For MLST-based categorization of the strains, the sequences of seven housekeeping genes (i.e., gapA, infB, mdh, pgi, phoE, rpoB, and tonB) were analyzed, and the PFGE patterns have been organized according to a dendogram of 35 XDR K. pneumoniae isolates based on MLST analysis. In red text are those isolates with no detectable carbapenemase genes. The gray box highlights the prevalence of the ST11 sequence type. FIGURE 1 | PFGE analysis of XDR K. pneumoniae isolates. In order to generate diagnostic genomic DNA fragmentation fingerprints, genomic DNA from each of the XDR K. pneumoniae isolates was digested using XbaI and subjected to pulsed-field gel electrophoresis. DNA fingerprints were revealed by Gel Red staining. For MLST-based categorization of the strains, the sequences of seven housekeeping genes (i.e., gapA, infB, mdh, pgi, phoE, rpoB, and tonB) were analyzed, and the PFGE patterns have been organized according to a dendogram of 35 XDR K. pneumoniae isolates based on MLST analysis. In red text are those isolates with no detectable carbapenemase genes. The gray box highlights the prevalence of the ST11 sequence type. FIGURE 1 | PFGE analysis of XDR K. pneumoniae isolates. In order to generate diagnostic genomic DNA fragmentation fingerprints, genomic DNA from each of the XDR K. pneumoniae isolates was digested using XbaI and subjected to pulsed-field gel electrophoresis. DS-Page of Outer Membrane Proteins SDS-Page of Outer Membrane Proteins The major porins of E. coli, OmpF and OmpC, provide for most of the flux of molecules up to ∼650 Da across the outer membrane (Nikaido et al., 1983; Sugawara et al., 2016) and thereby play a role in the susceptibility of E. coli to antibiotics (Nikaido, 2003; Zgurskaya et al., 2015). The homologous porins of K. pneumoniae, OmpK35 and OmpK36, have been highlighted as the primary channels through KPC-2 and other resistance determinants are often carried on plasmids (Kuai et al., 2014), and S1-PFGE revealed the presence of one or more plasmids in each of the isolated strains (Figure 2). The detected plasmids by S1-PFGE ranged in size from ∼50 to ∼390 kb. For an initial assessment of the plasmids, transconjugation experiments were established using E. coli J53 as the recipient. Carbapenemase genes from 12 strains were successfully transferred to the recipient E. coli J53, June 2017 | Volume 8 | Article 1230 Frontiers in Microbiology | www.frontiersin.org 6 XDR K. Pneumoniae Causing BSIs Bi et al. TABLE 3 | Antibiotic susceptibility of XDR K. pneumoniae isolates. Antibiotics MIC (mg/L) Percentage MIC50 MIC90 Range Susceptible/Non-susceptible β-lactams CAZ 128 >128 64 to >128 0/100 CTX >128 >128 32 to >128 0/100 β-lactam/Inhibitor SAM 64 >128 64 to >128 0/100 TZP >128 >128 64 to >128 0/100 Carbapenems IPM 64 64 8 to >64 0/100 MEM >64 >64 1 to >64 2.9/97.1 ETP >64 >64 4 to >64 0/100 Aminoglycosides AMK >256 >256 1 to >256 5.7/94.3 GEN >256 >256 8 to >256 0/100 TOB 256 >256 2 to >256 5.7/94.3 Quinolones CIP 32 64 1 to 128 2.9/97.1 LEV 16 64 4 to 64 0/100 Other FOS >512 >512 64 to >512 0/100 PB 1 1 0.25 to 128 94.3/5.7 TGC 0.5 1 0.25 to 1 100/0 CAZ, ceftazidime; CTX, cefotaxime; SAM, ampicillin/sulbactam; TZP, piperacillin/tazobactam; IPM, imipenem; MEM, meropenem; ETP, ertapenem; AMK, amikacin; GEN, gentamicin; TOB, tobramycin; CIP, ciprofloxaxin; LEV, levofloxacin; FOS, fosfomycin; PB, polymyxin B; TGC, tigecycline. BLE 3 | Antibiotic susceptibility of XDR K. pneumoniae isolates. a considerable cause of mortality in nosocomial infections accounting for ∼14%, ranking immediately after respiratory tract infections and incision infections in ICUs (Russotto et al., 2015). In this period from 2013 to 2015, K. pneumoniae was frequently isolated from these BSIs patients, and predominantly with a multiple drug resistant phenotypes. DS-Page of Outer Membrane Proteins It is a growing global reality, that XDR K. pneumoniae nosocomial infections are associated with delays in appropriate therapy, and therefore pose serious challenges to clinically effective therapeutic options worldwide (Lim et al., 2015). The increasing prevalence and global dissemination of these clinical XDR strains gravely threatens public health (Zhao et al., 2015). While our study has been conducted in a single medical center, the samples were sourced from the First Affiliated Hospital of Wenzhou Medical University, which is one of the largest comprehensive hospitals integrating medical care, clinical practice teaching and scientific research. The hospitals outpatient clinics service close to five million patients per annum, taking responsibility for the medical care of a 30 million population in southern Zhejiang and eastern Fujian areas. Environments such as this provide a valuable resource to track new developments in hospital acquired infections and monitor the dissemination of new resistance genes for ongoing studies. Respiratory infections could be the key source of XDR K. pneumoniae BSIs, which require a prolonged antibiotic therapy and are considered as an important factor for acquired resistance of pathogens (Ryan et al., 2015). The case-fatality rate attributed to BSIs caused by XDR K. pneumoniae here was 40% (14/35), the higher than the overall mortality rate (15–20%) associated with BSIs in previous studies (Russotto et al., 2015). The high ICU admission rate (n = 21, 60%) that was observed in the present study, may relate to hypoimmunity resulting from severe comorbidities and invasive care procedures (Woodford et al., 2004; Bouza et al., 2013; Martelius et al., 2016). The clinical retrospective data showed that 57% of cases received broad- spectrum antibiotics, including third-generation cephalosporin, carbapenems, and tigecycline. Recent studies have shown that carbapenems are generally considered as part of combination therapy when carbapenem MICs are <8 mg/L (Daikos et al., 2014), and this had become a standard treatment regime. However, 34 of the 35 isolates of XDR K. pneumoniae in this study were non-susceptible to meropenem and, even in combination therapy, meropenem was not protective against mortality of BSIs patients (P = 0.015). Thus, rapid typing and identification of specific BSIs phenotypes is essential to avoid unnecessary and inappropriate antimicrobial regimens. Our data showed that an alternative treatment regime of tigecycline in combination with other antimicrobial agents was significantly effective (P = 0.016). which beta-lactams cross the outer membrane (Kaczmarek et al., 2006). DS-Page of Outer Membrane Proteins OmpK35 and OmpK36 are highly abundant proteins of the outer membrane in K. pneumoniae, and can be readily detected by Coomassie blue staining after SDS- PAGE analysis of the outer membranes (Rath et al., 2009). A procedure was optimized to purify outer membranes from the control strain K. pneumoniae ATCC 13883, using sucrose gradient fractionation to separate outer membranes from inner membranes (Figure 4A). Immunoblotting for marker proteins F1β and BamB served as controls for the fractions (Figure 4A). Comparative analysis of outer membrane fractions isolated from the carbapenem-resistant, yet carbapenemase-negative strains FK688 and FK1934 using antibodies specific for OmpK35 and OmpK36 showed no detectable expression of OmpK35 and OmpK36 (Figure 4B). PCR primers designed to amplify regions of the corresponding loci failed to detect ompK35 and ompK36 in FK688 and FK1934 (data not shown). which beta-lactams cross the outer membrane (Kaczmarek et al., 2006). OmpK35 and OmpK36 are highly abundant proteins of the outer membrane in K. pneumoniae, and can be readily detected by Coomassie blue staining after SDS- PAGE analysis of the outer membranes (Rath et al., 2009). A procedure was optimized to purify outer membranes from the control strain K. pneumoniae ATCC 13883, using sucrose gradient fractionation to separate outer membranes from inner membranes (Figure 4A). Immunoblotting for marker proteins F1β and BamB served as controls for the fractions (Figure 4A). Comparative analysis of outer membrane fractions isolated from the carbapenem-resistant, yet carbapenemase-negative strains FK688 and FK1934 using antibodies specific for OmpK35 and OmpK36 showed no detectable expression of OmpK35 and OmpK36 (Figure 4B). PCR primers designed to amplify regions of the corresponding loci failed to detect ompK35 and ompK36 in FK688 and FK1934 (data not shown). The emergence and spread of XDR K. pneumoniae over the last decade is a major, global concern (Naparstek et al., 2012), and the findings of this specific study are relevant to problems faced by clinicians around the globe. In the last several years, antibiotic resistance mediated by plasmids has been increasing at a remarkable rate (Yang et al., 2011), especially through genes encoding carbapenemase, PMQRs and 16S-RMTase. Strikingly, most of the isolates in this study Frontiers in Microbiology | www.frontiersin.org DISCUSSION Braenderup H9812 digested with XbaI; Lanes 2–12 represent transconjugants of the corresponding number of donor isolates, all of the isolates code consistent with Table 3. (B) The corresponding Southern blot, hybridized with a DNA probe to the blaKPC−2 sequence. FIGURE 3 | Plasmid profiles of E. coli transconjugants. (A) In order to verify plasmids carried by the XDR K. pneumoniae isolates, transconjugation experiments were established using E. coli J53 as a recipient strain. Genomic DNA was isolated from the transconjugants, digested using S1 nuclease and subjected to pulsed-field gel electrophoresis. H = size marker strain Salmonella enterica ser. Braenderup H9812 digested with XbaI; Lanes 2–12 represent transconjugants of the corresponding number of donor isolates, all of the isolates code consistent with Table 3. (B) The corresponding Southern blot, hybridized with a DNA probe to the blaKPC−2 sequence. FIGURE 3 | Plasmid profiles of E. coli transconjugants. (A) In order to verify plasmids carried by the XDR K. pneumoniae isolates, transconjugation experiments were established using E. coli J53 as a recipient strain. Genomic DNA was isolated from the transconjugants, digested using S1 nuclease and subjected to pulsed-field gel electrophoresis. H = size marker strain Salmonella enterica ser. Braenderup H9812 digested with XbaI; Lanes 2–12 represent transconjugants of the corresponding number of donor isolates, all of the isolates code consistent with Table 3. (B) The corresponding Southern blot, hybridized with a DNA probe to the blaKPC−2 sequence. Using molecular analysis, we located blaKPC−2 on ∼50 and ∼160 kb transferable plasmids which co-harbored blarmtB and blaCTX−M−9. In consideration of the problems that smaller plasmids may not be detected by S1-PFGE, plasmids of randomly selected 10 strains and 6 transconjugants were extracted and separated by agarose gel electrophoresis. The result revealed the presence of smaller plasmids which were not detected by S1- PFGE in all of the 10 strains and 2 of the 6 transconjugants. The gel was then subject to Southern blot analysis, after transfer to a positively charged nylon membrane by the capillary method. The membrane was subject to hybridization with labeled blaKPC−2 probes, nevertheless, hybridization signals were only observed in large plasmids (>54.2 kb) (Figure S1). Figure S1 was available in supplementary data, and demonstrate that smaller plasmids didn’t mediate the widespread dissemination of resistant genes possessed KPC-2 and co-harbored three or more classes of resistance genes. Frontiers in Microbiology | www.frontiersin.org DISCUSSION Between 2013 and 2015, the incidence rate of all nosocomial infections in this major public hospital in southern China was 2.23%, comparable to other grade A tertiary hospitals that range from 2 to 4% (Mu et al., 2015; Zhao, 2015). The current study was motivated by the observation that bloodstream infection became Frontiers in Microbiology | www.frontiersin.org June 2017 | Volume 8 | Article 1230 7 Bi et al. XDR K. Pneumoniae Causing BSIs FIGURE 2 | Gel image of S1 PFGE result of all XDR K. pneumoniae isolates. Isolates were digested using S1 nuclease and subjected to pulsed-field gel electrophoresis. The gel was subjected to Gel Red staining and analyzed in a CHEF-Mapper XA PFGE system. H = size marker strain Salmonella enterica ser. Braenderup H9812 digested with XbaI. FIGURE 3 | Plasmid profiles of E. coli transconjugants. (A) In order to verify plasmids carried by the XDR K. pneumoniae isolates, transconjugation experiments were established using E. coli J53 as a recipient strain. Genomic DNA was isolated from the transconjugants, digested using S1 nuclease and subjected to pulsed-field gel electrophoresis. H = size marker strain Salmonella enterica ser. Braenderup H9812 digested with XbaI; Lanes 2–12 represent transconjugants of the corresponding number of donor isolates, all of the isolates code consistent with Table 3. (B) The corresponding Southern blot, hybridized with a DNA probe to the blaKPC−2 sequence. FIGURE 2 | Gel image of S1 PFGE result of all XDR K. pneumoniae isolates. Isolates were digested using S1 nuclease and subjected to pulsed-field gel electrophoresis. The gel was subjected to Gel Red staining and analyzed in a CHEF-Mapper XA PFGE system. H = size marker strain Salmonella enterica ser. Braenderup H9812 digested with XbaI. FIGURE 2 | Gel image of S1 PFGE result of all XDR K. pneumoniae isolates. Isolates were digested using S1 nuclease and subjected to pulsed-field gel electrophoresis. The gel was subjected to Gel Red staining and analyzed in a CHEF-Mapper XA PFGE system. H = size marker strain Salmonella enterica ser. Braenderup H9812 digested with XbaI. FIGURE 3 | Plasmid profiles of E. coli transconjugants. (A) In order to verify plasmids carried by the XDR K. pneumoniae isolates, transconjugation experiments were established using E. coli J53 as a recipient strain. Genomic DNA was isolated from the transconjugants, digested using S1 nuclease and subjected to pulsed-field gel electrophoresis. H = size marker strain Salmonella enterica ser. DISCUSSION The high prevalence rate of KPC-2 among these isolates exceeded that found in other investigations across the world (Bradford et al., 2004). Previous studies proposed that blaKPC−2 resides on transmissible plasmids, which frequently co-harbor other resistance elements (Endimiani et al., 2008), leading to MDR and XDR pathogens. Even where carbapenemase genes are not evident, carbapenem-resistant phenotypes were observed; while they carried AmpC β-lactamase genes (blaCMY and blaDHA−1), no carbapenemase genes were detected in two strains from this study, FK688 and FK1934. Notably, these two strains were not found to express OmpK35 and OmpK36. We suggest that the absence of the major porins in the bacterial outer membrane reduced permeability to carbapenem, thereby enhancing carbapenem resistance. Frontiers in Microbiology | www.frontiersin.org June 2017 | Volume 8 | Article 1230 8 Bi et al. XDR K. Pneumoniae Causing BSIs Since multiple resistant determinants rendering almost all antimicrobials ineffective and poor survival in patients infected with XDR K. pneumoniae, tigecycline and polymyxin B seemed to be the optional choices. Notably, multiple amino acid substitutions, including both gyrA (S83I, D87G) and parC (S80I) were observed among ST11 strains which was predominant clone except a single ST11 strain (2048/15), being apparently more than that detected in minor clone strains. Resistance mutations decreased the affinity of gyrase and topoisomerase IV for fluoroquinolones, and our findings also illustrate that favorable mutations and consequently superior fitness, closely associated with high-level resistance to fluoroquinolones, could contribute to the promotion of the major international high- risk clone (ST11) of multidrug-resistant K. pneumoniae. These findings are in complete agreement with those published by Tóth et al. (2014). FIGURE 4 | Remodeling of the outer membrane proteome in the XDR K. pneumoniae isolates. (A) Total membranes were isolated from K. pneumoniae ATCC 13883 and subjected to sucrose density fractionation. Membrane fractions were subject to SDS-PAGE, and then Coomassie blue staining (top panel) and immunoblotting (bottom panel) using antisera recognizing known outer (BamB) and inner (F1β) membrane proteins. (B) Whole cell lysates from K. pneumoniae ATCC 13883 and K. pneumoniae clinical isolates FK688 and FK1934 were analyzed by SDS-PAGE and western immunoblotting for OmpK35 and OmpK36. KPC-2-producing K. pneumoniae isolates have been reported worldwide, and the dominant KPC-producing clone ST258 is implicated in more than 70% of reported outbreaks in America (Kitchel et al., 2009). Other STs (ST1525, ST290, ST14, ST268, ST656, etc.) have not been reported to be MDR/XDR global clones. Frontiers in Microbiology | www.frontiersin.org DISCUSSION The predominant clone now is ST11, which is a variant of the pandemic ST258 clone and played an important role in the epidemic dissemination of blaKPC−2 (Cuzon et al., 2010). High homology of KPC-2-producing K. pneumoniae ST11 has been observed by PFGE, which indicated clonal dissemination in our hospital in recent years, reinforcing the viewpoint speculated by Qi et al. that ST11 K. pneumoniae could be considered as a plasmid scavenger that amplifies plasmid dissemination (Qi et al., 2011). FIGURE 4 | Remodeling of the outer membrane proteome in the XDR K. pneumoniae isolates. (A) Total membranes were isolated from K. pneumoniae ATCC 13883 and subjected to sucrose density fractionation. Membrane fractions were subject to SDS-PAGE, and then Coomassie blue staining (top panel) and immunoblotting (bottom panel) using antisera recognizing known outer (BamB) and inner (F1β) membrane proteins. (B) Whole cell lysates from K. pneumoniae ATCC 13883 and K. pneumoniae clinical isolates FK688 and FK1934 were analyzed by SDS-PAGE and western immunoblotting for OmpK35 and OmpK36. Smaller plasmids can be important resistance reservoirs harboring multiple determinants, and many of them are high copy number conferring the host bacterial strains high levels of resistance. Therefore, comprehensive analysis and study of smaller plasmids are essential for understanding the role of smaller plasmids play in developing of XDR strains. In addition, studying biology of virulence of XDR isolates, and gene environment of the plasmids (∼50 and ∼160 kb) harboring blaKPC−2 are worthwhile, and the lack of corresponding researches are deficiencies of present study, further explorations are still warranted in follow-up studies. blaKPC−2 in Wenzhou. However, investigation of other resistant genes harbored by smaller plasmids are still warranted. The genetic environment surrounding the blaKPC−2 gene which was located on various plasmids among the KPC- producing Enterobacteriaceae iaolated from China is primarily reported to be the integrin of Tn3-based transposon. The truncated blaTEM gene fragment is the representative structure of the Tn3 transposon (Luo et al., 2013). In present study, 6 isolates carrying blaKPC−2 which located in ∼50 kb transferable plasmids were detected to harbor blaTEM as well, so we speculate that the blaKPC−2-surrounding nucleotide sequence contain integron structure of Tn3-based transposon. REFERENCES produce beta-lactamase blaKPC−2 gene. Emerg. Infect. Dis. 16, 1349–1356. doi: 10.3201/eid1609.091389 produce beta-lactamase blaKPC−2 gene. Emerg. Infect. Dis. 16, 1349–1356. doi: 10.3201/eid1609.091389 Achtman, M., Willetts, N., and Clark, J. (1971). 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FUNDING The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb. 2017.01230/full#supplementary-material This work was supported by research grants from the National Natural Science Foundation of China (no. 81171614), the Health ACKNOWLEDGMENTS TZ, BL, and JC contributed to the design of the experiments. WB, HL, RD, BL, VT, and LC performed the experiment. WB, HL, and BL wrote the initial draft of the manuscript. TZ, TL, WB, HL, RD, BL, VT, JC, LC, JW, and RS contributed to the acquisition, analysis, interpretation of the data included in this manuscript. TZ, TL, WB, HL, BL, JC, LC, and RS revised the manuscript. All authors approves of the final manuscript being submitted and agree to be accountable for the work detailed in the submitted manuscript. We thank the team of the curators of the Institute Pasteur MLST system (Paris, France) for importing novel alleles, profiles and/or isolates at http://bigsdb.web.pasteur.fr. We acknowledge Dr. Takuya Shiota for antibodies recognizing OmpF/OmpK35 and OmpC/OmpK36. We thank Dr. Kerry Dunse for critical comments on the manuscript. CONCLUSION In summary, the complex phenotypes of these XDR K. pneumoniae strains were associated with multiple resistance determinants and remodeling of the outer membrane proteome. In addition, favorable gyrase and topoisomerase IV mutations and consequently superior fitness contributed to the promotion of the predominant clone (ST11) of multidrug-resistant K. pneumoniae in Wenzhou, China. The dissemination and epidemicity of clinical XDR K. pneumoniae strains result from horizontal transmission of multiple resistance determinants via IncF plasmids. KPC-2-producing K. pneumoniae ST11 played a crucial role. The clonal dissemination of XDR ST11 demonstrated that efficient screening, intensive surveillance, strict disinfection procedure and prompt quarantine measures are urgently needed to restrain the emergence and transmission The predominant blaKPC plasmid type was IncF, and was associated with K. pneumoniae ST258 (Chen et al., 2013). We speculate that most (7/12) transferable blaCTX−M and blaKPC−2 genes may be located on the IncF plasmid, which is capable of clonal expansion and horizontal dissemination among Enterobacteriaceae bacteria (Doumith et al., 2012). Previous studies have shown that individual patients can be positive for IncF plasmids for more than 3 years (Onnberg et al., 2014), which might reflect either the persistence of the pathogen clone, or persistence of the plasmid transmitted to other resident bacteria. ESBLs genes carried by plasmids are also detected in various lineages of the Enterobacteriaceae (Tham et al., 2012). June 2017 | Volume 8 | Article 1230 9 Bi et al. XDR K. Pneumoniae Causing BSIs Department of Zhejiang Province of the People’s Republic of China (no. 2011KYA106), the Zhejiang Provincial Program for the Cultivation of High-level Innovative Health Talents (no. [2012]241), and Program Grant 1092262 from the National Health and Medical Research Council, Australia. of XDR strains in hospital settings. The high mortality attributed to BSIs caused by XDR K. pneumoniae is an alert to clinicians to establish rational and effective combination drug therapy. REFERENCES 75, 373–376. doi: 10.1016/j.diagmicrobio.2013.01.006 ST1031 clinical isolates in China. Diagn. Microbiol. Infect. Dis. 75, 373–376. doi: 10.1016/j.diagmicrobio.2013.01.006 Nordmann, P., Cuzon, G., and Naas, T. (2009). The real threat of Klebsiella pneumoniae carbapenemase-producing bacteria. Lancet Infect. Dis. 9, 228–236. doi: 10.1016/S1473-3099(09)70054-4 Hu, T. Y., Qu, J. Y., and Li, X. J. (2014). 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Frontiers in Microbiology | www.frontiersin.org June 2017 | Volume 8 | Article 1230 REFERENCES Porin channels in Escherichia coli: studies with beta-lactams in intact cells. J. Bacteriol. 153, 232–240. June 2017 | Volume 8 | Article 1230 Frontiers in Microbiology | www.frontiersin.org 11 Bi et al. Bi et al. XDR K. Pneumoniae Causing BSIs armA genes in the same isolate. Diagn. Microbiol. Infect. Dis. 64, 57–63. doi: 10.1016/j.diagmicrobio.2009.01.020 armA genes in the same isolate. Diagn. Microbiol. Infect. Dis. 64, 57–63. doi: 10.1016/j.diagmicrobio.2009.01.020 during a short period of time in a Chinese teaching hospital: epidemiology study and molecular characteristics. Diagn. Microbiol. Infect. Dis. 82, 240–244. doi: 10.1016/j.diagmicrobio.2015.03.017 Zgurskaya, H. I., Weeks, J. W., Ntreh, A. T., Nickels, L. M., and Wolloscheck, D. (2015). Mechanism of coupling drug transport reactions located in two different membranes. Front. Microbiol. 6:100. doi: 10.3389/fmicb.2015.00100 Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Zhao, F., Zhang, J., Fu, Y., Ruan, Z., and Xie, X. (2015). Dissemination of extensively drug-resistant and KPC-2 producing Klebsiella pneumoniae isolated from bloodstream infections. J. Infect. Dev. Ctries 9, 1016–1021. doi: 10.3855/jidc.6679 Copyright © 2017 Bi, Liu, Dunstan, Li, Torres, Cao, Chen, Wilksch, Strugnell, Lithgow and Zhou. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Zhao, X. (2015). Investigation and analysis of prevalence rate of nosocomial infections in a three level of first-class hospital of traditional Chinese Medicine. Guangming J. Chin. Med. 24, 6110–6111. doi: 10.3969/j.issn.1003-8914.2015.06.027 Zhou, T., Zhang, Y., Li, M., Yu, X., Sun, Y., and Xu, J. (2015). An outbreak of infections caused by extensively drug-resistant Klebsiella pneumoniae strains June 2017 | Volume 8 | Article 1230 Frontiers in Microbiology | www.frontiersin.org 12
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The postoperative prognosis of elderly intertrochanteric fracture patients as evaluated by the Chang reduction quality criteria
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The postoperative prognosis of elderly intertrochanteric fracture patients as evaluated by the Chang reduction quality criteria Chongqing Emergency Medical Center (Chongqing University Central Hospital) xiaoxing Zhang  (  dszxx76@163.com ) Chongqing Emergency Medical Center (Chongqing University Central Hospital) Results The mortality were 24.68% and 15.42% at 1 year and total follow-up, respectively. In the total follow-up time and 1-year follow-up time, the mortality of CRQC-Excellent was significantly lower than that of CRQC- Acceptable (p.adj < 0.05), and was significantly lower than that of CRQC-Poor (p.adj < 0.05). After multi- factor adjustment, CRQC-Acceptable and Poor in were independent risk factors affecting the overall mortality and 1-year mortality. In addition, advanced age, comorbidities ≥ 1, ASA3 + 4, and prolonged preoperative waiting time were independent risk factors for survival in the total follow-up time. At 1-year follow-up, only ASA3 + 4 and prolonged preoperative waiting time were independent risk factors for survival. Subgroup analysis according to different characteristics at the total follow-up time and at the one-year follow-up time showed that in most subgroups as CRQC decreased was significantly associated with an increase in all-cause mortality (p for trend < 0.05). Conclusions This study highlights that CRQC-Acceptable and Poor are associated with increased all-cause mortality in elderly intertrochanteric fractures. We should try to achieve good reduction of these fractures. Objective The aim of this study was to investigate the relationship between the Chang reduction quality criteria (CRQC) and the outcome of elderly intertrochanteric fractures based on a subgroup of follow-up time. Methods Retrospective analysis of 389 elderly patients with intertrochanteric fractures treated surgically from January 2019 to June 2021, including 130 males and 259 females; age 84.64 (77.50-89.74) years. Patient survival was followed by telephone between admission to hospital for fracture and death, or until study deadline (June 1, 2022). According to the CRQC, were divided into Poor, Acceptable, Excellent three groups. Based on total follow-up time and 1-year follow-up, univariate and multivariate Cox proportional hazard models were used to assess the association between CRQC and all-cause mortality in elderly intertrochanteric fractures. Further subgroup analysis was performed according to different clinical and biological characteristics to make the results more accurate. Research Article Keywords: Chang reduction quality criteria, Elderly, Intertrochanteric fractures, Mortality Posted Date: August 1st, 2022 DOI: https://doi.org/10.21203/rs.3.rs-1893661/v1 License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/20 Page 1/20 Background Intertrochanteric fractures of the femur are more likely to occur in elderly individuals with osteoporosis, most of which are unstable, with high mortality and disability rates. Clinical treatment of these fractures Page 2/20 is difficult to some extent. With the aging of the population, the incidence of intertrochanteric fractures has been increasing annually [1-3]. Fixed early surgery is the current mainstream treatment and can allow patients to engage in early functional exercise and outdoor activities, reduce complications and improve quality of life, commonly used implants are typically attached to the marrow during include internal and external fixation [4]. External fixation and intramedullary fixation provide good biomechanical stability and are more suitable for elderly patients and patients with osteoporosis and unstable fractures, the latter are commonly performed with PFNA and INTERTAN fixation systems [5,6]. The Guidelines of The National Institute for Health and Care Excellence (NICE) emphasize that getting patients out of bed early after surgery can reduce mortality [7]. To achieve these goals, the fracture needs to be fixed in a stable structure that will fully support load-bearing, thereby reducing pain and improving function [8]. Poor stability after fracture fixation can lead to limb shortening, hip pain, dysfunction, and even resurgery [9,10], resulting in a delay in getting patients out of bed. Reduction quality is one factor determining stability after fracture fixation [11,12]. There are different criteria for evaluating the quality of intertrochanteric fracture reduction, the most widely used of which are the criteria developed by Baumgaertner et al (Baumgaertner reduction quality criteria, BRQC) [13,14]. Later, Chang et al, based on positive medial cortical support (PMCS, Fig. 1) and negative medial cortical support (NMCS, Fig. 1), proposed a new reset quality standard named the Chang reduction quality criteria (CRQC) [15] (Table 1). Studies have shown that the CRQC is more reliable than the BRQC in assessing stability after fracture fixation [16]. The main objective of this article is to assess the impact of reduction quality in regard to the CRQC on patient survival after the intramedullary nail fixation of intertrochanteric femoral fractures in elderly patients. To the best of our knowledge, there are no published studies on the CRQC in evaluating the reset quality after femoral intertrochanteric fracture and thus in assessing the impact of reset quality on mortality. Study design and patients A total of 389 patients with intertrochanteric fractures were admitted to the hospital between January 2019 and June 2021 for this study. All patients were fixed with INTERTAN or PFNA systems. The choice of internal fixation was based on surgeon preference and experience. The inclusion criteria were as follows: (1) diagnosis of intertrochanteric fracture (AO 31A1 or 31A2) [17]. (2) Age ≥ 65 years. (3) Low- energy fractures, fresh fractures not older than 3 weeks. (4) Complete medical history. The exclusion criteria were as follows: (1) Age < 65 years. (2) High energy fractures, old fractures, and pathological fractures. (3) Prior conservative treatment. (4) Refusal of or loss to follow-up. Table 1 Chang reduction quality criteria (CRQC) Page 3/20 Page 3/20 Item Score I. Alignment   a. Anteroposterior view: normal or slightly valgus neck-shaft anglea 1 b. Lateral view: less than 20° of angulation 1 II. Displacement   a. Anteroposterior view: neutral or positive medial cortical supportb 1 b. Lateral view: smooth anterior cortical contactc 1 Reduction quality   Excellent 4 Acceptable 2 or 3 Poor 0 or 1 Item Score I. Alignment   a. Anteroposterior view: normal or slightly valgus neck-shaft anglea 1 b. Lateral view: less than 20° of angulation 1 II. Displacement   a. Anteroposterior view: neutral or positive medial cortical supportb 1 b. Lateral view: smooth anterior cortical contactc 1 Reduction quality   Excellent 4 Acceptable 2 or 3 Poor 0 or 1 Follow-up and study endpoint Patients were followed up by telephone once a month for the first three months after discharge, then every three months until one year, and every six months thereafter. Follow-up time was defined as the time between hospitalization and the date of death or the last follow-up visit (June 30, 2022). Data collection We retrospectively recorded age, sex, fracture type, fracture orientation, number of comorbidities, American Society of Anesthesiologists (ASA) classification, type of anesthesia, preoperative waiting time, blood transfusion, preoperative hemoglobin, and CRQC for the patients. The comorbidity data of these patients were identified using the codes of the 10th Revision of the International Classification of Diseases. Page 4/20 Page 4/20 The main exposure variable was the reset quality, as assessed by the CRQC. The CRQC were assessed by two independent assessors (LJ and DX) blinded to each other's scores. Cases of disagreement were resolved with the assistance of a third assessor (HM). Statistical analysis IBM SPSS 26.0 (IBM Corp. New York, USA) were used for statistical analyses. The significance level was set to 0.05. Continuous variables are expressed as the mean ± standard deviation (SD) or median (interquartile range, IQR). The Shapiro‒Wilk test was used to assess the normality of the distribution of variables. The Kruskal‒Wallis H test was used for comparative analysis between the 3 groups of data that did not conform to a normal distribution. One-way ANOVA was used for comparative analysis between the 3 groups of normally distributed data. Categorical variables are expressed as frequencies (percentages) and were compared by the χ2 test. Hazard ratios (HR) and 95% confidence intervals (CIs) for the risk of death were calculated by one-way Cox regression analysis, incorporating the influencing factors (p< 0.10) into a multifactorial Cox proportional risk model. We also performed subgroup analyses for age, sex, fracture subtype, fracture orientation, number of comorbidities, ASA grade, blood transfusion, and hemoglobin level. For the subgroup analyses, we did not perform multivariate adjustment because of the very small number of events. Ethics approval This retrospective study involving human participants was conducted in accordance with the ethical standards of the institutional and national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. The study was approved by the Ethics Committee of the Central Hospital affiliated with Chongqing University. Informed consent was obtained from all participants. Patient characteristics Page 5/20 A total of 389 patients with intertrochanteric fractures were included in this study, and their characteristics are summarized in Table 1. The age of these participants was 84.64 (IQR, 77.50-89.74) years, with females accounting for the majority of patients (66.58%). AO 31A2 intertrochanteric fractures of the femur accounted for 79.69% of fractures, and 63.24% of fractures were on the right. The proportions of patients with no, one, and two or more comorbid diseases were 21.85%, 35.73% and 42.42%, respectively. Regarding ASA grades, 11.05% and 88.95% of patients were grades 1+2 and grades Page 5/20 3+4, respectively. Among the types of anesthesia, general anesthesia, combined spinal and epidural+spinal anesthesia, and nerve block were used on 37.28%, 59.64% and 3.08% of the patients, respectively. The preoperative waiting time was 3 (IQR, 2-5) days. The preoperative hemoglobin level was 107 (IQR, 93-119) g/l. A total of 56.30% of the patients received blood transfusions. All-cause mortality occurred in 96 patients during the total follow-up period (mortality rate: 24.68%). At the 1-year follow-up time, all-cause death had occurred in 60 patients (mortality: 15.42%). As shown in Table 2, there were no statistically significant differences in the comparison of sex, age, fracture subtype, orientation of the fracture, ASA score and preoperative waiting time among the 3 CRQC groups (Poor, Acceptable, Excellent), whereas statistically significant differences were found in the comparison of the number of comorbid diseases, mode of anesthesia, whether blood was transfused and hemoglobin level (P<0.05). As shown in Table 1 and Figure 1, at the total follow-up, the morbidity of the CRQC-Excellent group was significantly lower than that of the CRQC-Acceptable (16.67% vs. 31.91%, p.adj<0.05) and CRQC-Poor groups (16.67% vs. 53.85%, p.adj<0.05). The mortality of the CRQC- Acceptable group was lower than that of the CRQC-Poor group, but not significantly (31.91% vs. 53.85%, p.adj>0.05). At the one-year follow-up, the CRQC-Excellent group had significantly lower mortality than the CRQC-Acceptable (6.31% vs. 22.70%, p.adj<0.05) and CRQC-Poor groups (6.31% vs. 53.85%, p.adj<0.05), and mortality in the CRQC-Acceptable group was significantly lower than that in the CRQC-Poor group (22.70% vs. 53.85%, p.adj<0.05) (Fig. 2). Clinical variables predicting mortality The relationship between clinical variables and the prognosis of intertrochanteric fractures in elderly patients is listed in Tables 3 and 4. At the total follow-up, according to univariate Cox analysis, increasing age, fracture type (31A2), ≥1 comorbidity, ASA grades 3+4, longer preoperative waiting time, lower hemoglobin level, blood transfusion and lower CRQC grade were significantly associated with increased overall mortality (p< 0.10). At the 1-year follow-up, older age, fracture type (31A2), ASA grade 3+4, prolonged preoperative waiting time, decreased hemoglobin levels, blood transfusions and lower CRQC grade were found to be significantly associated with increased overall mortality by univariate Cox analysis (p< 0.10). The influencing factors screened by univariate Cox regression analysis were incorporated into the multivariate Cox proportional risk model. Increased age (HR 1.04, 95%CI 1.01-1.08), 1 comorbidity (HR 6.63, 95%CI 1.56-28.23), ≥2 comorbidities (HR 8.65, 95%CI 2.06-36.41), ASA grades 3+4 (HR 5.09, 95%CI 1.14-22.68), increased preoperative waiting time (HR 1.10, 95%CI 1.03-1.18), CRQC-Acceptable (HR 1.60, 95%CI 1.06-2.53), and CRQC-Poor (HR 6.67, 95%CI 3.48-12.77) were independent risk factors for all-cause mortality during the total follow-up (Table 2). ASA grade 3+4 (HR 5.07, 95%CI 1.08-23.84), increased preoperative waiting time (HR 1.12, 95%CI 1.03-1.21), and acceptable (HR 3.11, 95%CI 1.64-5.91) and poor CRQC grades (HR 14.80, 95%CI 6.83-32.09) were independent risk factors for all-cause mortality during the 1-year follow-up (Tables 3 and 4). Subgroup analyses Page 6/20 Page 6/20 To further verify whether the predictive values of the CRQC for mortality were consistent across populations, we performed subgroup analyses using forest plots, as shown in Figure 4. Consistent with the main analysis, subgroup analysis showed that in most subgroups, a lower CRQC grade was significantly associated with increased all-cause mortality (p for trend<0.05). However, only two subgroups, patients with ASA grades 1+2 (p=0.427) and patients with fracture type 31A2 (p=0.155), were exceptions at the total follow-up. At the 1-year follow-up, only one subgroup, patients with ASA grades 1+2 (p=0.427), was the exception (Figs 3 and 4). Table 2 Patient characteristics according to CRQC grade Page 7/20 Variable Total (n=389) CRQC grade p value Poor (n=26) Acceptable (n=141) Excellent (n=222) Age (years) 84.64 (77.50- 89.74) 85 (71.83- 89.19) 84 (77.75-89.74) 84.64 (77.88- 89.74) 0.745a Female, n(%) 259 (66.58) 18 (69.23) 90 (63.83) 151 (68.02) 0.681b 31A2, n (%) 310 (79.69) 24 (92.31) 116 (82.27) 170 (76.58) 0.107b Right-side fracture, n (%) 246 (63.24) 16 (61.54) 79 (56.03) 151 (68.02) 0.068b Comorbidities, n (%)         <0.001b  None 85 (21.85) 2 (7.69) 22 (15.60) 61 (27.48)   1 139 (35.73) 12 (46.15) 40 (28.37) 87 (39.19)   2 or more 165 (42.42) 12 (46.15) 79 (56.03) 74 (33.33)   ASA grade, n (%)         0.127b   1+2 43 (11.05) 6 (23.08) 13 (9.22) 24 (10.81)     3+4 346 (88.95) 20 (76.92) 128 (90.78) 198 (89.19)   Type of anesthesia, n (%)         0.017b General 145 (37.28) 10 (38.46) 60 (42.55) 75 (33.78)   Combined spinal and epidural+spinal 232 (59.64) 14 (53.85) 81 (57.45) 137 (61.71)   Nerve block 12 (3.08) 2 (7.69) 0 (0.00) 10 (4.50)   Preoperative waiting time (days) 3 (2-5) 4 (2-6.25) 3 (2-6) 3 (2-4) 0.097a HB (g/l) 107 (93- 119) 92.5 (77- 112.75) 104 (93.5-116.5) 108.5 (94.75- 120) 0.017a 1-year death, n (%) 60 (15.42) 14 (53.85) 32 (22.70) 14 (6.31) <0.001b Total death, n (%) 96 (24.68) 14 (53.85) 45 (31.91) 37 (16.67) <0.001b Discussion The key to a stable fracture fixation is reduction quality. Many studies have included restoration quality, but only as a confounding variable, rather than as the main object of research [18–22]. This study focuses on the CRQC, which are a relatively new set of criteria for assessing the quality of reduction following fracture fixation. We verified that compared with patients with excellent CRQC, those with acceptable CRQC had a 0.6- and 1.1-times increase in mortality at the total postoperative and 1-year follow-up, respectively, while those with poor CRQC showed a 5.67- and 13.80-times increase in mortality, respectively. In other words, fracture reduction quality appears to be an important predictor of postoperative mortality in elderly intertrochanteric fracture patients. Currently, however, when the patient's risk of death is high, the surgeon accepts a poor reduction, considering continuing the fixation and shortening the operation time to be more important than attempting to further improve the reduction. Similarly, the increased operative time, soft tissue dissection, and blood loss associated with open reduction relative to closed reduction may not be in the patient's best interest, or their functional needs may be lower, meaning they can better tolerate a poor reduction. The findings of this study urge us to better understand and focus more on the quality of the reduction. At present, there are two main standards for evaluating the postoperative reduction quality of intertrochanteric fractures: the CRQC and BRQC [16]. The greatest innovation of the CRQC lies in the introduction of the concepts of PMCS and NMCS [15, 23]. The CRQC require good reduction on anteroposterior (AP) views, meeting two conditions: 1. a displacement less than the bone cortex thickness; and 2. neutral or positive medial cortical support. The definition of good reduction thus excludes two possibilities: NMCS with displacement less than the cortical thickness or PMCS with displacement greater than the cortical thickness of the fracture. The CRQC require good reduction on lateral views and a smooth anterior cortex, meaning that the displacement must be less than half of the bone cortex thickness, emphasizing the strong support of the anterior cortex [24, 25]. Currently, most internal fixation materials do not immobilize small trochanter fragments, so CRQC does not explicitly require posterior cortical alignment [21]. The CRQC are also more reliable than the BRQC for three main reasons. First, the use of the BRQC may result in the loss of some details. ASA, American society of anesthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria, HR, Hazard ratio, CI, Confidence interval ASA, American society of anesthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria, HR, Hazard ratio, CI, Confidence interval ASA, American society of anesthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria, HR, Hazard ratio, CI, Confidence interval aKruskal‒Wallis H test aKruskal‒Wallis H test bχ2 test ASA, American society of anesthesiologists, CRQC, Chang reduction quality criteria, HB, Hemoglobin Table 3 Univariate and multivariate Cox regression analyses of factors associated with total follow-up all- cause mortality. Page 9/20 Variable Univariate Multivariate HR (95% CI) p value HR (95% CI) p value Age (per 1 year increase) 1.05 (1.02-1.08) <0.001 1.04 (1.01- 1.08) 0.006 Sex (Female vs. Male) 1.25 (0.83-1.88) 0.285     Fracture type (31A1 vs. 31A2) 1.86 (1.05-3.09) 0.033 1.63 (0.91- 2.92) 0.102 Fracture side (left vs. right) 0.82 (0.55-1.23) 0.342     Comorbidities         None 1.0 (Reference)   1.0 (Reference)   1 8.11 (1.93- 34.04) 0.004 6.63 (1.56- 28.23) 0.010 2 or more 16.86 (4.13- 68.91) <0.001 8.65 (2.06- 36.41) 0.003 ASA grade (1+2 vs. 3+4) 6.77 (1.67- 27.50) 0.007 5.09 (1.14- 22.68) 0.033 Type of anesthesia         General 1.0 (Reference)       Combine spinal and epidural+spinal 0.76 (0.51-1.15) 0.192     Nerve block 0.74 (0.18-3.08) 0.681     Preoperative waiting time (per 1 day increase) 1.12 (1.06-1.19) <0.001 1.10 (1.03- 1.18) 0.005 HB (per 1 g/l increase) 0.99 (0.98-1.00) 0.010 1.00 (0.99- 1.01) 0.907 Blood transfusion (no vs. yes) 2.18 (1.40-3.38) 0.001 1.69 (1.00- 2.87) 0.052 CRQC grade         Excellent 1.0 (Reference)   1.0 (Reference)   Acceptable 2.15 (1.39-3.32) 0.01 1.60 (1.02- 2.53) 0.043 Poor 5.86 (3.16- 10.88) <0.001 6.67 (3.48- 12.77) <0.001 ASA, American society of anesthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria, ASA, American society of anesthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria, Page 10/20 ASA, American society of anesthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria, HR, Hazard ratio, CI, Confidence interval esthesiologists, HB, Hemoglobin, CRQC, Chang reduction quality criteria, Discussion For example, in the BRQC, nonalignment includes three possible conditions: poor alignment only on the AP surface; poor alignment only on the side; and poor AP and lateral alignment; the BRQC cannot distinguish between these Page 11/20 Page 11/20 Variable Univariate Multivariate HR (95% CI) p value HR (95% CI) p value Age (per 1 year increase) 1.05 (1.01-1.08) 0.009 1.04 (1.00- 1.08) 0.066 Sex (Female vs. Male) 1.07 (0.63-1.82) 0.799     Fracture type (31A1 vs. 31A2) 2.46 (1.06-5.73) 0.036 1.94 (0.82- 4.56) 0.132 Fracture side (left vs. right) 0.75 (0.45-1.25) 0.275     Comorbidities         None 1.0 (Reference)       1 21624.41 (0- 2.59E+43 0.828     2 or more 55076.52 (0- 6.59E+43) 0.812     ASA grade (1+2 vs. 3+4) 3.87 (0.95-15.84) 0.060 5.07 (1.08- 23.84) 0.040 Type of anesthesia         General 1.0 (Reference)       Combine spinal and epidural+spinal 0.69 (0.41-1.16) 0.165     Nerve block 0.84 (0.20-3.54) 0.815     Preoperative waiting time (per 1 day increase) 1.13 (1.05-1.22) 0.001 1.12 (1.03- 1.21) 0.007 HB (per 1 g/l increase) 0.98 (0.97-0.99) 0.001 0.99 (0.98- 1.01) 0.229 Blood transfusion (no vs. yes) 3.04 (1.65-5.62) <0.001 1.63 (0.83- 3.19) 0.153 CRQC grade         Excellent 1.0 (Reference)   1.0 (Reference)   Acceptable 3.92 (2.09-3.32) <0.001 3.11 (1.64- 5.91) 0.001 Poor 13.39 (6.37-7.35) <0.001 14.80 (6.83- 32.09) <0.001 Page 12/20 conditions. In contrast, the CRQC use a more ideal, 4-point scoring system and retains more details [16]. Second, the CRQC reasonably adopt the concept of PMCS, which provides cortical support between the two main fragments and prevents further lateral sliding of the femoral head and neck fragments [16]. Third, using one or half cortical thickness to describe the displacement is better than using the actual distance of 4 mm because it can be measured directly with the naked eye through intraoperative C-arm fluoroscopy without the use of special tools. two main fragments and prevents further lateral sliding of the femoral head and neck fragments [16]. Third, using one or half cortical thickness to describe the displacement is better than using the actual distance of 4 mm because it can be measured directly with the naked eye through intraoperative C-arm fluoroscopy without the use of special tools. Our study found that mortality increased with age and the number of comorbidities during the total follow-up time. This conclusion has been confirmed in previous studies [26–29]. However, no corresponding results were observed at the one-year follow-up, which may have been caused by statistical error due to the small sample size. Discussion Some studies have reported that mortality is associated with higher ASA grades [30, 31]. Similarly, our study further demonstrated that patients with ASA grades 3 + 4 had a higher risk of death at the total - and 1-year follow-up than patients with ASA grades 1 + 2. However, this study had some limitations. This was a retrospective single-center study; large-sample, multicenter, randomized controlled studies are needed to confirm the results. Second, we are only evaluating medium-term outcomes because the number of deaths was relatively small, and it is impossible to assess short-term outcomes. Conclusion In conclusion, we demonstrate that postoperative mortality in elderly intertrochanteric fracture patients is associated with reduced reduction quality according to the CRQC. Therefore, we strongly recommend that orthopedic surgeons consider reduction quality when treating elderly intertrochanteric fracture patients to improve their outcomes. Availability of data and materials The datasets generated and/or analysed during the current study are not publicly available as they contain information that could compromise the privacy of research participants but are available from the corresponding author on reasonable request. Acknowledgements Page 13/20 Page 13/20 Not Applicable. Not Applicable. Funding Funding information is not available. Author details Department of Orthopaedic Surgery, Chongqing Emergency Medical Center (Chongqing University Central Hospital), Chongqing 400010, China Ethics approval and consent to participate This retrospective study involving human participants was conducted in accordance with the ethical standards of the institutional and national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. The study was approved by the Ethics Committee of the Central Hospital affiliated with Chongqing University. Informed consent was obtained from all participants. Author contributions All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by HM and LJ. The first draft of the manuscript was written by HM, DX made meaningful corrections to the structure of the article and guided the statistical methods and data processing, and all authors commented on previous versions of the manuscript. ZXX participated in the design of the study and proofread the manuscript as the corresponding author. All authors have read and approved the manuscript. Consent for publication Not Applicable. Competing interests The authors declare that they have no competing interests. References Page 14/20 Page 14/20 Page 14/20 1. Yang X, Wu Q, Wang X. Investigation of perioperative hidden blood loss of unstable intertrochanteric fracture in the elderly treated with different intramedullary fixations. Injury. 2017, 48(8): 1848-1852. 2. Angulo Tabernero M, Aguilar Ezquerra A, Ungria Murillo J, et al. Epidemiology of fractures of the proximal third of the femur: 20 years follow-up]. Rev Fac Cien Med Univ Nac Cordoba. 2015, 72(3): 145-151. 3. Wang J, Wei J, Wang M. 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National Institute for Health and Care Excellence Hip fracture–Management. London: Clinical guideline CG124, 2017. 8. Macdonald H, Brown R, Gronager M, Close J, Fleming T, Whitehouse M. Quality of fracture reduction is associated with patient survival at one year, but not 30 days, following trochanteric hip fracture fixation. A retrospective cohort study. Injury. 2022, 53(3): 1160-1163. 8. Macdonald H, Brown R, Gronager M, Close J, Fleming T, Whitehouse M. Quality of fracture reduction is associated with patient survival at one year, but not 30 days, following trochanteric hip fracture fixation. A retrospective cohort study. Injury. 2022, 53(3): 1160-1163. 9. Zlowodzki M, Brink O, Switzer J, et al. The effect of shortening and varus collapse of the femoral neck on function after fixation of intracapsular fracture of the hip: a multi-centre cohort study. J Bone Joint Surg [Br] 2008, 90-B:1487-1494. 9. Zlowodzki M, Brink O, Switzer J, et al. The effect of shortening and varus collapse of the femoral neck on function after fixation of intracapsular fracture of the hip: a multi-centre cohort study. J Bone Joint Surg [Br] 2008, 90-B:1487-1494. 10. Gordon M, Berntsson PO, Sjölund E, et al. Surg 2015, 135: 811-818. Surg 2015, 135: 811-818. 16. Mao W, Ni H, Li L, et al. Comparison of Baumgaertner and Chang reduction quality criteria for the assessment of trochanteric fractures. Bone Joint Res. 2019, 8(10): 502-508. 17. Marsh JL, Slongo TF, Agel J, et al. Fracture and Dislocation Classififi- cation Compendium—2007: orthopaedic trauma association classifification, database and outcomes committee. J Orthop Trauma. 2007, 21(suppl 10): S1–S163. 18. Jiamton C, Boernert K, Babst R, Beeres F, Link B. The nail-shaft-axis of the of proximal femoral nail antirotation (PFNA) is an important prognostic factor in the operative treatment of intertrochanteric fractures. Arch Orthop Trauma Surg 2018, 138: 339-349. 19. De Bruijn K, den Hartog D, Tuinebreijer W, Roukema G. Reliability of predictors for screw cutout in intertrochanteric hip fractures. J Bone Joint Surg [Am] 2012,94- A: 1266-1272. 20. Abram SG, Pollard TC, Andrade AJ. Inadequate 'three-point' proximal fixation predicts failure of the Gamma nail. Bone Joint J 2013, 95-B: 825-830. 21. Buyukdogan K, Caglar O, Isik S, Tokgozoglu M, Atilla B. Risk factors for cut-out of double lag screw fixation in proximal femoral fractures. Injury 2017, 48: 414-418. 22. Kashigar A, Vincent A, Gunton M, et al. Predictors of failure for cephalomedullary nailing of proximal femoral fractures. Bone Joint J 2014, 96-B: 1029-1034. 23. Cho MR, Lee JH, Kwon JB, et al. The effect of positive medial cortical support in reduction of pertrochanteric fractures with posteromedial wall defect using a dynamic hip screw. Clin Orthop Surg 2018, 10: 292-298. 24. Tsukada S, Okumura G, Matsueda M. 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The value of the tip-apex distance in predicting failure of fixation of peritrochanteric fractures of the hip. J Bone Joint Surg [Am] 1995, 77-A: 1058- 1064. 14. Baumgaertner MR, Curtin SL, Lindskog DM. Intramedullary versus extramedullary fixation for the treatment of intertrochanteric hip fractures. Clin Orthop Relat Res 1998, 348: 87-94. 14. Baumgaertner MR, Curtin SL, Lindskog DM. Intramedullary versus extramedullary fixation for the treatment of intertrochanteric hip fractures. Clin Orthop Relat Res 1998, 348: 87-94. Page 15/20 15. Chang SM, Zhang YQ, Ma Z, et al. Fracture reduction with positive medial cortical support: a key element in stability reconstruction for the unstable pertrochanteric hip fractures. Arch Orthop Trauma Page 15/20 15. Chang SM, Zhang YQ, Ma Z, et al. Fracture reduction with positive medial cortical support: a key element in stability reconstruction for the unstable pertrochanteric hip fractures. Arch Orthop Trauma Surg 2015, 135: 811-818. Kumar P, Law S, Sriram KB (2017) Evaluation of platelet lymphocyte ratio and 90-day mortality in patients with acute exacerbation of chronic obstructive pulmonary disease. J Thorac Dis 9(6): 1509– 1516. 27. Liu Y, Wang Z, Xiao W (2018) Risk factors for mortality in elderly patients with hip fractures: a meta- analysis of 18 studies. Aging Clin Exp Res 30(4): 323–330. 27. Liu Y, Wang Z, Xiao W (2018) Risk factors for mortality in elderly patients with hip fractures: a meta- analysis of 18 studies. Aging Clin Exp Res 30(4): 323–330. 28. Ercin E, Bilgili MG, Sarı C, et al. Risk factors for mortality in geriatric hip fractures: a compressional study of different surgical procedures in 785 consecutive patients. Eur J Orthop Surg Traumatol 2017, 27: 101-6. 28. Ercin E, Bilgili MG, Sarı C, et al. Risk factors for mortality in geriatric hip fractures: a compressional study of different surgical procedures in 785 consecutive patients. Eur J Orthop Surg Traumatol 2017, 27: 101-6. 29. Khan MA, Hossain FS, Ahmed I, Muthukumar N, Mohsen A. Predictors of early mortality after hip fracture surgery. Int Orthop 2013, 37: 2119-24. 30. Gurger M. Factors impacting 1-year mortality after hip fractures in elderly patients: A retrospective clinical study. Niger J Clin Pract 2019, 22: 648-51. Page 16/20 Page 16/20 31. Gremillet C, Jakobsson JG. Acute hip fracture surgery anaesthetic technique and 30-day mortality in Sweden 2016 and 2017: A retrospective register study. F1000Res 2018, 7: 1009. 31. Gremillet C, Jakobsson JG. Acute hip fracture surgery anaesthetic technique and 30-day mortality in Sweden 2016 and 2017: A retrospective register study. F1000Res 2018, 7: 1009. Figures Figure 1 Postoperative X-ray of intertrochanteric fracture. (A) X-ray showed positive medial cortical support, meaning that the inferior edge of the medial cortex of the femoral head-neck fragment was medial to the superior edge of the medial cortex of the femoral shaft with a displacement of less than one cortical thickness. (B) X-ray showed negative medial cortical support, meaning that the inferior edge of the medial cortex of the femoral head-neck fragment was lateral to the superior edge of the medial cortex of the femoral shaft, regardless of displacement distance. (C) X-ray showed neutral medial cortical support, meaning that the medial cortex of head–neck fragment and the femoral shaft were smoothly contacted. Postoperative X-ray of intertrochanteric fracture. (A) X-ray showed positive medial cortical support, meaning that the inferior edge of the medial cortex of the femoral head-neck fragment was medial to the superior edge of the medial cortex of the femoral shaft with a displacement of less than one cortical thickness. (B) X-ray showed negative medial cortical support, meaning that the inferior edge of the medial cortex of the femoral head-neck fragment was lateral to the superior edge of the medial cortex of the femoral shaft, regardless of displacement distance. (C) X-ray showed neutral medial cortical support, meaning that the medial cortex of head–neck fragment and the femoral shaft were smoothly contacted. Page 17/20 Figure 2 Column diagram comparing mortality in elderly intertrochanteric fracture patients at the 1 year and total follow-up for different Chang reduction quality criteria (CRQC) grades were analyzed using the chi-square test. Figure 2 Column diagram comparing mortality in elderly intertrochanteric fracture patients at the 1 year and total follow-up for different Chang reduction quality criteria (CRQC) grades were analyzed using the chi-square test. Page 18/20 Page 18/20 igure 3 orest plot of the subgroup analysis estimating the association between the C riteria (CRQC) grade and total follow-up mortality based on different characte etween subgroups were analyzed by Cox regression analysis. The black rhom azard ratio (HR), and the black horizontal lines represent the 95% confidence Figure 3 Forest plot of the subgroup analysis estimating the association between the Chang reduction quality criteria (CRQC) grade and total follow-up mortality based on different characteristics. Differences between subgroups were analyzed by Cox regression analysis. The black rhombuses represent the hazard ratio (HR), and the black horizontal lines represent the 95% confidence interval (CI). Figure 3 Figure 3 Forest plot of the subgroup analysis estimating the association between the Chang reduction quality criteria (CRQC) grade and total follow-up mortality based on different characteristics. Differences between subgroups were analyzed by Cox regression analysis. The black rhombuses represent the hazard ratio (HR), and the black horizontal lines represent the 95% confidence interval (CI). Page 19/20 Figure 4 Forest plot of the subgroup analysis estimating the association between the Chang reduction quality criteria (CRQC) grade and 1-year follow-up mortality based on different characteristics. Differences between subgroups were analyzed by Cox regression analysis. The black rhombuses represent the hazard ratio (HR), and the black horizontal lines represent the 95% confidence interval (CI). Forest plot of the subgroup analysis estimating the association between the Chang reduction quality criteria (CRQC) grade and 1-year follow-up mortality based on different characteristics. Differences between subgroups were analyzed by Cox regression analysis. The black rhombuses represent the hazard ratio (HR), and the black horizontal lines represent the 95% confidence interval (CI). 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Ein repräsentativer Bau des 19. Jahrhunderts auf dem Land: der wiederbelebte Bahnhof Eckartshausen-Ilshofen Besonders vorbildliche Sanierungen Die fünf Preisträger des Denkmalschutzpreises Baden-Württemberg 2022 Gerhard Kabierske Denkmalschutz und Denkmalpflege im Baden-Württemberg sind in den letzten Jahren nicht einfacher geworden. Die unbefriedigende Stellensituation beim Landesamt für Denkmalpflege macht eine ausreichende Beratungstätigkeit für Denkmaleigentümer schon geraume Zeit kaum mehr möglich. Vorstöße, daran etwas zu ändern, haben mit Verweis auf die Haushaltslage keine Chance umgesetzt zu werden. Die Covid-19-Pandemie hat die Situation noch zugespitzt, denn wie sollte eine qualitative Denkmalpflege vom Homeoffice aus, ohne persönliche Inaugenscheinnahme der Kulturdenkmale und ohne den persönlichen Kontakt zur Bauherrschaft betrieben werden? Und von Seiten der Politik und der Ministerialverwaltung weht der Wind auch rau, wird doch neuerdings immer 18 stärker ein völlig ungerechtfertigter Widerspruch zwischen Umweltschutzbelangen und Denkmalpflege gesehen. Die geplante Änderung des Denkmalschutzgesetzes wird mit ihrem undifferenzierten grünen Licht für Sonnenkollektoren, Windräder und Dämmmaßnahmen an Kulturdenkmalen oder in deren Umgebung zwar wegen ihres geringen Anteils von Denkmalen und Anlagen bei den gesamten Baulichkeiten im Land an der Klimasituation nichts ändern, aber unsere historischen Stadtbilder ganz wesentlich negativ beeinflussen. In einer gemeinsamen Stellungnahme haben der Schwäbische Heimatbund und der Landesverein Badische Heimat gegen die Änderungen Stellung genommen – offensichtlich ohne Gehör zu finden. Schwäbische Heimat 2023|1 Umso wichtiger ist es für die beiden Vereine, den Denkmalschutz in Baden-Württemberg zu unterstützen und ihre Anerkennung jenen privaten Eigentümern und Eigentümerinnen auszusprechen, die besonders vorbildlich bei einer Gesamtsanierung oder Umnutzung ihres historisch bedeutsamen Kulturdenkmals vorgegangen sind und damit einen wichtigen Beitrag zur Tradierung der vielfältigen Baukultur im Land geleistet haben. Der bereits seit 1978 vergebene Denkmalschutzpreis soll dafür ein deutliches Zeichen setzen. Als Anerkennung erhalten die ausgezeichneten Eigentümer einen Geldpreis in Höhe von 5.000 Euro sowie eine Bronzeplakette zur Anbringung an ihrem Gebäude. Zudem ist die Auszeichnung mit Urkunden für sie sowie für beteiligte Architekten, Restauratoren und Handwerker verbunden. Wie bereits seit 2006 ist die Finanzierung des Preises, für den die Ministerin für Landesentwicklung und Wohnen Nicole Razavi die Schirmherrschaft übernommen hat, der großzügigen Unterstützung durch die Wüstenrot Stiftung zu verdanken. Das Juryverfahren konnte 2022 glücklicherweise ohne Corona-Einschränkungen stattfinden. Auf die Ausschreibung im Frühjahr gingen 65 Einsendungen ein. Die Jury, die sich aus Dr. Anette Busse für die Wüstenrot Stiftung, Prof. Dr. Ulrike Plate für das Landesamt für Denkmalpflege, Dr. Diana Wiedemann für die Architektenkammer Baden-Württemberg, Ulrich Gräf, Dr. Bernd Langner und Dr. Karsten Preßler für den Schwäbischen Heimatbund, Dr. Gerhard Kabierske für den Landesverein Badische Heimat sowie Frank Mienhardt für den Städtetag BadenWürttemberg zusammensetzte, traf nach Vorprüfung und Arbeitssitzung eine engere Wahl von elf Objekten. Diese wurden bei einer dreitägigen Juryrundfahrt von über tausend Kilometern vom Main bis zum Bodensee besichtigt und schließlich die fünf Preisträger bestimmt: das ehemalige Jägerhaus des Klosters Salem in Bermatingen, der Wildenhof in Lenzkirch-Raitenbuch, ein Fachwerkhaus in Maulbronn-Zaisersweiher, das frühere Pfarrhaus in Wangen-Oberwälden sowie der ehemalige Bahnhof Eckartshausen-Ilshofen. Die Preise werden im Rahmen einer Festveranstaltung am 24. April 2023 in der Klosterkirche Salem überreicht, zu der der Schwäbische Heimatbund und der Landesverein Badische Heimat alle Interessierten herzlich einladen. Die Bauten und Sanierungen werden hier im Folgenden vorgestellt. Zeugnis klösterlichen Bauens des 18. Jahrhunderts – das sanierte Jägerhaus des Klosters Salem in Bermatingen (Bodenseekreis) »Wenn das einmal zum Verkauf steht, machen wir das«, sagten sich Yvonne Eisele und Sven Nolle, die seit Jahren in einem benachbarten Haus wohnten, in dem Yvonne Eisele auch aufgewachsen war. Beim Traumobjekt des Ehepaars handelte es sich nicht um irgendein Gebäude des im nördlichen Hinterland des Bodensees gelegenen Ortes Bermatingen, sondern um das sogenannte »Jägerhaus«, das zusammen mit dem auf dem Grundstück liegenden Backhaus und einer Torkelscheuer den lokalen Klosterhof der nur wenige Kilometer entfernten Zisterzienserabtei Salem bildete. Deren Wohlstand noch im 18. Jahrhundert dokumentieren nicht nur die monumentalen Klosterbaulichkeiten in Salem, sondern ebenso die vielen stattlichen Funktionsgebäude, die das Kloster auf seinem Territorium errichten ließ. Beispiele für die besondere Baukultur, die die Abtei entfaltete, sind auch das Rebleutehaus in Sipplingen und das Torkelgebäude in Mittelstenweiler, deren Sanierungen in den letzten Jahren bereits mit dem Denkmalschutzpreis ausgezeichnet worden sind. Vorbildlich restauriert und als Wohnhaus weitergenutzt: das ehemalige Jägerhaus des Klosters Salem in Bermatingen. Vorne der Zugang zum riesigen Weinkeller unter dem Gebäude Kulturerbe und Denkmalschutz 19 sich rechts und links die Räume reihen wie in der Klausur eines barocken Klostergebäudes. Die Ausstattung überrascht in ihrer handwerklichen Solidität und der künstlerischen Ausstattung. Der Mittelflur zeigt kräftiges Sichtfachwerk und überaus üppig gestaltete Türen mit barocken Ohrgewänden und Verdachungen. Ein in den Flur vorspringender ehemaliger Kamin trägt auf dem Sturz der Ofenbedienungstür die Jahreszahl der Erbauung des Hauses. Die seitlichen steinernen Wangen mit eingemeißeltem Beschlagwerk des 16. Jahrhunderts stammen Überrascht durch seine Größe und Klarheit: der Gewölbehalle des Weinkellers Das 1721 errichtete Bermatinger Jägerhaus diente nicht nur als Wohnung für den in Klosterdiensten stehenden Jäger, sondern auch zur Verwaltung der unmittelbar gegenüber ansteigenden weitläufigen Rebflächen am Leopoldberg und zur Unterbringung der Rebleute, die dort den Weinbau betrieben. Von der Bedeutung des Weinbaus zeugt vor allem der mächtige Weinkeller, der eindrucksvoll korbbogenförmig überwölbt ist und Licht über hochgelegene Fenster in Stichkappen erhält. Hier hatten riesige Holzfässer Platz. Von einem kleinen separaten Schutzhaus mit Satteldach und einem reich gestalteten Holztor direkt vor dem Jägerhaus führt eine breite einläufige Treppe steil hinunter ins tiefe Gewölbe. Der Keller bildet den langrechteckigen, podiumsartigen Sockel für das geräumige eingeschossige Fachwerkgebäude mit hohem Walmdach, welches, nur von kleinen Schleppgaupen belichtet, unausgebaut ist. Das rot gestrichene Fachwerk macht einen überaus schmucken Eindruck. Eselsrücken zieren den Schwellbalken, und an den Hausecken in die Eckpfosten geschnitzte Abtsstäbe belegen sinnfällig, wer einst hier der Bauherr und Eigentümer war. Das Innere ist, typisch für die Nutzbauten des Klosters, über einen durchgehenden Mittelflur erschlossen, an dem Funktion und Repräsentation: der Mittelflur, der die Räume erschließt, mit Sichtfachwerkwänden und Stuckdecke Am Riedweg 1/1 Salem-Neufrach Tel. 0 75 53-9 24 00 WWW.WIRTH-ET.DE 20 Schwäbische Heimat 2023|1 Der Dachstuhl als Fitnessraum: offengelassen und nur der Boden gedämmt. In der Mitte zwischen den verzogenen Kaminen eine alte Räucherkammer ganz offensichtlich von einem älteren Klostergebäude und sind hier wiederverwendet worden. Die Decken werden im Flur wie in den meisten Räumen von Hohlkehlen eingefasst und von einfachen stuckgerahmten Rund- und Vierpassformen akzentuiert. Ohne Ausbau dient der Dachstuhl als Fitnessraum 2019 sollten sich die lang gehegten Hoffnungen von Yvonne Eisele und Sven Nolle erfüllen. Im Zuge wirtschaftlicher Umstrukturierungen der Verwaltung des markgräflich-badischen Hauses, das seit 1803 das Erbe des aufgelösten Klosters Salem angetreten hatte, wurde das Kulturdenkmal zum Kauf angeboten. Zuletzt war das Gebäude zu Wohnzwecken sowie als Weinverkaufsstelle genutzt worden; der Gewölbekeller ist jährlich Schauplatz des großen Bermatinger Weinfests. Die Familie erwarb das Anwesen und erwies sich, so die einhellige Meinung der Jury, in ihrer denkmalbezogenen Einstellung als würdige Wahrerin der Haustradition. Die Bereitschaft, das Haus nicht in mehrere Wohnungen aufzuteilen, sondern es trotz des nicht alltäglichen Grundrisses ohne größere Eingriffe selbst zu bewohnen, ermöglichte es, die alte Struktur zu bewahren. Diese konnte durch Entfernung einer später eingezogenen trennenden Wand im Flur sogar wieder deutlicher herausgeschält werden. Ebenso wurden im Bereich von Bad und Toilette sowie im großen rückwärtigen Raum, der über die gesamte Hausbreite reicht, spätere Veränderungen rückgebaut. Beispielhaft ist vor allem auch der Verzicht auf einen Ausbau des weiträumigen Dachstuhls mit seiner eindrucksvollen Holzkonstruktion. Er erhielt nur einen kleinen containerartigen Einbau für eine Sauna und die dafür notwendigen sanitären Einrichtungen. Passend dazu wird er unbeheizt als Fitnessraum genutzt. Mit Hilfe des in Denkmalpflegefragen erfahrenen Teams aus der Architektin Corinna Wagner, dem Zimmereibetrieb Holzbau Schmäh und dem Restaurator Jürgen Schulz-Lorch sowie unter Beteiligung des Natursteinres- Wir gratulieren zum Denkmalschutzpreis SWen Markdorfer Straße 26 Kulturerbe und Denkmalschutz | 88682 Salem-Neufrach 21 | 07553 / 7565 DAS FENSTER Mehr als ein Loch in der Wand. Eine Öffnung zur Erde, zum Wasser, zum Himmel. Eine Öffnung zum Licht, zur Zuversicht, zur Hoffnung. Eine Öffnung zu den Menschen, zum Leben, zur Liebe. Eine Öffnung zu kostbaren Erinnerungen – wir helfen Ihnen, diese Fenster für die Zukunft zu bewahren. homa-rw.de 22 Schwäbische Heimat 2023|1 taurators Peter Wiest, des Malers Jürgen Dilpert und des Stuckateurbetriebs Ziegler wurde das Haus 2020/21 nach einer genauen Bauanalyse und Schadenskartierung vorbildlich saniert. Auch wenn der Bau in keinem besorgniserregenden Zustand war, zeigten sich doch beim Holzwerk und bei den Stufen der Eingangstreppe viele Schadstellen, die handwerklich vorbildlich repariert wurden. Bei der Dämmung wurde auf natürliche Materialien Wert gelegt. Die neuen Fenster wurden nach dem Vorbild eines einzeln erhalten gebliebenen Beispiels wahrscheinlich aus dem 19. Jahrhundert nachgebaut. Ausbauteile für einen Windfang an der Haustür, die Küche und den Sanitärbereich wurden bewusst zeitgemäß gestaltet, ohne die historische Substanz zu beeinträchtigen. Langer Atem und engagierte Eigentümer – die Sanierung des Wildenhofs in Lenzkirch-Raitenbuch (Landkreis Breisgau-Hochschwarzwald) Der Wildenhof in Raitenbuch zählt zu den eindrucksvollsten Höfen des Hochschwarzwalds: Er imponiert bereits durch seine schiere Größe. Das gewaltige Dach, unter dem er sich in einen Taleinschnitt schmiegt, misst nicht weniger als 1.100 Quadratmeter Fläche. Aber auch die geradezu archaisch-rustikale Anmutung der massiven StänderBohlenkonstruktion ist außergewöhnlich. Wie auch die Inschrift über dem Eingang zum Wohnteil überliefert, wurde der Hof im Jahr 1728 errichtet. Ursprünglich war er Mittelpunkt eines großen Gutes mit Ackerbau und Viehzucht. Der weitläufige hangseitige Bereich, der ursprünglich für Ställe genutzt wurde, zeugt noch heute davon, ebenso der riesige Raum der Tenne unter dem Dach, in die Heuwagen von der Bergseite her einfahren konnten. Die herausragende Stellung des Wildenhofs innerhalb der Tradition der Schwarzwaldhöfe wurde früh erkannt. Bald Ein mächtiges Zeugnis bäuerlicher Baukultur im Schwarzwald: der Wildenhof in Lenzkirch-Raitenbuch nach der Sanierung nach dem Zweiten Weltkrieg wurde er als Kulturdenkmal von besonderer Bedeutung eingetragen, war aber damals schon ein Sorgenkind. Bereits für die 1860er-Jahre lässt sich nachweisen, dass der zugehörige Landbesitz durch Verkauf stark zusammengeschmolzen war. Die wechselnden Eigentümer konnten daher eine adäquate Bauunterhaltung nicht mehr gewährleisten. Zudem führten unzureichende Gründung sowie Hang- und Winddruck dazu, dass sich die Holzkonstruktion dramatisch in Richtung Tal verschob. Um 1,30 Meter hängt die talseitige Fassade mit dem Krüppelwalm gegenüber der Vertikalen über, mit vielen konstruktiven Folgen für das Baugefüge. So konnten die Ställe schon lange kaum mehr genutzt werden, Das Herz des Wohnteils: die große, in ihrer Dimension wiederhergestellte Rauchküche Kulturerbe und Denkmalschutz 23 Im quer durch das Haus führenden Gang am besten zu erkennen: die starke Verformung des Hofes durch Berg- und Winddruck, vor der statischen Sicherung ein großes Problem und ein Teil der Bohlenbalkenwände sowie vor allem die Stubenausstattung des Wohnteils, der für zwei Familien aufgeteilt worden war, gingen früh verloren. Mit Unterstützung der Denkmalpflege wurde 1956 die undichte Schindeldachfläche mit Faserzementplatten überdeckt, um wenigstens das Regenwasser abzuhalten. Immer noch in bescheidenem Umfang landwirtschaftlich genutzt, befand sich der Hof in den späten 1980er-Jahren in einem denkbar schlechten Zustand. Martin Wider, Schreiner- und Zimmermeister sowie Restaurator im Handwerk, dem das Schicksal des Hofes am Herzen lag, erwarb ihn 1990 und wagte eine ambitionierte Rettungsaktion. Auf Grundlage einer genauen Be- Dem Bauherrn die Sicherheit zu geben, das Richtige zu tun Seit über 30 Jahren steht der Name, Martin Wider, für Denkmalpflege und Bauen im Bestand im südwestdeutschen Raum. Mit viel Leidenschaft und innovativem handwerklichem Knowhow war sein Restauratorenbetrieb im Hochschwarzwald federführend daran beteiligt, wertvolle Bausubstanz zu restaurieren und zu modernisieren. Nach der Übergabe der Zimmerei an seinen Sohn gründete Martin Wider 2020 die Martin Wider BiB GmbH, in der er sein geballtes Wissen und seine langjährige Erfahrung künftigen Bauherren zu Verfügung stellt. Für öffentliche und private Bauherren übernimmt er die Aufgaben von der Bauherrenvertretung bis zur Bauprojektierung und Bauleitung. Dazu gehören ebenso die professionelle Beratung in schwierigen Fragestellungen der Denkmalpflege, das Aufstellen und die Verfolgung eines tragfähigen Kostenrahmens sowie die Begleitung in der termingerechten und qualitätsbewussten Umsetzung der Bauprojekte. 24 standsaufnahme und eines Sanierungskonzepts, das Ulrich Schnitzer, Spezialist für Schwarzwaldhöfe an der Universität Karlsruhe, mit Beteiligung des Landesdenkmalamts entwickelt hatte, sollte der Wildenhof statisch gesichert, dabei seine überlieferte Struktur bewahrt und ihm das historische Gesamtbild zurückgegeben werden. Um dem Hof eine tragfähige wirtschaftliche Grundlage zu ermöglichen, wurde in den innen neu gegliederten bergseitigen Stallteil und in die ehemaligen Knechtkammern Widers Schreinerwerkstatt eingebaut und die riesige Tenne zu Lagerzwecken hergerichtet. In mehreren Etappen, vor allem in den 1990er-Jahren und dann noch einmal um 2006 und 2016, trieb Wider mit Engagement die um- Martin Wider BiB GmbH ERHALTEN BEWAHREN NUTZEN – Beratung, Gutachten und Schadensanalysen – Bauprojektierungen und Planung – Definition von Nutzungsanforderungen – Erarbeiten von Nutzungs- und Restaurierungskonzepten – Bauleitung – Vertretungs- und Unterstützungsmandate öffentlicher und privater Bauherren – Antragswesen (Denkmalförderungen und KfW – Anträge) – Kostenschätzung und Kostenkontolle Im Kaisergrund 8, 79859 Schluchsee, Tel: +49 176 1011 9811, m.wider@wider-bib.de, www.wider-bib.de Schwäbische Heimat 2023|1 fangreichen Arbeiten voran. Dabei wurden nachträgliche An- und Einbauten entfernt, durch den Einbau von Stützkonstruktionen unter dem Dach die Statik in Ordnung gebracht. Im vorderen Bereich des Hauses wurden für die privaten Wohnbedürfnisse Widers die Räume des ehemaligen Leibgedings für den Altbauern hergerichtet, während die Sanierung der Stuben des eigentlichen Wohnteils aus finanziellen Gründen liegenbleiben musste. Eine Außenwand musste neu aufgerichtet werden 2020 kaufte das Unternehmerehepaar Jürgen und Maria Grieshaber den Hof. Mit großem persönlichem und finanziellem Engagement waren sie nun die Garanten für die Fortführung des Projekts. Das ursprüngliche Sanierungskonzept von Ulrich Schnitzer wurde weiterverfolgt, die Planung der 1990er-Jahre jedoch für die Wohnzwecke der neuen Eigentümer durch Florian Rauch in Basel überarbeitet. Rauch selbst ist als Architekt am Denkmal kein Unbekannter. Schon 2002 erhielt er für den eigenen Schwarzwaldhof den Denkmalschutzpreis. Für die Realisierung zeichneten weiterhin Martin Wider und seine Holzfirma verantwortlich, was Kontinuität gewährleistete. Auch die abschließende Etappe der Sanierung des Wohnteils des Wildenhofs unter dem Ehepaar Grieshaber stellte sich als sehr anspruchsvoll und komplex dar. Der Gewölbekeller musste stabilisiert werden, bestehende Fundamente wurden ergänzt, die Primärkonstruktion statisch in Ordnung gebracht und die völlig verformte Außenwand demontiert und neu aufgerichtet. Besonderer Wert wurde dabei auch auf die Rekonstruktion der ursprünglichen Stubenfenster mit Schiebeflügeln und auf deren Dichtigkeit gelegt. Überhaupt spielte der Einbau moderner Haustechnik, die nicht ins Auge fallen sollte, eine wichtige Rolle – von Dämmmaßnahmen, einer neuen Holzpelletheizung mit Fußboden-, Fußleisten- und Wandradiatoren bis hin zum Einbau einer die Bausubstanz schonenden und leicht rückbaubaren Sonderlösung für einen behindertengerechten Aufzug, eine durch einen Holzverschlag verkleidete Hebebühne. Die Jury zeigte sich von dem Ergebnis der Sanierung eines bedeutenden, aber besonders schwierigen Objekts beeindruckt, die nur mit langem Atem und als Gesamtleistung von mehreren Eigentümern und beteiligten Architekten und Handwerkern bewerkstelligt werden konnte. Statische Sicherung, Erhaltung von Originalsubstanz, Rückbau von späteren Veränderungen, Rekonstruktion von Verlorenem, Adaption an heutige Funktionen und Energiestandards, Qualität der handwerklichen Leistung sowie eine angemessene Gestaltqualität neuer Teile erfolgten beim Wildenhof auf hohem Niveau, womit dem Objekt eine besondere Beispielhaftigkeit zukommt. Abweichend von der üblichen Vergabe erhalten Jürgen und Maria Grießhaber als die heutigen sowie Martin Wider als frühere Eigentümer gemeinsam den Preis. Kulturerbe und Denkmalschutz Handwerklich perfekte Zimmermannsarbeit, inzwischen schon wieder vom Wetter gezeichnet: der im ersten Bauabschnitt der 1990er-Jahre wiederhergestellte Außengang unter dem weit überstehenden Dach Rekonstruktion nach erhaltenem Vorbild: die Fenster der großen Eckstube 25 Vor dem Untergang gerettet – ein historisches Fachwerkhaus in Maulbronn-Zaisersweiher (Enzkreis) 2016 wurde Detlev Frodermann über eine Internetanzeige auf ein Fachwerkhaus aufmerksam. Schon der erste Besuch in Zaisersweiher, einem Ortsteil von Maulbronn, begeisterte ihn und seine Frau. Der zweigeschossige Bau mit hohem Satteldach und steilem Giebel zur Straße stellte sich als das besonders schmucke Wohnhaus eines ehemaligen landwirtschaftlichen Anwesens im Ortskern unweit der Kirche heraus. Durch eine große Toreinfahrt gelangte man ursprünglich von der Straße in den rückwärtigen Bereich mit freistehendem Stall und Scheune. Der Grundriss zeigt ein durch den Grundstückszuschnitt bedingtes verschobenes Rechteck. In Erwin Huxholds Publikation über das Bürgerhaus im Kraichgau war das Äußere bereits gewürdigt worden als ein unversehrtes Beispiel für Fachwerkfassaden der ersten Hälfte des 18. Jahrhunderts: Auffällig vor allem durch die aufwändigen Zierfachwerkbrüstungen unter den leicht erkerartig vortretenden Fenstern des Obergeschosses, das zwar bäuerlich-derbe, aber ungewöhnlich plastische Formen aufweist. Beim Blick auf den Zustand des Hauses stellte sich 2016 freilich Ernüchterung ein. Seit nahezu vierzig Jahren war das einst stolze Anwesen nicht mehr bewohnt worden und entsprechend heruntergekommen. Mehrere Eigentümer hatten sich in dieser Zeit die Klinke in die Hand gegeben und waren mit verschiedenen Sanierungsüberlegungen UNESCO-Welterbe Kloster Maulbronn Ganzjährig Führungen Sonderführungen Familienspaß Museen in Maulbronn Klostermuseum Museum auf dem Schafhof Steinhauerstube Schmie Literaturmuseum Kunstsammlung Heinrich Märkte und Veranstaltungen 08.-10.04. Lebendiges Kunsthandwerk Mai-Sept. Klosterkonzerte 08./09.07. Fleckenfest Zaisersweiher 04.-06.08. WeinSommer Maulbronn 09./10.09. Kräuter- und Erntemarkt 08.10. Erlebnistag im Kloster 09./10.12. Weihnachtsmarkt Weitere Infos: Stadt Maulbronn, Tel.: 07043/103-0, info@maulbronn.de, www.maulbronn-erleben.de 26 Oben ein Bild des Niedergangs: das Fachwerkhaus in Maulbronn-Zaisersweiher vor der Sanierung, heute ist es wieder ein Schmuckstück für den Ort. gescheitert. Wasser drang über das kaputte Dach ins Innere, der hüfthohe Sockel aus Sandsteinquadern war brüchig und an den Ecken abgesunken, der Putz bröckelte von den Fachen. Das Wetter hatte dem Holzwerk an den Oberflächen stark zugesetzt. Doch trotz schwerer Schäden selbst an tragenden Teilen war das Gefüge noch einigermaßen stabil, da man für die Konstruktion ausschließlich Eichenbalken verwendet hatte. Für die zugehörige Doppelscheune im hinteren Teil des Grundstücks gab es jedoch keine Rettung mehr. Sie war nach einem Teileinsturz von den Denkmalbehörden zum Abbruch freigegeben worden. Da überdies auch das talseitige Nachbarhaus abgerissen worden war, drohte dem Ortskern von Zaisersweiher an empfindlicher Stelle der Verlust des historisch gewachsenen malerischen Straßenbilds. Schwäbische Heimat 2023|1 Die Stube im Obergeschoss mit alter Decke und reparierten Fenstern Frodermanns ließen sich von der auf den ersten Blick hoffnungslosen Situation nicht abschrecken, nicht einmal vom völlig vermüllten Hausinneren. Man hatte gute Kenntnisse, was Holzbau anbelangt, und wusste zudem den Bruder Thomas Frodermann mit im Boot. Gemeinsam besitzen sie in Stuttgart-Weilimdorf ein Zimmerergeschäft, das auf die Sanierung von Kulturdenkmalen spezialisiert ist. Die beiden Brüder fühlten sich von der außergewöhnlichen Aufgabe herausgefordert und entschlossen sich zum Kauf des Objekts, um an ihm ihre handwerklichen Fähigkeiten zu demonstrieren und es denkmalgerecht zu sanieren. Die Originalsubstanz war weitestgehend erhalten Man ließ sich die dafür erforderliche Zeit. Die insgesamt vierjährige Planungs- und Bauphase begann parallel zur notwendigen Entrümpelung vorbildlich mit einer genauen Baudokumentation: verformungsgerechtes Aufmaß, Farbbefunduntersuchung außen und innen, eine detaillierte Schadensdokumentation des Holzwerks sowie ein vom Stuttgarter Architekturbüro Strebewerk erstelltes Instandsetzungskonzept bildeten für die Bauherren die selbstverständliche Grundlage für die Realisierung der Sanierungsmaßnahme. Dabei wurde dendrochronologisch auch die Datierung des Hauses geklärt. Das Holz war 1731 geschlagen worden, die von Huxold angenommene Datierung bestätigte sich damit. Nachgewiesen wurde gleichfalls, dass die Originalsubstanz weitestgehend ohne Umbauten erhalten geblieben war. Nur eine Wand zwischen einem werkstattartigen Raum im Erdgeschoss und der innen liegenden Treppe war verschoben worden, um im nicht unterkellerten Bau eine Grube schaffen zu können. Diese Wand wurde an ihre ursprüng- Kulturerbe und Denkmalschutz Blick von der ehemaligen Durchfahrt auf die Treppe 27 liche Stelle zurückversetzt, um der Treppe wieder mehr Raum zu verschaffen. Ansonsten wurden größere Eingriffe vermieden. Das Dach erhielt durch zwei neue Schleppgauben mehr Licht. Die Durchfahrt, bereits seit langem geschlossen, wurde durch ein neues Tor zur Straße und einen Glasabschluss zum Hof klimatisch dem Hausinneren zugeschlagen und durch zusätzliche Oberlichtöffnungen an der Längsseite besser belichtet. Der einzige große Raum im Haus ist nun als Wohnbereich genutzt. In allen Gewerken wurde nach den restauratorischen Grundlagen auf besonders sorgfältige handwerkliche Weise repariert. Die bestehenden bauzeitlichen Lehmausfachungen mit Staken konnten weitestgehend erhalten werden, abgängige Fachen und solche mit modernen Baumaterialien des 20. Jahrhunderts wurden entfernt und durch Lehmsteine ersetzt. Nachdem zwei originale, im Umriss balusterartig gesägte Bretter der ursprünglichen Treppenwangen gefunden worden waren, wurden diese rekonstruiert. Natürlich wurde an Belange der Gegenwart gedacht: Zur Wärmeisolierung wurden die reparierten alten Fenster zu Kastenkonstruktionen ausgebaut, an den Außenwänden eine Innendämmschale angebracht und mit Lehm verputzt. Der sichtbar gebliebene Dachstuhl erhielt eine außenseitige Bretterschalung mit Aufsparrendämmung, deren Erscheinungsbild am Giebelortgang durch eine plastisch gegliederte Gestaltung geschickt minimiert wurde. Das Haus ist wieder zu einem Schmuckstück für das Dorf geworden und hat die Chance, auch weitere Generationen zu beherbergen. Seit 2020 bewohnen Detlev Frodermann und seine Frau das Haus, dessen Sanierung nach Meinung der Jury Schule machen sollte. Reparatur als denkmalpflegerisches Ideal – das ehemalige Pfarrhaus in Wangen-Oberwälden (Landkreis Göppingen) Marlene und Johannes Widmann waren erst um die Dreißig, als sie 2017 das frühere Pfarrhaus in Oberwälden, heute ein Ortsteil von Wangen bei Göppingen, erwarben. Beide kannten das laut Bauinschrift am Kellerabgang 1787 errichtete Gebäude gut, da Marlene Widmann in Oberwälden aufgewachsen war. Beide schätzen das malerische Ortsbild des Dorfes am Rand des Schurwaldes, zumal es sich stark abhebt von der verstädterten und zersiedelten Umgebung des nahen Fils- und Neckartals. Das schlichte, wohlproportionierte spätbarocke Gebäude mit seinem Krüppelwalmdach ist ein wichtiges Element des baulichen Ensembles, das sich um die bis ins Mittelalter zurückgehende Nikolauskirche und den Dorffriedhof schart. In seinem engen Bezug zur Kirche bei gleichzeitiger Dominanz gegenüber den alten Bauernhäusern ist es in Oberwälden bis heute geradezu ein Idealbild geblieben für diese im Schwäbischen ehedem so wichtige Bauaufgabe. Hier war ein Mittelpunkt des kulturellen und religiösen Lebens im Dorf, in diesem Milieu war die 1823 gebo- Der Enzkreis Feiern Sie Wir werden 50 mit uns! Wir bedanken uns für die gute Zusammenarbeit FRANKFURTER STRASSE 65, 75433 MAULBRONN WWW.HEINRICH-BAUUNTERNEHMUNG.DE TEL.: 07043-9253-0 FAX: 07043-9253-50 28 Die neue Badeinrichtung fügt sich in die alte Raumstruktur. Schwäbische Heimat 2023|1 Das Pfarrhaus von Oberwälden nach der behutsamen Sanierung: noch immer ein Mittelpunkt des Ortes, überragt von der Turmspitze der Nikolauskirche rene Luise Pichler als Pfarrerstochter aufgewachsen, die später als Autorin historischer Romane bekannt werden sollte. Von der repräsentativen Front des zweigeschossigen Hauses mit seinem zentralen Eingang hat man zwischen den zugehörigen Nebengebäuden von Pfarrscheuer und Wasch- und Backhaus einen grandiosen Blick über unverbaute Natur auf den Hohenstaufen, den Rechberg und die Schwäbische Alb. Hier zu wohnen war der Traum der jungen Familie. Das Haus gehörte der Gemeinde Wangen, stand aber schon seit einigen Jahren leer, da man kein Nutzungskonzept hatte. Zwar war es nicht in baufälligem Zustand und noch bis in die 1980er-Jahre waren Maßnahmen zum Erhalt durchgeführt worden, doch wuchs schon Efeu durch die Fenster. Außerdem gab es wegen der Hanglage des unteren Geschosses in den Sockelzonen Feuchtigkeitsprobleme, die bereits zu Schäden am Holzwerk führten. Eine Kostenschätzung für notwendige Sanierungsmaßnahmen schreckte die Ortsverwaltung über Jahre ab, selbst tätig zu werden. Da die Widmanns Interesse anmeldeten, entschloss sich die Gemeinde, das Haus gegen Höchstgebot zum Verkauf anzubieten. Es gelang dem Ehepaar schließlich, den Zuschlag zu erlangen. Mit alter Aura für moderne Wohnansprüche Es kam dem Kulturdenkmal zugute, dass die neuen Eigentümer ein Gespür für den Wert der überkommenen Besonderheiten des Hauses besaßen und ihr Nutzungskonzept sich bestens mit der Struktur des Hauses vereinbaren ließ, dessen Bausubstanz sich auch im Inneren trotz früherer Erneuerungen weitgehend erhalten hatte. Nur die ursprüngliche Treppe war im späten 19. Jahrhundert durch eine neue ersetzt worden. Im Erdgeschoss mit den massiv gemauerten Außenwänden sollte neben der unge- Kulturerbe und Denkmalschutz wöhnlich großen Eingangshalle und den bestehenden Wirtschaftsräumen eine kleine separate Wohnung geschaffen werden. Das aus verputztem Fachwerk bestehende Obergeschoss wurde für die großzügige Wohnung der Eigentümer vorgesehen, bei der sich die Räume rechts WIR BAUEN MIT HOLZ AUCH FÜR SIE Fon 07331/83231, Hauptstraße 40, 73329 Kuchen 29 HERZLICHEN GLÜCKWUNSCH Historische Historische Werte Werte erhalten erhalten ormati Inf ormati Inf nf or d nf ern or dern en en on on HIE HIER R a Foto: Gerhard Kabierske Modernisieren Sie Ihre historische Immobilie Modernisieren Sie Ihremit "Geprüften Restauratoren historische Immobilie mit im Zimmererhandwerk". "Geprüften Restauratoren Wir verbinden traditionelles im Zimmererhandwerk". Handwerk mit modernster Wir verbinden traditionelles Technologie. Handwerk mit modernster Technologie. a Der Landkreis Göppingen gratuliert den Preisträgern recht herzlich zum Denkmalschutzpreis! Preisgekrönte Denkmalsanierung von Leibbrand. Verband der Restauratoren im Zimmererhandwerk e.V. Verband der Restauratoren im Zimmererhandwerk Helmuth-Hirth-Straße 7 e.V. Verband der Restauratoren 73760 Ostfildern 43 e.V. im Zimmererhandwerk Hackländerstrasse 70184 Stuttgart Telefon 0711-23996-50 Hackländerstrasse 43 Fax Stuttgart 0711-23996-60 70184 Telefon 0711-23996-50 E-Mail 0711-23996-60 info@restauratoren-verband.de Fax Telefon 0711-23996-50 Internet www.restauratoren-verband.de E-Mail info@restauratoren-verband.de Fax 0711-23996-60 Internet www.restauratoren-verband.de E-Mail info@restauratoren-verband.de Wir freuen uns mit den Besitzern über die Auszeichnung mit dem Denkmalschutzpreis Baden-Württemberg 2022 für unsere Arbeit am ehemaligen Pfarrhaus in WangenOberwälden. Unsere Restauratoren sanieren nach den Richtlinen des WTA und haben jahrzehntelange Erfahrung in der Sanierung von Fachwerk- und Denkmalschutzobjekten. U. Leibbrand GmbH Lutherstr. 65 · 73614 Schorndorf Fon 07181·92015-0 · www.leibbrand.de 30 Schwäbische Heimat 2023|1 Der lichte große Wohnraum mit umlaufender Lamperie und aufgearbeitetem Parkett im Obergeschoss: Der neue Küchenblock wurde frei hineingestellt, ohne den Raumeindruck zu zerstören. und links eines Mittelflurs reihen. Im bereits zuvor ausgebauten Dachgeschoss wurde eine weitere Wohnung eingerichtet, die wie jene im Erdgeschoss die Möglichkeit zur Vermietung bietet. Veränderungen am Grundriss bestanden einzig in der Entfernung zweier nachträglich eingezogener Wände im Erd- und im Dachgeschoss und einem Türdurchbruch an einer Stelle, an der früher wahrscheinlich bereits eine Öffnung bestanden hatte. Die Fachwerkkonstruktion der Innenwände wurde nicht angetastet, ebenso blieb der Spitzboden unausgebaut, wobei am Dach und im Bereich des Erdgeschosses bauphysikalisch richtige Dämmmaßnahmen mit Zellulosefasern und Lehmverputz zur Verbesserung der Energiebilanz durchgeführt wurden, ohne das Erscheinungsbild zu beeinträchtigen. Anstelle der alten Gasthermen im Haus wurde in der bereits früher sanierten und als Hobbywerkstatt genutzten Pfarrscheuer ein umweltfreundlicher Kombikessel für Scheitholz und Holzpellets installiert, der über eine Leitung das Gebäude zentral mit Wärme versorgt. Der hinzugezogene Architekt Volker Sawall aus Geislingen sowie die Handwerker erwiesen sich als äußerst kompetent im Umgang mit der vorhandenen Bausubstanz. Zunächst wurde durch die Verbesserung der Drainage der Sockelzone das in den Außenmauern hochsteigende Hangwasser vom Haus ferngehalten. Die weitere Sanierung ging durchweg von der Erhaltung und Reparatur des Bestehenden aus. Ob die Verbundfenster aus den 1950erJahren, die Klappläden, die originalen Türen, die Dielenund Parkettböden aus verschiedenen Zeiten sowie die umlaufenden Lamperien – das Holzwerk wurde handwerklich mit Sorgfalt aufgearbeitet. Die Beschläge aus verschiedensten Zeiten wurden dabei wiederverwendet, ob Türklinken aus der Erbauungszeit oder dem späten 19. Jahrhundert oder die Fensteroliven der Nachkriegszeit. Kulturerbe und Denkmalschutz Putz und Stuck, aber auch unter späteren Bodenbelägen zum Vorschein gekommene große Steinplatten wurden ebenso fachgerecht ergänzt. Neue Teile wie beim Küchenoder Bädereinbau sind in bewusst modernen Formen gehalten, wobei eine zurückhaltende Gestaltung verhindert, dass die Kontraste zwischen Alt und Neu zu stark ins Auge springen. Die Jury war von diesem vorbildlichen Beispiel des Umgangs mit einem Kulturdenkmal überzeugt, das durch seine unaufdringliche Angemessenheit besticht. Das Pfarrhaus wird einerseits in seiner alten Aura weitertradiert und gleichzeitig heutigen Wohnansprüchen gerecht. Hier war Platz für Fässer: der Gewölbekeller unter einem Teil des Gebäudes mit einem breiten Zugang von außen und einer internen Treppe in den Eingangsbereich 31 Ausgezeichnet! ESSEN, TAGEN, FEIERN UND GENIEßEN im renovierten und stilvoll eingerichteten Bahnhof | Restaurant und Barbetrieb | Regionale Spezialitaten | Hochzeiten und Familienfeste | Firmenevents | Vereinssitzungen | Modern eingerichtete Apartments mit komplett ausgestatteter Küche | Kostenfreies W-Lan und Flat-TV | Wöchentliche Reinigung | Handtuch- und Bettwäschewechsel Restaurant & Boardinghouse Am Bahnhof 1 74532 Ilshofen-Eckartshausen Tel. 07904 - 9438210 info@bahnhofmann.de www.bahnhofmann.de 32 Schwäbische Heimat 2023|1 Ein »Tor zur Welt« – Wiederbelebung des Bahnhofs in Eckartshausen-Ilshofen (Landkreis Schwäbisch Hall) Für Claudia und Rüdiger Hofmann war es eine Herzensangelegenheit, den Bahnhof von Eckartshausen-Ilshofen an der Bahnstrecke von Schwäbisch Hall nach Crailsheim wieder zum Leben zu erwecken, zumal das relativ große Gebäude, das auch als Bahnstation für das nahegelegene Ilshofen und einen weiteren Einzugsbereich in Hohenlohe diente, heute noch in besonderer Weise das Ortsbild des kleinen Eckartshausen prägt. Rüdiger Hofmann war hier aufgewachsen, und für ihn hatte der Bahnhof in seiner Jugend, an der wichtigen Ostwestverbindung von Heilbronn nach Nürnberg gelegen, nichts anderes als den Anschluss an die weite Welt bedeutet. Die Bahnhofsgaststätte, die sich darin befand, empfand er als wichtigen Mittelpunkt der Dorfgemeinschaft. Dieser Bahnhof war 1864–67 im Zuge der Trassierung der Kochertalbahn nach Plänen der Bahnbauverwaltung im damals üblichen Stil der Funktionsbauten der KöniglichWürttembergischen Staatseisenbahnen errichtet worden: mit Rundbogenfenstern und -türen im Erdgeschoss sowie hochrechteckigen Fenstern im Obergeschoss, profiliert eingeschnitten in die Verkleidung der Fassaden mit großen Steinquadern aus regionalem Sandstein. Über einem zweiten, nur kniestockartigen Geschoss schließt ein flach geneigtes und kräftig überstehendes Dach den kubischen Baukörper ab. Im Erdgeschoss waren neben der Bahnhofsgaststätte der Schalter- und Warteraum untergebracht, in den Obergeschossen Wohnungen für Bahnbeamte und Bahnarbeiter. Mehr als 120 Jahre erfüllte der Bahnhof seine Funktion, sah glänzende Tage, wenn der württembergische König hier zu Manövern auf dem nahen Truppenübungsplatz ausstieg, aber auch tragische, als gegen Ende des Zweiten Weltkriegs ein mit völlig entkräfteten KZ-Häftlingen beladener Güterzug hier tagelang auf dem Gleis stand oder Tieffliegerangriffe auf die Bahnlinie erfolgten, von denen noch zahlreiche Einschusslöcher an den Fassaden zeugen. Wie viele andere Landbahnhöfe war auch der Bahnhof in Eckartshausen in den letzten Jahrzehnten vom Niedergang geprägt, obwohl die Bahntrasse keineswegs aufgege- Kulturerbe und Denkmalschutz Ein repräsentativer Bau des 19. Jahrhunderts auf dem Land: der wiederbelebte Bahnhof Eckartshausen-Ilshofen, vorne das sich unterordnende neue Technikgebäude mit der Heizung ben wurde. Zunächst nahmen Modernisierungen, wie etwa der Einbau neuer Fenster, keine Rücksicht mehr auf die bauliche und gestalterische Qualität der Architektur. Dann zog sich die Deutsche Bahn mehr und mehr von der zunehmend vernachlässigten Immobilie zurück, die ihre ursprünglichen Aufgaben verlor. Schon 1994 wurde der Schalterverkauf zugunsten eines simplen Automaten auf dem Bahnsteig eingestellt, ebenso wurde die Bahnhofswirtschaft geschlossen. Direkt neben den Gleisen fiel der Bahnhof für zwei Jahrzehnte in triste Agonie, was der Bausubstanz nicht gut bekam. Massive Schäden am Holzwerk des Daches waren die Folge. Das Unternehmerehepaar Hofmann verfolgte betrübt die Entwicklung und ergriff sofort die Initiative, als bekannt wurde, dass die Bahn das inzwischen denkmalgeschützte Gebäude in Berlin versteigern lassen wollte. Sie steigerten mit und erhielten den Zuschlag. Ihr Ziel war es, den Bahnhof so weit als möglich in seinen Ursprungszustand zu versetzen und dabei eine wirtschaftliche wie denkmalver- 33 Nach Jahren der Leerstands: die Bahnhofswirtschaft lädt wieder zum Verweilen ein. trägliche Nutzung zu finden. Erste Überlegungen für den Umbau zu einem Hotel wurden nicht weiterverfolgt, als klar wurde, dass dafür starke Eingriffe in die Substanz notwendig und das Erscheinungsbild beeinträchtigende Anbauten unerlässlich sein würden. Schließlich wurde 2016–18 eine Sanierung als Boardinghaus realisiert. Im Erdgeschoss reaktivierte man die alte Bahnhofswirtschaft und erweiterte sie um die Fläche der ehemaligen Schalterhalle und den Wartesaal. Die früheren Dienstwohnungen im Ober- und Dachgeschoss wurden zu kleineren Wohneinheiten für temporäre Mietnutzungen umgebaut. Sie werden vor allem von zeitweise in Ilshofen tätigen Mitarbeitern der international agierenden Metallbaufirma genutzt, der Rüdiger Hofmann als Geschäftsführer vorsteht. Spätere Veränderungen wurden rückgebaut, Befunduntersuchungen zur ursprünglichen Farbigkeit durchgeführt, verloren gegangene Gestaltqualität bei Fenstern und Türen durch Nachbauten gemäß den noch vorhandenen originalen Elementen wiederhergestellt. Besonders 14 Erforschen und Erhalten Jahresbericht der Bau- und Kunstdenkmalpflege 4/2021 15 Ruhe und Bewegung – ein anmutiges Paar Mutter mit Kind – ein Kooperationsprojekt zwischen Landesamt für Denkmalpflege und Staatlicher Akademie der Bildenden Künste Stuttgart: forschen – konservieren – erhalten 54 von Jochen Ansel Erforschen und Erhalten BAUDENKMALE & KUNSTDENKMALE Jahresbericht der Bau- und Kunstdenkmalpflege 4/2021 2 Klassizistisches Kleinod 01 O B J E K T : Skulpturengruppe Maria mit Kind S T A N D O R T : ehem. Klosterkirche St. Georg, Schlossbezirk 8, 88416 Ochsenhausen (Lkr. Biberach) E I G E N T Ü M E R : Kath. Kirchengemeinde St. Georg M A S S N A H M E : Untersuchung und Konservierung B E T E I L I G T E : Institut für Konservierungswissenschaften an der Staatlichen Akademie der Bildenden Künste, Prof. Dr. Wibke Neugebauer, Prof. Dr. Anna von Reden, Dipl.-Rest. Peter Vogel, Anna Egeler und Chiara Schweizer; Universität Konstanz, Lisa Braun 55 in Baden-Württemberg Ochsenhausen Zur Restaurierung der Wandmalereien im Spiegelsaal des Leimener Rathauses von Ruth Cypionka ◀1 BASILICA MINOR – FOLGEN DER E R N E N N U N G Seit 2019 trägt die ehemalige Klosterkirche St. Georg in Ochsenhausen den von Papst Franziskus verliehenen Titel „Basilica minor“. Die aus diesem Anlass in die Wege geleitete Neugestaltung des Altarbereichs lenkte die Aufmerksamkeit auf die Skulptur der Maria mit Jesuskind, ein Werk des Ulmer Schnitzers Niklaus Weckmann. Dieser wirkte zwischen 1481 und 1526 und prägte den Ulmer Stil maßgeblich. Von ihm geschaffene Schnitzretabel sind im Alpenraum Italiens, Österreichs und der Schweiz anzutreffen. Mit ihren mehr als 500 Jahren zählt die in Ochsenhausen hochverehrte Marienfigur zu den ältesten Ausstattungsstücken der Kirche. Da der Einbau der neuen Stufen- und Podestanlage im Altarraum der Kirche umfangreiche Evakuierungs- und Sicherungsarbeiten an den Seitenaltären und am Kreuzaltar bedingte, musste auch die Marienfigur ihren angestammten Platz verlassen, was eine Bewertung ihres Erhaltungszustands nötig machte. Dabei stellten die Restauratoren des Landesamts für Denkmalpflege Ablösungen in den Farblagen fest, viele Farbverluste waren bereits eingetreten – ein Schadensprozess, den es zu stoppen galt. 2 1 11 aufwändig erwies sich die Sanierung der Hausteinverkleidung der Fassaden, deren untere Teile stark verwittert waren. Dabei wurde das passende Steinmaterial durch Zweitverwendung von Quadern aus einer alten Mauer in der Nachbarschaft des Bahnhofs gewonnen. Das Grundstück mit der Mauer hatte die Familie Hofmann dafür eigens hinzugekauft. Die Jury beurteilt diese Sanierung als besonders beispielhaft, da sie zeigt, dass die Umnutzung eines Bahnhofs, die häufig zu fragwürdigen Ergebnissen führt, in denkmalverträglicher Weise geschehen kann und nicht automatisch zu unwiederbringlichen Substanzverlusten führen muss. Besonders gefiel, wie den strikten baurechtlichen Auflagen für Brandschutz, Küchentechnik und Dämmmaßnahmen nachgekommen wurde, ohne das Gesamtbild zu stören. So wurde der zweite Fluchtweg durch den Einbau einer weiteren inneren Treppe geschaffen, die spiegelsymmetrisch zur bestehenden angelegt wurde und weder von außen noch im Inneren in Erscheinung tritt. Für die moderne holzbetriebene Heizungsanlage wurde O B J E K T : Rathaus P R O J E K T : Sanierung Rathaus S T A N D O R T : Rathausstr. 8, 69181 Leimen (RheinNeckar-Kreis) E I G E N T Ü M E R : Stadt Leimen M A S S N A H M E : Restaurierung der Wandmalereien B E T E I L I G T E J O C H E N : Ansel, Restaurator, LAD; Böke & Fritz, Diplomrestauratoren für gefasste Holzobjekte und Wandmalerei, Eppingen; Stadt Leimen F Ö R D E R U N G : Fördermittel des Landes und der Denkmalstiftung Baden-Württemberg Leimen Das heutige Rathaus in Leimen – ein elfachsiger, zweigeschossiger Bau mit dreiachsigem Mittelrisalt und vorgelagertem Balkon – besticht schon äußerlich durch seine Größe und strenge klassizistische Gliederung mit rustiziertem Erdgeschoss und ebensolchen Eckpilastern unter einem ausgebauten Mansarddach. Der wohlhabende jüdische Hoffaktor Aaron Elias Seligmann (1747–1824) ließ sich 1794 diesen repräsentativen Bau errichten, der gestalterisch engen Bezug auf Peter Anton von Verschaffelts Adelpalais Bretzenheim in Mannheim nimmt. Seligmann, der nicht nur das Salzmonopol für die Kurpfalz innehatte, sondern auch die in Leimen florierende Tabakindustrie begründete, setzte sich hiermit ein Denkmal, das nicht nur seinen wirtschaftlichen, sondern auch gesellschaftlichen Aufstieg und die beginnende politische Emanzipation der jüdischen Bevölkerung in der Epoche der Aufklärung veranschaulichte. 1841 erwarb die Gemeinde Leimen das sogenannte Palais Seligmann und richtete darin ihr Schul- und Rathaus ein; die Rathausnutzung besteht bis heute. D E R S P I E G E L S A A L Im Zentrum des Palais liegt in der Beletage der über eine zweiläufige, repräsentative Treppenanlage erschlossene Festsaal mit vorgelagertem Balkon. Er ist mit mythologischen Wandgemälden auf Leinwand, die von gemalten Architekturgliederungen und Supraporten en grisaille gerahmt werden, sowie mit zwei Kaminen und Spiegeln ausgestaltet. Die Malereien werden dem Mannheimer Maler Peter Ferdinand Deurer (1777–1844) zugeschrieben. Dieses eindrucksvolle klassizistische Kunstkabinett, dessen Bildinhalte sich streng an antikes Formengut anlehnen, war zu seiner Entstehungszeit äußerst modern und sollte die große Kunstkennerschaft und hohe Bildung des Auftraggebers Seligmann zur Schau stellen. 2017 wurde entschieden, den vielgenutzten, vor allem bei Hochzeitspaaren beliebten, aber in die Jahre gekommenen Saal zu restaurieren. Der Jahresbericht der Bau- und Kunstdenkmalpflege in Baden-Württemberg stellt jeweils bemerkenswerte Beispiele aus dem Schatz von über 90.000 Bau- und Kunstdenkmalen vor. Im aktuellen 4. Band (2021) sind Objekte aus allen Epochen enthalten – vom mittelalterlichen Beinhaus in Wertheim bis zur Bundesanwaltschaft in Karlsruhe. Die Jahresberichte können auch zur Fortsetzung bestellt werden – im Buchhandel sowie bei www.thorbecke.de wm1226_anzeige.indd 1 Erforschen und Erhalten (2021) 256 Seiten, reich bebildert, Paperback, 21 x 30 cm € 28,- [D] / ISBN 978-3-7995-1565-8 23.01.23 12:56 34 Schwäbische Heimat 2023|1 in deutlicher Entfernung vom Gebäude ein sich unterordnendes Funktionsgebäude errichtet. Ebenso positiv wurde bewertet, wie es durch kluge Planung im Obergeschoss nur durch wenige Vermauerungen bzw. Türdurchbrüche möglich war, kleinere Wohneinheiten zu schaffen, ohne die ursprüngliche Struktur des Gebäudes grundlegend zu beeinträchtigen. Impulse für eine abwechslungsreiche Freizeit Impulse für eine abwechslungsreiche Freizeit Unsere schön gelegene Stadt bietet: Unsere schön Stadt Impulse fürgelegene eine abwechslungsreiche Freizeit • Gute Gastronomie- und • Reizvolle Ausflugs- und bietet: Unsere schön gelegene Wandermöglichkeiten Hotelbetriebe • Reizvolle AusflugsundStadt • Gute Gastronomie- und bietet: • Radfahren, Freibadbesuch, • Stauferburgruine Leofels Wandermöglichkeiten Hotelbetriebe • Gute Gastronomie- und • Reizvolle Ausflugs- und Tennis, Angeln Infos unter: • Radfahren, Freibadbesuch, • Stauferburgruine Leofels Wandermöglichkeiten HotelbetriebeIlshofen, • Theater, Ausstellungen, Stadtverwaltung Tennis, Angeln Infos unter: • Radfahren, Stauferburgruine Leofels Haller Str. 1, 74532 Ilshofen Kleinkunst Freibadbesuch, • • Theater, Ausstellungen, Stadtverwaltung Ilshofen, Tennis, Angeln Infos • Ilshofener Herbst- und Tel.: 0unter: 79 04/7 02-0 Haller Str. 1, 74532 Ilshofen • Kleinkunst Theater, Ausstellungen, Stadtverwaltung Ilshofen, Töpfermarkt, Ostermarkt, info@ilshofen.de Haller 1, 74532 Kleinkunst www.ilshofen.de Stadtfest Herbst- und Tel.: 0 Str. 79 04/7 02-0Ilshofen • Ilshofener • Töpfermarkt, Ilshofener Herbstund Tel.: 0 79 04/7 02-0 info@ilshofen.de Ostermarkt, Töpfermarkt, Ostermarkt, info@ilshofen.de www.ilshofen.de Stadtfest www.ilshofen.de Stadtfest Blick in die ehemalige Eingangshalle, nun auch gastronomisch genutzt: restaurierte wandfeste Ausstattung und nach Befund rekonstruierte Farbigkeit Über den Autor Gerhard Kabierske studierte Kunstgeschichte und Provinzialrömische Archäologie an den Universitäten Freiburg und München. Er promovierte bei Johannes Langner in Freiburg über den badischen Jugendstil-Architekten Hermann Billing. Von 1988 bis 1993 war er Stadtkonservator bei der Unteren Denkmalschutzbehörde Karlsruhe und von 1993 bis 2020 tätig am Südwestdeutschen Archiv für Architektur und Ingenieurbau (saai) an der Universität Karlsruhe bzw. am Karlsruher Institut für Technologie Kulturerbe und Denkmalschutz (KIT). Schwerpunkt seiner Arbeit bildeten der Aufbau des Archivs zu einer der größten Einrichtungen seiner Art im deutschsprachigen Bereich sowie Ausstellungen und Publikationen zur Architektur des 19. und 20. Jahrhunderts. Seit 2000 ist er Vertreter des Landesvereins Badische Heimat in der Jury für den Denkmalschutzpreis Baden-Württemberg, seit 2006 deren Vorsitzender. Einladung zur Preisverleihung Der Festakt zur Verleihung des Denkmalschutzpreises findet in der Klosterkirche Salem am 24. April 2023 statt. Details siehe im SHB Intern S. 101. 35
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Human Papillomavirus (Hpv) Infection In Rural And Tribal Populations Of The World With A Special Focus On The Prevalence In India
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Journal of Biomedical and Allied Research ISSN: 2582-4937 Rashid S, et al., 2022- J Biomed Allied Res Review Article ISSN: 2582-4937 Rashid S, et al., 2022- J Biomed Allied Res Review Article 2Jazan University, Jizan, Saudi Arabia *Corresponding Author: Dr. Shazia Rashid, Ph.D. Assistant Professor, J3-412, Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India. Christina Choudhary1, Kanubha Sharma1, Sajad Ahmad Dar2, Shazia Rashid1* Christina Choudhary1, Kanubha Sharma1, Sajad Ahmad Dar2, Shazia Rashid1* Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India 1Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University Uttar Pradesh, India Abstract Received Date: 04-23-2022 Human papilloma virus (HPV) infection is one of the major causes of cervical cancer which is one of the common causes of death in women across the globe and is the fourth most prevalent cancer in women representing 7.5% of female cancer deaths globally and more than 85% of these occur in underdeveloped regions. In India, cervical cancer is responsible for the highest cancer deaths among women which can be attributed to multiple pregnancies, open relationships, inadequate sanitation and cleanliness, behavioral habit and lifestyle, smoking, poor nutrition, and long-term contraceptive use. These factors have been associated as risk factors for cervical cancer. This review discusses issues faced by women in tribal and rural areas of India due to poor economic conditions, different lifestyles to mainstream population, socioc and lack of access to healthcare facilities. The review also focusses on the tribal populations the prevalence rates in these tribal groups. The current initiatives taken by government and n organizations (NGOs) to prevent and control the HPV infection and reduce the cervical can also been highlighted. The review emphasizes the urgent need for preferential care for wom tribal communities of the world. Accepted Date: 05 Published Date: 05 Copyright© 2022 b rights reserved. Th distributed under Commons Attribu unrestricted us reproduction in a original author and Accepted Date: 05-4-2022 Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Published Date: 05-20-2022 Copyright© 2022 by Choudhary C, et al. All rights reserved. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. vical cancer; HPV; Risk factors; HPV prevalence; tribal; rural; Government initiatives; NGO- Keywords: Cervical cancer; HPV; Risk factors; HPV prevalence; tribal; rural; Government initiatives; NGO- initiatives. Introduction underlying infectious diseases, smoking, poor diet and long-term use of oral contraceptives [8,9]. The population of the world is divided into the urban, rural, and tribal populations. An area is known as the rural sector when the population of that area is less than 5,000, the density of population less than 400 per sq km, and more than 25% males are engaged in agricultural areas. The tribal population accounts for 5% of the global population [1] and about 19.3% of the global population lives in rural areas [2]. India is a diverse country that has 29 States and 7 Union Territories. The current population of India according to the 2019 Census is 1.37 billion, out of which 70 percent lives in a rural area [3,4]. India is home to a large tribal population which is approximately 8.6% of the Indian population and about 65% people live in rural areas whereas 35% people live in the urban area [5]. These factors are particularly more common in the rural and tribal belts of India. Multiple pregnancies Some tribal communities live in open relationships and in addition women are prone to having successive pregnancies in a year, which leads to higher parity, abortions, poor health, and susceptibility to infections. In a study conducted among the tribal adolescent girls of different tribes from three different states of India–Madhya Pradesh (Hoshangabad), Chhattisgarh (Narainpur and Kondagaon) and Jharkhand (Jamshedpur) it was found that they have persistent HPV infection due to several factors among which multiple pregnancies were also a major factor [8,10]. One of the common causes of death across the globe is cervical cancer. It is the fourth most prevalent cancer in women representing 7.5% of female cancer deaths globally with more than 85% of these occurring in underdeveloped regions [6]. About 20% of cancer deaths are caused due to Human papilloma virus (HPV) infection and it is a common cause of death for women belonging to Eastern, Middle, and Western Africa, Central America and South East Asia [7]. In India, cervical cancer is responsible for highest cancer deaths among women in rural areas. Age is another important risk factor. In many tribal communities, women become sexually active at a very early age of 10-12 years. It has been observed that women in their late teens and mid-30s are more prone to cervical cancer. Due to lack of education and poor awareness, researchers propose that engaging in sexual activity at a young age makes the cervix highly vulnerable to HPV infection as a result of the changes during puberty [11,12]. Women who undergo full-time pregnancy at a very young age are more susceptible to cervical cancer [8]. A study carried out in different tribal areas of Madhya Pradesh, Jharkhand, and Chhattisgarh, reported that the mean age of women getting married was Risk factors of cervical cancer The common risk factors for HPV infection are age, multiple sexual partners, multiple pregnancies, poor sanitation and hygiene, Multiple partners It has been seen that some of the tribal communities mostly live in open relationships with multiple partners in preference to the traditional one partner marriage system, which increases their risk of acquiring HPV infection [10]. According to the study by Peedicayil et al in 2016, out of 809 women who took part in the study, 0.7% of them had multiple partners and 3% of them had used oral contraceptives [13]. A higher HPV prevalence rate has been observed in women with gynecological symptoms increasing their risk of developing cervical cancer [14]. Poor sanitation and hygiene Due to poor economic conditions and decreased awareness, women in rural and tribal areas usually lack resources and information to maintain sexual hygiene particularly during menstruation. This makes them vulnerable to poor sexual health and prone to sexually transmitted infections, like HPV leading to increased risk of cervical cancer [9,15]. In a study conducted across the tribal areas of Chhattisgarh, Madhya Pradesh, Jharkhand, it was observed that most of the women who were tested positive for HPV infection had very poor sanitation and hygiene particularly during the time of menstruation, repeated use old cloth pieces along with cow dung ash and other unhygienic materials in their sanitary pad during menstrual period making them more susceptible to cervical cancer [10,16,17]. Behavioral pattern and lifestyle 18.1 years, and 43% of women became sexually active before the age of 18 [10]. The prevalence of HPV in any area of inhabitation depends on the lifestyle and behavior of the inhabitants to a large extent. People living in tribal areas often live in remote areas with lack contact with the outside world [10]. Most of the rural and tribal areas in India lack health care facilities because they live in secluded and remote areas. In addition, they are less likely to access medical care due to their beliefs and prefer natural products procured locally for treatment [9,15]. Increased susceptibility to diseases such as tuberculosis, pneumonia, malaria, anemia and poor immune system are reported in the tribal areas of Madhya Pradesh, Jharkhand, and Chhattisgarh. Chlamydia infection is a kind of bacterial infection in the reproductive tract, which helps the HPV to thrive on the cervix, leading to a higher risk of cervical cancer [9,10,18,19]. Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Poor diet Due to poor economic conditions in the tribal areas, there is lack of nutritious food specially required by women during pregnancy and childbirth which may cause anemia, malnutrition and weight loss in women and could be linked to high prevalence of HPV infection [10]. Smoking In rural areas, consumption of tobacco in different forms is very common among men and women. It has been observed that women who smoke are more prone to cervical cancer than non-smokers. Smoking tobacco and other such substances damage the DNA of the cervix and lower the immunity to fight HPV infection [19]. According, to a study conducted among tribal people, people in these areas consume a lot of locally fermented beverages called mahua and tadi which contain toxic chemicals and hence, maybe the reason for high HPV prevalence in this region [18]. prolonged use of intrauterine contraceptive devices can lead to actinomycosis, pelvic inflammatory disease and subsequent possible malignancies [21]. However, Indian tribal women have been reported to have no or very limited knowledge about oral contraception and the use of contraceptive methods is also very limited [22]. Long term use of oral contraceptives There are limited studies carried out to determine the HPV infection prevalence in tribal population in India and on a global level. Some major tribes/ tribal groups of India and different continents are listed in Table 1 and Table 2 respectively. Oral contraceptives are the hormonal medications taken to prevent pregnancy. Various studies show that women using oral contraceptives for 5 or more years are more prone to cervical cancer, as these pills induce a change in susceptibility of cervical cells and result in persistent infection [20]. Moreover, Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 result in persistent infection [20]. Moreover, Indian States Tribe/ Tribal Groups Andhra Pradesh Nakkala, Kurvikaran, Kondhs, Kodi, Kodhu, Desaya Kondhs, Dongria Kondhs, Kuttiya Kondhs, Tikiria Kondhs, Yenity Kondhs, Kuvinga, Porja, Parangiperja Arunachala Pradesh Sulung Bangni, Sulung, Laju, Havi Tangsa, Liju Nocte, Lish Monpa Assam Syntheg, Chakma Andaman & Nicobar Islands Jarawas, Sentinelese, Shom Pens Bihar Banjara, Birhor, Parhayia, Korwa, Kora, Mudi-kora Chhattisgarh Saonta, Saunta Dadra & Nagar Haveli Naikda or Nayaka, Kathodi Jammu & Kashmir Bakarwal Jharkhand Parhaiya, Birhor, Savar, Baiga, Korwa Kerala Cholanaickan Odisha Mankirdia, Mankria, Mankidi, Koya, Gumba Koya, Koitur Koya, Kamar Koya, Musara Koya, Dharua, Dhuruba, Dhurva, Korua, Parenga, Didayi, Didai Paroja, Didai, Bondo Poraja, Bonda Paroja, Banda Paroja, Paroja, Parja, Bodo Paroja, Barong Jhodia Paroja, Chhelia Paroja, Jhodia Paroja, Konda Paroja, Paraja, Ponga Paroja, Sodia Paroja, Sano Paroja, Solia Paroja, Gandia, Omanatya, Omanatyo, Amanatya Rajasthan Garasia(except Rajput in that region), Kathodi, Katkari, Dhor Kathodi, Dhor Katkari, Son Kathodi, Son Katkari Uttar Pradesh Agariya, Baiga, Saharya, Raji West Bengal Gorait Table 1: Tribes in each state of India [23]. Continent Tribe/ Tribal Groups References Asia Veddas (Sri Lanka), Jarawa (Andaman Islands, India), Naga (north-eastern India and north-western Myanmar), Lhop (northwest Bhutan), Bodo (Nepal), Giraavaru (Maldives). Long term use of oral contraceptives Burmans, Karen, Shan, Rakhine, Karenni, Chin, Kachin and Mon (Burma/Myanmar) Tibetans, Uighurs (China), Ainu, Okinawans (Japan), Orang asli (Malaysia), Igorot, Lumad, Mangyan (Phillipines) [24] Africa Zulu (South Africa), Maasai (East Africa), San Bushmen (Western Botswana and Makgadikgadi), Yoruba (Nigeria and Southern Benin), Xhosa (Eastern- Cape-Province of South Africa), Hausa (West Africa), Himba (Northern Namibia), Oromo (southern parts of Ethiopia, Northern Kenya, some parts of Somalia), Kalenjin (Western highlands of Kenya), Chaga (Tanzania) [25] Europe Saami (Scandinavia and Russia) [26] South America Mapuche, Kolla, Toba, Guarani, Wichi, Mocovi, Haurpe, Comechingen, Tehuelche, Charrua, Pilaga (Argentina), Quechua, Aymara, Chiquitano, Mojeno (Bolivia), Atacama (Chile), Awa, Chachi, Tsachila (Ecuador), Wayuu, Pemon, Warao (Venezuela) [27] North America Alaska natives, Pacific islands American (United States), Nahua Mazahua, Otomi, Mixtecs (Mexico) Table 2: Tribal groups present in different continents of the world. Tribe/ Tribal Groups Table 2: Tribal groups present in different continents of the world. tribal areas of southern coastal Karnataka, reported a higher prevalence of HPV infection among tribal women (40.6%) than general population (14.3%) [31]. HPV infection with type 16 type was found in indigenous Nicobarese tribe, in Andaman and Nicobar Islands, with a prevalence of 2.3% [32]. In rural areas of West Bengal, a higher prevalence of risk factors related to cervical cancer was reported by Gupta et al, (2012). The prevalence of HPV 16 and 18 in rural areas of eastern India was found to be 7.5% and 9.6% respectively [33]. A study carried out by Sharma et al. (2015) in tribal areas of three Indian states: Madhya Pradesh, Jharkhand and Chhattisgarh reported 12.9% overall prevalence of HPV infection in tribal girls of these regions with more than 65% of them infected with HR-HPV types predominantly HPV16 indicating. The study reported a very high prevalence of HPV infection in adolescent and young adult tribal girls possibly due to different socio-sexual behavior, indicating a serious health Cervical cancer is one of the most common cancers in women in India especially in rural and tribal areas, where the HPV infection is increasing at an alarming rate. However, the HPV prevalence and incidence studies reported in rural and tribal populations of India are limited. In India, the initial reports of the incidence of cervical cancer were reported from the rural areas of Barshi in Maharashtra in 1987 [28]. Other rural areas affected in the state of Maharashtra included Paranda and Bhum Tahsils [28]. Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Long term use of oral contraceptives In 2007, rural areas of Ahmedabad and Gujrat were reported to be affected by cervical cancer. About 700 different cases were reported from Ratnagiri district in Mumbai in 2009. In the following years, several rural areas such as Sevagram, Konkan in Maharashtra reported the incidence of cervical cancer [29]. In Aizawl district of Mizoram, the prevalence of HPV virus was reported to be 15.94% and 11.08% in rural areas of Meghalaya [30]. A population-based study was conducted in the Mozambique are affected by high incidences of invasive cervical cancer and HPV appears to be more common among women with normal cytology than in more developed parts of the world, with a prevalence of 24 percent on average [39]. According to the WHO report, the rate of cervical cancer is found to be higher in Eswatini, followed by Malawi in-regions of sub-Saharan Africa [40]. It was due to the lack of technical, infrastructural, financial and human resources needed for the cytological screening of HPV and the method of Visual Inspection using acetic acid (VIA) used for cytological screening due to low income, resulting in higher HPV [41]. The main reason for this difference in incidence rates is the effective implementation of HPV screenings and vaccination programs by the developed countries compared to developing countries [42]. Table 3 lists the major studies carried out in the rural and tribal populations of the world. concern for Indian tribal women. Apart from India, cervical cancer is the second most common cancer after breast cancer to affect women aged 15–44 years in the European Union with 33 000 cases of cervical cancer and 15 000 deaths each year [34]. It is twice as high in Latin America compared with the worldwide average and is associated with 68,220 new cases of cervical cancer per year with incidence rates range from 20 to 80 per 100,000 women and 31,712 cervical cancer- associated deaths occur each year [35]. The incident rates of HPV in sub-Saharan region are very high, especially in Abuja, Nigeria, (with HPV prevalence of 37%), where the proportion of HPV positive women is same in all groups, from 10 years to 65 years of age (or more) [36,37]. The higher HPV rate was due to the high tobacco use, lack of cervical cancer screening, and unattended precancerous lesions [38]. Long term use of oral contraceptives The sub-Saharan Africa regions of Guinea, Zambia, Tanzania, Malawi, and Continents/ Countries Tribe/ Tribal Groups Prevalence Reference Southeast Asia Tibetan group, Hani women (China) 14% [43] South America Guarani (Argentina) 64% [44] Tanzania (Eastern-Africa) Mwanza 11.60% [45] Europe North Sami (sami group) (Finland) 21% [43,46] Latin America Alaska Native tribal women 16% [43,47] Table 3: Prevalence of HPV in different continents/ countries Table 3: Prevalence of HPV in different continents/ countries Table 3: Prevalence of HPV in different continents/ countries from various rural and urban registries [48]. This provides the map for designing and implementing screening and management programs effectively. Another committee that works on the cancer control is the Indian Academy of Pediatrics committee. Its purpose is to raise awareness, educate patients and parents on HPV infection and risk of cervical cancer and sensitizing pediatricians to play an active role in cervical cancer prevention program [49]. The three prophylactic vaccines: quadrivalent HPV vaccine, bivalent HPV vaccine, and the monovalent HPV Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Government and Non-Government initiatives The government of India has developed specific programs and initiatives to screen and manage the increasing rate of HPV infection among rural and tribal women in India to reduce the cervical cancer burden in this population. Indian Council of Medical Research (ICMR) established the National Cancer Registry program, which acts as a surveillance system for cancer and collects information about the cancer prevalence vaccines are available commercially are for the prevention of HPV infection against HPV genotypes 16,18,6 and 11 [50]. Gardasil, Gardasil 9, and Cervarix are used for the prevention of HPV infection from HPV genotypes 16 and 18. Apart from these HPV genotypes, Gardasil prevents infection caused by HPV 6 and 11, which is responsible for 90% of genital warts. Gardasil 9 prevents HPV 31,33,45,52, and 58 besides 6,11,16, and 18 [51,52]. In India, Gardasil was the first HPV vaccine approved for use in 2006 [53]. HPV vaccination is recommended for women from 9 to 26 years before the onset of any sexual activity [54]. However, these vaccines provide protection for only certain HPV types but not all [54]. Also, some side effects like pain, redness, or swelling in the arm where the shot was given and fever, dizziness, nausea, headache or feeling tired, muscle or joint pain have been reported after the vaccination. rticle be discovered only after the true implementation of these vaccines in India [57]. Some of the states in India have initiated HPV screening and vaccination programs. Delhi was the first state in India to launch free HPV vaccination as a part of the Public Health Program for girls of the age of 11-13 years at Delhi State Cancer Institute through its framework in the east and west regions of Delhi [58]. WHO has supported the Government of Punjab (Bhatinda) for HPV vaccination programme in 2016 [59]. In 2009, a vaccination trial for cervical cancer was conducted by Andhra Pradesh Minister for Health and Family Welfare in collaboration with ICMR and PATH, a non-profit organization in the USA in Khammam district. A similar project was also launched by the Gujrat government in Vadodara district. Most of the vaccinated girls belonged to the tribal communities whose parents were agricultural laborers [60]. However, this trial was suspended by the state governments when six deaths of young girls were reported in the weeks following the vaccination. Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Government and Non-Government initiatives It was later discovered that the reason for their death was due to other factors unrelated to the HPV vaccine, such as poisoning, drowning, malaria, or snakebite [55]. Various non-governmental organizations (NGOs) like Biocon Foundation and SAMA work to spread awareness about HPV infection and its vaccination. Biocon Foundation provides Pap smears tests to economically poor communities in India and it conducted its first test in Karnataka in 2016. Since then, it has been successful in screening more than 3000 women in India [55]. SAMA is a research group that works for the health and welfare of women. In 2010, SAMA reported the side In India, the National Technical Advisory Group on Immunization recommended the HPV vaccine for young women to be included in the National Immunization Program [55] to ensure easy access and affordability for the economically and socially deprived sections of the society. However, factors like high vaccine costs, duration of vaccine use, vaccine acceptance, and disease prioritization have prevented the vaccine to become a part of the National Immunization Program [56]. For a mass HPV vaccination program, affordability and accessibility are of major concern and for region-specific issues; a cost-effective second- generation vaccine may be needed [17]. WHO recommends that HPV vaccination must be included in the National Immunization Program and the operational difficulties can vaccination as soon as enter seventh grade of their school [65]. effects of the HPV vaccine given to young girls, which included cramps, heavy bleeding, and early onset of menstruation [53]. The Government schemes and initiative can have both positive and negative impact on people worldwide. The prophylactic vaccines for HPV have met with mixed acceptance globally. However, policy-level interventions have been effective in increasing public health benefit. Government policies and mandates may result in improved HPV vaccination coverage and reduced disease burden and alternative policies that improve unhindered access to HPV vaccination may allow success as well [65]. The HPV vaccines have been licensed almost in all the countries across the globe. More than 80 countries have introduced HPV vaccine in the National Immunization Programs. In most programs, a school-based approach is used to deliver the vaccine to the targeted adolescents with additional efforts using field clinics, and primary health centers to cover girls who missed vaccination and do not attend schools [59,66]. Government and Non-Government initiatives To encourage the research into HPV, the National Institutes of Health, USA and National Cancer Institutes, UK provides grants and funds to enhance the healthcare delivery system and studies its characteristics [8]. Many countries across the world have introduced HPV vaccination in their National Immunization Program, including Australia, Canada, USA, and various other European countries [61]. In 2007, Australia commenced the National HPV vaccination program and National HPV vaccination Register (NHPVR) that delivers HPV vaccine to young girls and monitors and reports the coverage of HPV vaccine [62]. Along with it, the National Cervical Screening Program was also introduced by the Australian government to review cervical screening in different areas [63]. In European countries, the Council of the European Union recommends that the screening programs for cervical cancer are implemented using a systematic population- based approach with quality assurance at all appropriate levels and the test to be used should be the pap test with age groups not less than 20 and not more than 30 [64]. In the United States, the Advisory Committee on Immunization Practices recommends that all the young girls (between age groups of 11-12) should receive the HPV vaccine [61]. Following this, the Cervical Cancer Prevention Act was also introduced which proposed that girls should be given HPV Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 References 1. Basaninyenzi U. Indigenous people. The World Bank. 2021. 1. Basaninyenzi U. Indigenous people. The World Bank. 2021. 3. Area and population-Statistical yearbook 2018. Ministry of Statistics and Programme Implementation, Gov India. 2019. 4. Census of India. Rural and Urban population distribution. Gov India. 2011. 4. Census of India. Rural and Urban population distribution. Gov India. 2011. 4. Census of India. Rural and Urban population distribution. Gov India. 2011. 5. Statistical Profile of Scheduled Tribes in India. Ministry of Tribal affairs statist 6. Ferlay J, Colombet M, Soerjomataram I, Mathers C, Parkin DM, Piñeros M, et al. Estimating the global cancer incidence and mortality in 2018: GLOBOCAN sources and methods. Int J Cancer. 2019;144(8):1941-53. PubMed | CrossRef 6. Ferlay J, Colombet M, Soerjomataram I, Mathers C, Parkin DM, Piñeros M, et al. Estimating the global cancer incidence and mortality in 2018: GLOBOCAN sources and methods. Int J Cancer. 2019;144(8):1941-53. PubMed | CrossRef 7. Sabeena S, Bhat PV, Kamath V, Arunkumar G. Global human papilloma virus vaccine implementation: An update. J Obstet Gynaecol Res. 2018;44(6):989-97. PubMed | CrossRef 7. Sabeena S, Bhat PV, Kamath V, Arunkumar G. Global human papilloma virus vaccine implementation: An update. J Obstet Gynaecol Res. 2018;44(6):989-97. PubMed | CrossRef 8. American Cancer Society, Risk Factors for Cervical Cancer. 2020. 9. Travasso C. Prevalence of HPV is high among Indian tribal girls and young women, study finds. BMJ. 2015;350. PubMed | CrossRef 9. Travasso C. Prevalence of HPV is high among Indian tribal girls and young women, study finds. BMJ. 2015;350. PubMed | CrossRef 10. Sharma K, Kathait A, Jain A, Kujur K, Raghuwanshi S, Bharti AC, et al. Higher prevalence of human papillomavirus infection in adolescent and young adult girls belonging to different Indian tribes with varied socio-sexual lifestyle. PLoS One. 2015;10(5). PubMed | CrossRef 10. Sharma K, Kathait A, Jain A, Kujur K, Raghuwanshi S, Bharti AC, et al. Higher prevalence of human papillomavirus infection in adolescent and young adult girls belonging to different Indian tribes with varied socio-sexual lifestyle. PLoS One. 2015;10(5). PubMed | CrossRef 11. Mabelele MM, Materu J, Ng’ida FD, Mahande MJ. Knowledge towards cervical cancer prevention and screening practices among women who attended reproductive and child health clinic at Magu district hospital, Lake Zone Tanzania: a cross-sectional study. BMC Cancer. 2018;18(1):1-8. PubMed | CrossRef 11. Mabelele MM, Materu J, Ng’ida FD, Mahande MJ. Conclusion The review highlights the status of HPV prevalence in rural and tribal areas of India and at global level. Most of the tribal populations of the world live in secluded and inaccessible areas and follow more open sexual relationships with women becoming sexually activity early, after menarche; and have multiple sexual partners and are multiparous. As these population groups are located in distant areas and are economically deprived, they have limited access to healthcare facilities and may follow different social norms and religious beliefs which is compounded by poverty, illiteracy, ignorance, hostile environment, poor sanitation, lack of safe drinking water, blind beliefs and prejudices particularly in developing and underdeveloped countries. As the economic and socio-cultural milieu of this population is different; the women are at an increased risk of HPV infection. In order to improve the health and reduce mortality in women in these rural and tribal areas, government organizations should adopt rigorous measures to create awareness and promote screening by setting up awareness workshops and screening camps about HPV infection and cervical cancer and the importance of maintaining good sexual health and hygiene. The government should develop policies to ensure the screening and vaccination of adolescent girls and young women in these areas and also improve the health care facilities in the rural and tribal areas of the country. The government organizations can support and work along with non-governmental organizations and NGOs to promote the awareness and help reduce cancer burden in rural and tribal women. 1. Basaninyenzi U. Indigenous people. The World Bank. 2021. | 4; ( ) | p J 4( ) 4 | Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 2. Census. New census data show differences between urban and rural populations. US Census Bureau. 2016. 3. Area and population-Statistical yearbook 2018. Ministry of Statistics and Programme Implementation, Gov India. 2019. References Knowledge towards cervical cancer prevention and screening practices among women who attended reproductive and child health clinic at Magu district hospital, Lake Zone Tanzania: a cross-sectional study. BMC Cancer. 2018;18(1):1-8. PubMed | CrossRef 12. Risk factors for Cervical Cancer. CCS. 2017. 13. Peedicayil A, Abraham P, Prasad J, Jeyaseelan L, Abraham S, Kurian S, et al. Community prevalence of human papillomavirus by self-collected samples in South India. Indian J Gynecol Oncol. 2016;14(1):1-5. CrossRef 13. Peedicayil A, Abraham P, Prasad J, Jeyaseelan L, Abraham S, Kurian S, et al. Community prevalence of human papillomavirus by self-collected samples in South India. Indian J Gynecol Oncol. 2016;14(1):1-5. CrossRef 14. De Sanjosé S, Diaz M, Castellsagué X, Clifford G, Bruni L, Muñoz N, et al. Worldwide prevalence and genotype distribution of cervical human papillomavirus DNA in women with normal cytology: a meta-analysis. Lancet Infect Dis. 2007;7(7):453-9. 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Indian J Med Paediatr Oncol. 2016;37(04):278-85. Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 References Akarolo-Anthony SN, Maso LD, Igbinoba F, Mbulaiteye SM, Adebamowo CA. Cancer burden among HIV- positive persons in Nigeria: preliminary findings from the Nigerian AIDS-cancer match study. Infect Agent Cancer. 2014;9(1):1-7. PubMed | CrossRef 37. Akarolo-Anthony SN, Maso LD, Igbinoba F, Mbulaiteye SM, Adebamowo CA. Cancer burden among HIV- positive persons in Nigeria: preliminary findings from the Nigerian AIDS-cancer match study. Infect Agent Cancer. 2014;9(1):1-7. PubMed | CrossRef | 38. Cancer of the cervix in the African Region, Regional Committee for Africa. WHO. 2011. 38. Cancer of the cervix in the African Region, Regional Committee for Africa. WHO. 2011. 39. De Vuyst H, Alemany L, Lacey C, Chibwesha CJ, Sahasrabuddhe V, Banura C, et al. The burden of human papillomavirus infections and related diseases in sub-saharan Africa. Vaccine. 2013;31:32-46. PubMed | CrossRef 40. Cervical Cancer. WHO. 2020. 39. De Vuyst H, Alemany L, Lacey C, Chibwesha CJ, Sahasrabuddhe V, Banura C, et al. The burden of human papillomavirus infections and related diseases in sub-saharan Africa. Vaccine. 2013;31:32-46. PubMed | CrossRef 40. Cervical Cancer. WHO. 2020. Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 41. Aina IO, Raul SM, Padilla LA, Mthethwa-Hleta S, Preko PO, Jolly PE. Sociodemographic factors, health seeking behaviors, reproductive history, and knowledge of cervical screening among women in Swaziland. Infect Agent Cancer. 2020;15(1):1-9. PubMed | CrossRef 42. Chan CK, Aimagambetova G, Ukybassova T, Kongrtay K, Azizan A. Human papillomavirus infection and cervical cancer: epidemiology, screening, and vaccination—review of current perspectives. J Oncol. 2019. PubMed | CrossRef 43. Baloch Z, Yue L, Yuan T, Feng Y, Tai W, Liu Y, et al. Status of human papillomavirus infection in the ethnic population in Yunnan Province, China. Biomed Res Int. 2015. PubMed | CrossRef 44. Tonon SA, Picconi MA, Zinovich JB, Nardari W, Mampaey M, Badano I, et al. Human papillomavirus cervical infection in Guarani Indians from the rainforest of Misiones, Argentina. Int J Infect Dis. 2004;8(1):13-9. PubMed | CrossRef 45. Houlihan CF, Baisley K, Bravo IG, Kapiga S, de Sanjosé S, Changalucha J, et al. The incidence of human papillomavirus in Tanzanian adolescent girls before reported sexual debut. J Adolesc Health. 2016;58(3):295-301. PubMed | CrossRef 46. References Soininen L, Järvinen S, Pukkala E. Cancer incidence among Sami in northern Finland, 1979–1998. Int J Cancer. 2002;100(3):342-6. PubMed | CrossRef 47. Schmidt-Grimminger DC, Bell MC, Muller CJ, Maher DM, Chauhan SC, Buchwald DS. HPV infection among rural American Indian women and urban white women in South Dakota: an HPV prevalence study. BMC Infect Dis. 2011;11(1):1-8. PubMed | CrossRef 48. Summary report on HPV and cervical cancer statistics in India. WHO. HPV Info Centre. 2007 49. Choudhury P. Preventing cervical cancer: pediatricians role. Indian Pediatr. 2009. PubMed 50. Wang R, Pan W, Jin L, Huang W, Li Y, Wu D, et al. Human papillomavirus vaccine against cervical cancer: Opportunity and challenge. Cancer Lett. 2020;471:88-102. PubMed | CrossRef 51. 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MMWR Morb Mortal Wkly Rep. 2019;19(11):3202-6. PubMed | CrossRef 55. Cousins S. A woman’s worth: health, stigma and discrimination in India. Sage Publications Pvt. L 55. Cousins S. A woman’s worth: health, stigma and discrimination in India. Sage Publications Pvt. Limited. 2020. 56. Chatterjee S, Chattopadhyay A, Samanta L. HPV and cervical cancer epidemiology-current status of HPV vaccination in India. Asian Pac J Cancer Prev. 2016;17(8):3663-73. PubMed 56. Chatterjee S, Chattopadhyay A, Samanta L. HPV and cervical cancer epidemiology-current s vaccination in India. Asian Pac J Cancer Prev. 2016;17(8):3663-73. PubMed 57. Rathi A, Singh SV. HPV Vaccine Scenario in India - A Short Report. Madridge J Vaccines. 2018;2(1):62-63. CrossRef 58. Mehrotra R, Hariprasad R, Rajaraman P, Mahajan V, Grover R, Kaur P, et al. | 4; ( ) | p J 4( ) 4 | Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article Rashid S | Volume 4; Issue 1 (2022) | Mapsci-JBAR-4(1)-024 | Review Article Citation: Choudhary C, Sharma K, Dar SA, Rashid S. Human Papillomavirus (HPV) Infection in Rural and Tribal Populations of the World with a Special Focus on the Prevalence in India. J Biomed Allied Res. 2022;4(1):1-12. DOI: https://doi.org/10.37191/Mapsci-2582-4937-4(1)-024 64. Stockholm, Guidance for the Introduction of HPV vaccines in EU countries. 2008. 63. Canfell K, Sitas F, Beral V. Cervical cancer in Australia and the United Kingdom: comparison of screening policy and uptake, and cancer incidence and mortality. Med J Aust. 2006;185(9):482-6. PubMed | CrossRef 65. Brandt HM, Pierce JY, Crary A. 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Associations of quality of life with physical activity, fruit and vegetable consumption, and physical inactivity in a free living, multiethnic population in Hawaii: a longitudinal study
˜The œinternational journal of behavioural nutrition and physical activity
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Chai et al. International Journal of Behavioral Nutrition and Physical Activity 2010, 7:83 http://www.ijbnpa.org/content/7/1/83 RESEARCH Open Access Associations of quality of life with physical activity, fruit and vegetable consumption, and physical inactivity in a free living, multiethnic population in Hawaii: a longitudinal study Weiwen Chai1*, Claudio R Nigg2, Ian S Pagano1, Robert W Motl3, Caroline Horwath4, Rod K Dishman5 Abstract Introduction: High intake of fruit and vegetables and being physically active are associated with reduced risk of chronic diseases. In the current study, we examined the associations of physical activity, fruit and vegetable consumption, and TV/video watching (indicator for physical inactivity) with perceived quality of life (QOL) in a sample of free living adults. Methods: A cohort (N = 139) from a random, multi-ethnic sample of 700 adults living in Hawaii was evaluated at 3-month intervals for the first year and 6-month intervals for the second year. QOL was assessed from self-reports of mental or physical health at the end of the study. Results: Overall, the cohort participants appeared to maintain relatively constant levels of physical activity, fruit and vegetable intake, and TV/video watching. Physical activity was positively related to mental health (p-values < 0.05), but not physical health, at all time points regardless of participants’ fruit and vegetable consumption and hours of TV/video watching. Neither mental nor physical health was associated with fruit and vegetable intake or TV/video watching. Conclusion: Our study supports that physical activity is positively associated with mental health. Fruit and vegetable consumption and TV/video watching may be too specific to represent an individual’s overall nutritional status and physical inactivity, respectively. Introduction High intake of fruit and vegetables and being physically active are associated with reduced risk of chronic diseases such as heart disease, diabetes, and cancers [1-5]. Despite interventions to increase physical activity in the general population, only 30% of US adults aged 18 years or older are sufficiently active during their leisure time according to recent surveys [6]. National campaigns such as 5-A-Day have increased awareness of the health benefits associated with fruit and vegetables; however, the increase in consumption of these foods * Correspondence: wchai@crch.hawaii.edu 1 Cancer Research Center of Hawaii, University of Hawaii, (1236 Lauhala Street), Honolulu, (HI 96813), USA Full list of author information is available at the end of the article has been relatively modest compared to the decrease in fat intake [7]. Quality of life (QOL), a conceptualization reflecting an individual’s physical and mental well-being, has emerged as an important consideration in disease treatment and prevention. Research on QOL and physical activity has predominantly focused on elderly populations or populations with chronic diseases such as cardiovascular diseases, arthritis, pulmonary diseases, and cancer [1]. Although evidence consistently suggests a positive association between physical activity and QOL in these populations [8,9], the relation may not be reproducible in younger, disease-free individuals. In comparison to the physical activity domain, fewer studies have assessed the impact of fruit and vegetable intake on QOL and © 2010 Chai et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Chai et al. International Journal of Behavioral Nutrition and Physical Activity 2010, 7:83 http://www.ijbnpa.org/content/7/1/83 most of them were also conducted in diseased populations [10-14]. Physical inactivity has drawn far less research attention than physical activity; nevertheless, its adverse health effects may be as important as the beneficial effects of physical activity. It was reported that TV watching, a commonly used indicator of inactivity was associated with obesity [15,16]. Understanding behavioral patterns involving nutrition, physical activity, and inactivity and how they influence QOL is essential to public health as positive outcomes would provide the general public with a motivation to adopt healthy lifestyles, thereby reducing risk and incidence of chronic diseases. In the current study, we examined the associations of fruit and vegetables consumption, physical activity, and inactivity with QOL in a sample of free living adults in Hawaii. Methods Participants and procedures This longitudinal, cohort study used a random sample of 700 adults (18 years or older) from Hawaii. A sub-sample of 139 (20%) participants who completed QOL survey at the end of the study was used for analysis (QOL cohort). The detailed procedure was described previously [17]. In brief, the questionnaire was programmed into a computer assisted telephone interview system and participants were recruited using random digit dialing procedures. A qualified individual whose birthday was closest to the date of the phone call was asked to participate. A total of 700 adults were recruited and informed consent was obtained from the participants. The University of Hawaii Institutional Review Board approved all study procedures. At baseline (T-1), 3month intervals (T-2, T-3, T-4, and T-5) for the first year and 6-month intervals (T -6 and T-7) for the second year, assessments (30-minute interviews) regarding participants’ physical activities and nutritional behaviors were performed. A survey of QOL was sent out at the end of the study (T-7); 139 (20%) participants completed the survey. Measures of physical activity Physical activity was assessed using the International Physical Activity Questionnaire (IPAQ) which records physical activity as hours and additional minutes of participation during the past 7 days in activities rated according to multiples of metabolic equivalents (METS). IPAQ assesses frequency and duration of walking (3.3 METS) and moderate (4.0 METS) and vigorous (8.0 METS) physical activity, appropriate for categorization of individuals as meeting public health guidelines for sufficient regular physical activity. The total weekly Page 2 of 6 physical activity levels, expressed as MET_hr/wk, were calculated as the sum of walking and moderate and vigorous physical activity for the week. The IPAQ has acceptable measurement properties for monitoring population levels of physical activity among 18- to 65year-old adults in diverse settings [18]. Measures of physical inactivity Physical inactivity/sedentary behavior was measured according to the amount of time (hours) each participant spent on watching TV/video on an average day as previously described [19]. Data suggest that TV/video watching far exceeds the time spent in any other leisure activity and represents the principal sedentary behavior in the United States [20]. Measures of fruit and vegetable intake The National Cancer Institute (NCI) Fruit and Vegetable screener was used in our study to assess the frequency and amount of consumption of 9 categories of fruits and vegetables (fruit, fruit juices, salad, beans, French fries, other potatoes, tomato sauce, vegetable soups, and other vegetables) over the previous month [21]. Computation of total daily servings of fruit and vegetables was described elsewhere [21]. This questionnaire provides estimated median daily servings of fruit and vegetables similar to those from 24-hour recalls [21]. Measures of QOL QOL was measured using a SF-12 Health Survey (SF12). The SF-12 is a multipurpose short-form with 12 questions, all selected from the SF-36 Health Survey [22]. Scale sores were estimated for four health concepts (physical functioning, role physical, role emotional, and mental health) using two items each, whereas the remaining four (bodily pain, general health, vitality, and social functioning) were represented by a single item. All 12 items were used to calculate the physical (PCS) and mental (MCS) component summary scores by applying a scoring algorithm empirically based on the data of a US general population survey [22,23]. SF-12 was chosen in the current study since overall physical and mental health were the key outcomes of interest. Statistical analysis Repeated-measures MIXED model was used to evaluate if physical activity, fruit and vegetable intake, or hours on TV/video watching were affected by time. Mean values at T-2, 3, 4, 5, 6 or 7 were compared to that at baseline (T-1). Partial correlation was used to assess the associations of QOL outcomes (MCS or PCS) with physical activity, fruit and vegetable consumption, or TV/video watching. Chai et al. International Journal of Behavioral Nutrition and Physical Activity 2010, 7:83 http://www.ijbnpa.org/content/7/1/83 The basic model and the full model adjusted for ethnicity, gender, age (continuous), body mass index (BMI; continuous), and education (continuous) were tested. The results were similar for both models (data not shown). We also used General Linear Model (GLM) to examine the interactions between physical activity, fruit and vegetable intake, and TV/video watching in relation to MCS or PCS. T-test was used to assess the differences in the above three behavioral variables between the total random sample and QOL cohort at baseline. In order to examine whether QOL outcomes were associated with certain behavioral patterns, we classified study participants into 9 profiles. The reason for this approach was to further explore the potential/suggestive associations which might not be detected by the above statistical analyses using continuous variables. The classification criteria were described as follow. A participant was classified as “average” if all his/her values (as means calculated from the 7 time points) for physical activity, fruit and vegetable intake, and TV/video watching were within 0.5 SD from the corresponding cohort means. The remaining categories (for “non-average” participants) were defined according to whether a participant’s value for a certain behavioral variable was greater than 0.5 SD above or less than 0.5 SD below the cohort mean (e.g., high for physical activity, > cohort mean for physical activity + 0.5 SD; high for fruit and vegetable intake, > cohort mean for fruit and vegetable intake + 0.5 SD; low for TV/video watching, Page 3 of 6 < cohort mean for TV/video watching - 0.5 SD). SAS software (SAS Institute, Cary, North Carolina) was used for all analyses. All tests were two sided, and P < 0.05 was considered statistically significant. Results Table 1 shows baseline characteristics for the total random sample and QOL cohort. Although QOL cohort participants were more likely to be older, females, and Caucasians and less likely to be Pacific Islanders compared to the total random sample, there were no significant differences in baseline physical activity levels, fruit/ vegetable consumption, and hours of TV/video watching between the two populations. It appeared that both populations had relatively high fruit and vegetable intakes at baseline (6.7 for QOL cohort and 7.4 for the total random sample). Overall, physical activity levels, fruit and vegetable intake, and hours of TV/video watching remained relatively constant over the 2-year experimental period. However, physical activity levels were significantly lower at T-3 and T-6 than that at baseline. Participants also had significantly lower fruit and vegetable intakes at T-4 and T-6 compared to baseline (Table 2). Increasing weekly physical activity levels was significantly associated with increasing MCS at all time points (T-1 to T-7; P-values < 0.05). There were no significant associations between MCS and daily fruit and vegetable Table 1 Selected baseline characteristics of the study participants Characteristics Age (y), mean (SD) BMI (kg/m2), mean (SD) Total random sample (N = 700) QOL cohort (N = 139) 47.0 (17.1) 25.9 (5.6) 55.3 (15.5) 24.7 (4.7) Education (y), mean (SD) 14.6 (2.8) 15.6 (2.9) Median household income ($) 40-50,000 40-50,000 Gender, n (%) Male 256 (36.6) 36 (25.9) Female 438 (62.6) 103 (74.1) Caucasian Pacific islanders 261 (37.3) 155 (22.1) 59 (42.4) 20 (14.4) Asian 218 (31.1) 43 (30.9) Other 60 (8.6) 15 (10.8) In excellent/very good/good/or fair health, n (%) 655 (95.0) 133 (95.7) Physical activity (MET_hr/wk), mean (SD) 67.5 (66.2) 63.0 (59.2) Fruit and vegetable (servings/d), mean (SD) 7.4 (6.5) 6.7 (4.2) P = 0.10* TV/video (hr/d), mean (SD) 2.5 (2.0) 2.3 (1.7) Ethnicity, n (%) P = 0.46* P = 0.18* Note. QOL = quality of life; BMI = body mass index; MET = metabolic equivalent. * T-test was performed to examine the differences between the total random sample and QOL cohort in weekly physical activity levels, daily fruit and vegetable consumption, and daily hours of TV/video watching at baseline. Chai et al. International Journal of Behavioral Nutrition and Physical Activity 2010, 7:83 http://www.ijbnpa.org/content/7/1/83 Page 4 of 6 Table 2 Levels of physical activity, fruit and vegetable intake, and TV/video watching for participants of QOL cohort (N = 139) at the 7 time points Time points Physical activity P* (MET_hr/wk) Baseline (T-1) 63.0 ± 4.7 3-month (T-2) 6-month (T-3) 55.6 ± 4.7 48.5 ± 4.8 Fruit and vegetable P* TV/video (serving/d) 6.7 ± 0.4 0.11 0.001 P* (hr/d) 2.3 ± 0.1 7.0 ± 0.4 6.7 ± 0.4 0.51 0.94 2.4 ± 0.1 2.2 ± 0.1 0.44 0.46 9-month (T-4) 58.5 ± 4.7 0.35 5.8 ± 0.4 0.04 2.3 ± 0.1 0.97 12-month (T-5) 56.0 ± 4.8 0.13 6.0 ± 0.4 0.12 2.3 ± 0.1 0.94 18-month (T-6) 54.0 ± 4.8 0.048 5.5 ± 0.4 0.01 2.3 ± 0.1 0.95 24-month (T-7) 61.9 ± 4.8 0.87 6.6 ± 0.4 0.79 2.2 ± 0.1 0.50 Note: Values are presented as mean ± SE; QOL = quality of life. MET = metabolic equivalent. * P value for difference between T-1 (baseline) and T-2, T-3, T-4, T-5, T-6, or T-7 from repeated-measures MIXED model. consumption. No significant associations were also observed between MCS and daily hours of TV/video watching except for T-3 and T-7, where an inverse association was observed. PCS was not associated with physical activity, fruit and vegetable intake, or hours of TV/ video watching (Table 3). There were no significant interactions between physical activity, fruit and vegetable consumption, and TV/video watching in relation to MCS or PCS (P-values > 0.05). The QOL outcomes for the 9 behavioral profiles were listed in Table 4. We did not perform statistical analyses due to small sample size for certain behavioral profiles. Consistent with our overall findings, participants who had average or above average physical activity levels were also characterized by higher MCS scores regardless of their status of fruit and vegetable consumption and/ or TV/video watching. Discussion Our results indicated that physical activity was predictive of positive mental health irrespective of participants’ other behaviors such as fruit and vegetable intake and TV/video watching. This observation is in agreement with other prospective studies that showed physically active adults had lower risk of mental distress than inactive adults when measures like the SF-12, including its parent measure, the SF-36, are used [1,24]. However, those studies did not uniformly adjust for diet or sedentary behaviors that might confound the association between perceived distress and physical activity [1,24]. The results are plausible given the large literature from prospective cohort studies and randomized controlled trials that regular physical activity is associated with reduced symptoms of depression and anxiety, which represent the main content areas of the mental health scale of the SF-12. Although limited, there is emerging evidence to support neurobiological mechanisms whereby physical activity can reduce feelings of Table 3 Correlations of physical activity, fruit and vegetable intake, and TV/video watching with QOL outcomes at the 7 time points* Time points MCS PCS r P r P Baseline Physical activity 0.21 0.02 0.01 0.96 (T-1) Fruit and Vegetable -0.02 0.81 -0.02 0.79 TV/video -0.00 0.99 0.02 0.82 3-month Physical activity 0.21 0.02 0.06 0.50 (T-2) Fruit and Vegetable TV/video 0.02 -0.14 0.84 0.14 0.03 0.04 0.75 0.66 6-month Physical activity 0.21 0.02 0.08 0.37 (T-3) Fruit and Vegetable 0.09 0.28 -0.07 0.42 TV/video -0.24 0.008 0.14 0.12 9-month Physical activity 0.25 0.006 0.09 0.30 (T-4) Fruit and Vegetable TV/video -0.06 -0.01 0.50 0.96 0.07 0.07 0.41 0.45 12-month Physical activity 0.21 0.02 0.04 0.70 (T-5) Fruit and Vegetable 0.13 0.14 -0.06 0.51 TV/video -0.02 0.87 -0.07 0.45 18-month Physical activity 0.24 0.009 0.12 0.21 (T-6) Fruit and Vegetable TV/video 0.12 -0.18 0.19 0.05 0.03 -0.06 0.71 0.49 24-month Physical activity 0.24 0.01 0.05 0.56 (T-7) Fruit and Vegetable 0.09 0.35 -0.04 0.65 TV/video -0.21 0.02 -0.06 0.55 Note. QOL = quality of life; MCS = mental component summary for SF.-12; PCS = physical component summary for SF-12; r = correlation coefficient * Partial correlations were performed and results were adjusted for ethnicity, gender, age, body mass index, and education. Chai et al. International Journal of Behavioral Nutrition and Physical Activity 2010, 7:83 http://www.ijbnpa.org/content/7/1/83 Page 5 of 6 Table 4 QOL outcomes for behavioral profiles Behavioral profiles* Behavioral parameters mean (SD) PA FV TV/video low low low 11 23.6 (8.8) 3.4 (1.0) 1.7 (0.8) 49.9 (9.1) 44.1 (10.4) low low low high high low 13 16 15.6 (8.4) 21.3 (9.1) 2.7 (0.9) 7.8 (2.0) 3.7 (1.7) 1.6 (0.7) 48.4 (11.0) 44.5 (11.8) 48.7 (10.6) 49.0 (10.3) low high high 14 23.3 (12.3) 7.1 (1.6) 3.7 (1.1) 48.7 (10.9) 45.6 (12.4) high high high 10 134.8 (57.2) 7.8 (2.8) 3.6 (0.8) 47.0 (9.3) 54.5 (6.7) high high low 32 92.6 (38.9) 8.6 (3.0) 1.3 (0.8) 48.3 (8.3) 53.7 (6.9) high low high 6 80.1 (56.0) 4.4 (0.5) 4.1 (0.5) 51.0 (4.3) 54.2 (7.1) high low low 3 44.9 (6.0) 3.0 (0.3) 0.6 (0.5) 46.9 (8.8) 54.6 (3.6) 34 54.6 (14.9) 5.8 (1.6) 2.0 (1.8) 50.4 (8.6) 51.9 (8.3) Average† N PA (MET_hr/wk) FA (serving/d) QOL measures mean (SD) TV/video (hr/d) PCS MCS Note. QOL = quality of life; PA = physical activity; FV = fruit and vegetable intake; PCS = physical component summary for SF-12; MCS = mental component summary for SF-12; MET = metabolic equivalent. * ‘high’ refers to the participant’s value for PA, FV or TV/video was greater than 0.5 SD above the cohort mean for the respective variables; ‘low’ refers to the participant’s value for PA, FV, or TV/video was less than 0.5 SD below the cohort mean for the respective variables. † Participants were classified as ‘average’ if their values for PA, FV, and TV/video were all within 0.5 SD from the corresponding cohort means. depression or anxiety by positive influences on the central nervous system [25,26] Alternatively, physical activity may also influence mental health through social interactions due to the mutual support and social relationships that are provided when engaging in physical activity with others. No associations were found between participants’ physical health and levels of physical activity. Previous research conducted in elderly or chronically diseased populations demonstrated strong evidence that exercise improved individuals’ physical conditions [1]. It is suggested that older adults and those with chronic diseases tend to have poorer physical health which creates challenges and requires specific needs concerning physical activity [1]. Consequently, results obtained from these populations may not be generalized to populations with different age and physical conditions. The mean participant age in our study was 55.3 ± 15.5 years. Approximately 96% reported that their health was excellent, very good, good, or fair. Thus, the lack of association observed in the current study could be partially attributed to our younger and healthier study population (essentially, a ceiling effect). In our study, neither physical nor mental health was associated with fruit and vegetable consumption. Similar to physical activity domain, previous studies demonstrating positive associations between nutrition and QOL were also predominately conducted in diseased populations. In our study, the average intakes of fruit and vegetables at each time point were high, all exceeding the currently recommended 5 servings/day. As a consequence, the ability to detect the potential associations may be limited due to the high intake (another ceiling effect). Furthermore, food and nutrition can affect people’s lives through many ways. Instead of focusing on individual dietary component, we need to consider the roles of other factors such as meal preparation, additional food groups, dinning environment, social interaction, and cultural aspects of food and diet. Overall, TV/video watching was not associated with mental or physical heath in the current study. The inverse association with MCS observed at T-3 and T-7 is intriguing and requires further investigation. It was suggested that depression and sedentary lifestyle have bidirectional relationships [27]. Another study by Patten et al. [28] showed that major depressive episodes were associated with an increased risk of transition from an active to an inactive pattern of activity. However, physical inactivity in the above studies was measured according to participant’s physical activity levels or daily energy expenditure instead of quantifying the time spent in sedentary behaviors such as TV/video watching. There were several limitations to the current study. First, although we used validated self-reported measures, objective indicators may provide more accurate evaluations of behaviors. Second, QOL was only assessed at the end of the study (T-7), resulting in a low response rate for the survey (20%). However, in light of the evidence that participants maintained relatively constant levels of the behavioral parameters and the key variables from QOL cohort were not considerably different from the entire sample, we presume that our findings would persist over the 2-year study period. Finally, we did not measure other sedentary behaviors such as work-related physical inactivity which could be relevant to QOL outcomes. In conclusion, the results from this longitudinal study indicated physical activity, superior to fruit and vegetable consumption and physical inactivity, is a main player Chai et al. International Journal of Behavioral Nutrition and Physical Activity 2010, 7:83 http://www.ijbnpa.org/content/7/1/83 influencing individual’s mental health. Our findings are novel and support future investigations in a larger study involving repeated measurements of QOL and multibehavioral frame work. Abbreviations QOL: Quality of life; SF-12: Short Form Health Survey; MCS: mental component summary for SF-12; PCS: physical component summary for SF12; MET: metabolic equivalent; SD: standard deviation; SE: standard error. Acknowledgements Financial support for this study was received from the National Cancer Institute Grant R01 CA109941 and R25 CA 90956. Author details 1 Cancer Research Center of Hawaii, University of Hawaii, (1236 Lauhala Street), Honolulu, (HI 96813), USA. 2Department of Public Health Studies, University of Hawaii, (1960 East West Road), Honolulu, (HI 96822), USA. 3 Department of Kinesiology and Community Health, University of Illinois Champaign Urbana, (906 S. Goodwin Ave), Champaign, (IL 61820), USA. 4 Department of Human Nutrition, University of Otago, (33 Union Street), Dunedin, New Zealand. 5Department of Kinesiology, University of Georgia, (330 River Road), Athens, (GA 30602), USA. Authors’ contributions All of the authors made substantial contributions to the study concept and design or analysis and interpretation of the data and have reviewed and approved the final manuscript for submission. Specifically, WC designed the analysis, analyzed the results, and was the primary author of every section of the text. ISP aided in the design of the analysis and performed much of the initial statistical analyses. CRN, RWM, CH, and RKD were instrumental in the design of the study, and commented on and approved the manuscript. Competing interests The authors declare that they have no competing interests. Received: 24 June 2010 Accepted: 22 November 2010 Published: 22 November 2010 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. References 1. Bize R, Johnson JA, Plotnikoff RC: Physical activity level and health-related quality of life in the general adult population: a systematic review. Prev Med 2007, 45:401-415. 2. Friedenreich CM, Orenstein MR: Physical activity and cancer prevention: etiologic evidence and biological mechanisms. J Nutr 2002, 132:3456S-3464S. 3. Harding AH, Wareham NJ, Bingham SA, Khaw K, Luben R, Welch A, Forouhi NG: Plasma vitamin C level, fruit and vegetable consumption, and the risk of new-onset type 2 diabetes mellitus: the European prospective investigation of cancer–Norfolk prospective study. Arch Intern Med 2008, 168:1493-1499. 4. Ness AR, Powles JW: Fruit and vegetables, and cardiovascular disease: a review. Int J Epidemiol 1997, 26:1-13. 5. Peto J: Cancer epidemiology in the last century and the next decade. Nature 2001, 411:390-395. 6. Barnes P: Physical activity among adults: United States, 2000 and 2005. Hyattsville, MD: US Department of Heath and Human Services, CDC; 2007. 7. Greene GW, Rossi SR: Stages of change for reducing dietary fat intake over 18 months. J Am Diet Assoc 1998, 98:529-534, quiz 535-526. 8. 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Vallis M, Ruggiero L, Greene G, Jones H, Zinman B, Rossi S, Edwards L, Rossi JS, Prochaska JO: Stages of change for healthy eating in diabetes: relation to demographic, eating-related, health care utilization, and psychosocial factors. Diabetes Care 2003, 26:1468-1474. Corle DK, Sharbaugh C, Mateski DJ, Coyne T, Paskett ED, Cahill J, Daston C, Lanza E, Schatzkin A: Self-rated quality of life measures: effect of change to a low-fat, high-fiber, fruit and vegetable enriched diet. Ann Behav Med 2001, 23:198-207. Andersen RE, Crespo CJ, Bartlett SJ, Cheskin LJ, Pratt M: Relationship of physical activity and television watching with body weight and level of fatness among children: results from the Third National Health and Nutrition Examination Survey. JAMA 1998, 279:938-942. Salmon J, Bauman A, Crawford D, Timperio A, Owen N: The association between television viewing and overweight among Australian adults participating in varying levels of leisure-time physical activity. Int J Obes Relat Metab Disord 2000, 24:600-606. Dishman RK, Thom NJ, Rooks CR, Motl RW, Horwath C, Nigg CR: Failure of post-action stages of the transtheoretical model to predict change in regular physical activity: a multiethnic cohort study. Ann Behav Med 2009, 37:280-293. Craig CL, Marshall AL, Sjostrom M, Bauman AE, Booth ML, Ainsworth BE, Pratt M, Ekelund U, Yngve A, Sallis JF, Oja P: International physical activity questionnaire: 12-country reliability and validity. Med Sci Sports Exerc 2003, 35:1381-1395. Buckworth J, Nigg C: Physical activity, exercise, and sedentary behavior in college students. J Am Coll Health 2004, 53:28-34. Dietz WH: The role of lifestyle in health: the epidemiology and consequences of inactivity. Proc Nutr Soc 1996, 55:829-840. Thompson FE, Subar AF, Smith AF, Midthune D, Radimer KL, Kahle LL, Kipnis V: Fruit and vegetable assessment: performance of 2 new short instruments and a food frequency questionnaire. J Am Diet Assoc 2002, 102:1764-1772. Ware JE, Kosinski M: User’s manual for the SF-12v2™ Health Survey. 2007. Kontodimopoulos N, Pappa E, Niakas D, Tountas Y: Validity of SF-12 summary scores in a Greek general population. Health Qual Life Outcomes 2007, 5:55. Martin CK, Church TS, Thompson AM, Earnest CP, Blair SN: Exercise dose and quality of life: a randomized controlled trial. Arch Intern Med 2009, 169:269-278. Physical Activity Guidelines Advisory Committee: Physical Activity Guidelines Advisory Committee Report, 2008. Washington, D.C.: U.S. Department of Health and Human Services, 2008; 2008. Dishman RK, O’Connor PJ: Lessons in exercise neuroloogy: The case of endorphins. Mental Health and Physical Activity 2009, 2:4-9. Roshanaei-Moghaddam B, Katon WJ, Russo J: The longitudinal effects of depression on physical activity. Gen Hosp Psychiatry 2009, 31:306-315. Patten SB, Williams JV, Lavorato DH, Eliasziw M: A longitudinal community study of major depression and physical activity. Gen Hosp Psychiatry 2009, 31:571-575. doi:10.1186/1479-5868-7-83 Cite this article as: Chai et al.: Associations of quality of life with physical activity, fruit and vegetable consumption, and physical inactivity in a free living, multiethnic population in Hawaii: a longitudinal study. International Journal of Behavioral Nutrition and Physical Activity 2010 7:83.
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Highly individual- and tissue-specific expression of glycoprotein group A and B blood antigens in the human kidney and liver
BMC immunology
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© The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. The Creative Commons Public Domain Dedication waiver (http://​creat​iveco​ mmons.​org/​publi​cdoma​in/​zero/1.​0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Open Access Abstract Background:  Currently, research on the quantitative distribution of ABO antigens in different organs and tissues remains limited. We aimed to examine the individual characteristics of blood group glycoprotein A and B antigen expression in human kidneys and livers. Methods:  We obtained human samples, including the renal artery, renal vein, renal tissue, hepatic artery, hepatic vein, portal vein, and hepatic tissue, from 24 deceased organ transplant donors. The expression of the blood group antigens glycoprotein A and B was analysed and compared by Western blotting. Results:  There was no significant difference in the expression between blood group glycoprotein A and B antigens at any of the seven sites (p > 0.05). The expression of both A and B antigens was highest in renal tissue and the portal vein and was lowest in the renal artery. A large difference in glycoprotein antigen expression was observed among various donors or different regions of the same individual. Univariate analysis revealed that glycoprotein A/B antigens were affected by the age and sex of donors and were significantly higher in males and in young people. Conclusions:  Our study found that blood group glycoprotein antigen expression showed certain trends and distinct distribution in the kidney, liver, and vessels among individuals and in different regions of the same individual, which may explain the different clinical outcomes of patients who received ABO-incompatible transplantation. rds:  ABO incompatible transplantation, Blood group antigen, Kidney, Liver, Western blot Keywords:  ABO incompatible transplantation, Blood group antigen, Kidney, Liver, W complement activation [1]. Thus, pre-existing anti-donor ABO antibodies in recipient blood must be removed before ABOi transplantation, and antibody rebound must be prevented after transplantation [2, 3]. Currently, clini- cal preconditioning protocols exclusively consider the anti-donor ABO antibody titre, which must be reduced to the “safe” range (e.g., ≤ 1:16 in most transplant cen- tres) on the transplant day [4–6]. Performing organ transplantation in ABO-incompatible cases continues to pose a significant challenge [7]. Even when the ABO anti- body titre was “safe” on the day of transplantation, some ABOi recipients still experienced AMR or even hyper- acute rejection [8, 9]. In contrast, some ABOi allografts Highly individual‑ and tissue‑specific expression of glycoprotein group A and B blood antigens in the human kidney and liver Xianding Wang1,2†, Fan Zhang4†, Yamei Jiang3†, Zilin Xu4, Xiaobing Feng1,2, Linde Li1,2, Yu Fan1,2, Turun Song1,2, Yunying Shi5, Zhongli Huang1,2 and Tao Lin1,2* Introductionh The transplantation of ABO-incompatible (ABOi) donor allografts into recipients with naturally occurring anti- A or B antibodies may sometimes result in antibody- mediated rejection (AMR); this process is initiated by antibodies binding to A or B antigens present on the vascular endothelium within the graft and subsequent *Correspondence: kidney1234@163.com †Xianding Wang, Fan Zhang are co-first authors 1 Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Number 37, Guoxue Alley, Chengdu 610041, Sichuan, China Wang et al. BMC Immunol (2021) 22:66 https://doi.org/10.1186/s12865-021-00456-2 Wang et al. BMC Immunol (2021) 22:66 https://doi.org/10.1186/s12865-021-00456-2 *Correspondence: kidney1234@163.com †Xianding Wang, Fan Zhang are co-first authors 1 Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Number 37, Guoxue Alley, Chengdu 610041, Sichuan, China Full list of author information is available at the end of the article For blood groups that were positive for antigen A, namely, groups A and AB, further tests were performed with anti-A1 lectin to determine the subtype of the blood A antigen (A1 or A2). survived without AMR when the posttransplant ABO antibody titre gradually increased to the preoperative level [10, 11]. It is unclear why these two contrasting events occur. To date, most studies have focused on the anti-donor ABO antibody titre of recipients, and very little is known about the influence of the donor expression pattern of A/B antigens on posttransplant AMR incidence. It is hypothesized that, in addition to ABO antibodies, the onset and absence of AMR in these ABOi recipients may also be attributed to the individual pattern of distribution, subtype, and levels of ABO blood group antigens within the allograft. Several previous studies have described the expression pattern of organ- surface A/B antigens. On the vascular endothelial cells of the human heart, only type II A/B antigens were expressed, and type III/IV structures were not detected. Conversely, in children who received ABOi heart transplants, ABO antibodies specific for type II antigens—the only A/B antigen subtypes expressed in heart tissue—were absent, demonstrating the high speci- ficity of B cell tolerance to donor blood group antigens [12–14]. In the human renal vascular bed, a previous study reported that there were three different A antigen expression patterns (major, minor, and minimal staining distribution), while all kidneys showed a B antigen pat- tern that was similar to the major pattern of A antigen but was slightly weaker [15]. These expression profiles have important implications that should be considered in clinical settings of ABOi transplantation. Eligibility criteria Th li ibili The eligibility criteria for deceased donors were as fol- lows: (1) written consent obtained from the next of kin, (2) 18–65  years old, (3) ABO blood group, (4) organ donation after cardiac or brain death, (5) normal terminal serum creatinine [< 110  µmol/l (female) or < 140  µmol/l (male)], (6) normal terminal serum alanine aminotrans- ferase [< 40  IU/L (female) or < 50  IU/L (male)], and (7) the donated kidneys and livers were used for subsequent ABO-compatible organ transplantation and had normal graft function. Exclusion criteria included (1) acute kidney or liver injury before donation, (2) a medical history of chronic kidney disease or hepatitis B or C virus infection, (3) active infection needing antibiotic treatment, and (4) renal or liver parenchyma damage or lithiasis revealed by ultrasound. However, these previous studies are limited because A/B antigen quantification was performed with only immunohistochemistry (IHC), which may be particu- larly difficult to interpret. A/B antigens are expressed in tissues as portions of glycolipids and glycoproteins. Highly individual- and tissue-specific expression of gly- colipid group A and B blood antigens was found in previ- ous studies [16], but no studies have used Western blot analysis to quantify glycoprotein A/B antigens; previ- ous studies used tissue samples in which red blood cells (RBCs) were present at high levels, making it impossible to distinguish between erythrocytic and tissue sources of ABO blood group antigen expression with Western blot- ting. Thus, the purpose of this study was to evaluate the hypothesis that the quantitative glycoprotein A/B antigen expression in RBC-free human kidneys and livers (the two most common organs used for ABOi transplanta- tion) varies greatly among individuals as well as among different sites in an individual based on Western blotting. © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. The Creative Commons Public Domain Dedication waiver (http://​creat​iveco​ mmons.​org/​publi​cdoma​in/​zero/1.​0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Wang et al. BMC Immunol (2021) 22:66 Page 2 of 9 (No. 2019SHEN282). All organ donation cases were con- ducted according to the protocols for China Categories I, II, and III donors [17]. All kidney [renal artery, renal vein, renal tissue (by a 14-gauge BARD MAX-CORE disposable core biopsy instrument)] and liver [hepatic artery, hepatic vein, portal vein, hepatic tissue (by wedge resection)] samples were obtained from deceased organ transplant donors. The donor kidney and liver were per- fused before and immediately after being removed surgi- cally (to remove residual red blood cells) and preserved in an RBC-free histidine-tryptophan-ketoglutarate solu- tion. For blood groups that were positive for antigen A, namely, groups A and AB, further tests were performed with anti-A1 lectin to determine the subtype of the blood A antigen (A1 or A2). (No. 2019SHEN282). All organ donation cases were con- ducted according to the protocols for China Categories I, II, and III donors [17]. All kidney [renal artery, renal vein, renal tissue (by a 14-gauge BARD MAX-CORE disposable core biopsy instrument)] and liver [hepatic artery, hepatic vein, portal vein, hepatic tissue (by wedge resection)] samples were obtained from deceased organ transplant donors. The donor kidney and liver were per- fused before and immediately after being removed surgi- cally (to remove residual red blood cells) and preserved in an RBC-free histidine-tryptophan-ketoglutarate solu- tion. Western blot analysis Total protein was extracted from tissue samples, the tis- sues were homogenized, and centrifuged at 4  °C. The supernatants were used for Western blot assays. Proteins were separated by 10% SDS-PAGE and then transferred onto PVDF membranes (Amersham, GE Healthcare, Chicago, IL). After being blocked with 5% nonfat milk, membranes were incubated with an anti-blood group A antibody (1:1000, BIOSCOT, Merck Millipore) at 4  °C overnight, with a mouse monoclonal anti-β-actin anti- body (1:10,000, ab8245) used as the internal reference, followed by a subsequent incubation with a goat anti- rabbit secondary antibody (1:8000, Santa Cruz Biotech- nology, Santa Cruz, CA, USA). The visualization of the protein bands was performed with enhanced chemilu- minescence kits (Santa Cruz Biotechnology). The band intensity was quantified using Image Lab 6.0.1 Software (Bio-Rad Laboratories, Inc). The relative expression of blood group antibodies is represented by the ratio of the Tissue samplesh This study protocol was reviewed and approved by the Biomedical Ethics Committee, West China Hospital Wang et al. BMC Immunol (2021) 22:66 Wang et al. BMC Immunol (2021) 22:66 Page 3 of 9 Table 1  Clinical parameters of included deceased organ transplant donors BMI Body Mass Index Feature N = 24 Blood type [n (%)] A 13 (54.2%) B 6 (25%) AB 2 (8.3%) O 3 (12.5%) Gender [n (%)] Male 15 (62.5%) Female 9 (37.5%) Age (years) [mean ± sd] 50.29 ± 12.32 Height (meters) [mean ± sd] 1.64 ± 0.08 Weight (kilograms) [mean ± sd] 62.67 ± 12.76 BMI (kg/m2) [mean ± sd] 23.04 ± 4.00 Cause of death [n (%)] Head trauma 13 (54.2%) Stroke 10 (41.7%) Central nervous system tumor 1 (4.2%) band intensity between the experimental band and inter- nal reference. band intensity between the experimental band and inter- nal reference. H&E and immunohistochemical staining Specimens from human kidneys and livers were fixed in formalin and embedded in paraffin. For H&E stain- ing, 4-µm slices were stained with H&E for histologi- cal examination. For immunohistochemistry of blood group A antigens, samples were rehydrated, washed with TBS, and blocked with TBS containing 10% FCS and 1% BSA, followed by incubation for 16 h in TBS containing 1% BSA and primary antibodies for blood group A or B antigens. Tissue sections were washed twice with TBS, and then HRP-conjugated anti-IgG secondary antibod- ies were added to TBS. After washing twice, sections were counterstained with Mayer’s haematoxylin, and images were analysed with a Nikon eclipse 90i digital microscope. Statistical analysis Experimental data are presented as the mean ± stand- ard deviation (sd) or median (range). Mean values of the groups with normally distributed data were compared using Student’s t-tests or ANOVA, whereas Wilcoxon rank-sum tests and Friedman M tests were used for com- parisons of non-normally distributed data. All statistical analyses were conducted using R (version 3.4.4), and a P-value below 0.05 was considered significant. in the hepatic artery, 0.64 ± 0.53 in the hepatic vein, 0.71 ± 0.61 in the renal vein, 1.16 ± 0.90 in renal tissue, and 1.56 ± 1.23 in the portal vein, in increasing order. The mean intensities of B antigen among the 6 type B donors and 2 type AB donors were 0.43 ± 0.36 in the renal artery, 0.61 ± 0.44 in hepatic tissue, 1.06 ± 0.78 in the renal vein, 1.10 ± 0.98 in the hepatic artery, 1.89 ± 1.10 in the por- tal vein, 2.87 ± 3.20 in the hepatic vein, and 3.20 ± 2.92 in renal tissue, in increasing order. There was a 6.24-fold difference in the mean glycoprotein A antigen intensity between the lowest- and highest-intensity sites and a corresponding 7.44-fold difference in the glycoprotein B antigen intensity.f Results h In this study, we obtained 168 tissue samples from 24 deceased organ donors, including 13 (54.2%) donors in group A, 2 (8.3%) donors in group AB, 6 (25%) donors in group B, and 3 (12.5%) donors in group O; there were 15 (62.5%) males and 9 (37.5%) females, with a mean age of 50.29 ± 12.32 years (Table 1). All the donors in groups A and AB belonged to the A1 subtype. The mean height was 1.64 ± 0.08 m, and the mean weight was 62.67 ± 12.76 kg, with a mean body mass index (BMI) of 23.04 ± 4.00 kg/ m2. The deceased donors died of a variety of causes: head trauma (n = 13, 54.2%), stroke (n = 10, 41.7%), and central nervous system tumours (n = 1, 4.2%). Much wider individual differences in blood group anti- gen intensities were observed at the same site of various donors as well as at different sites of the same donor. The Friedman M test was then used and indicated that there were differences in the distribution among the seven sites of the glycoprotein A antigen group (p < 0.001), but there was not a significant difference in the glycoprotein B antigen group (p = 0.544). Individual differences were significantly different in both the glycoprotein A antigen group (p = 0.004) and B antigen group (p = 0.002). The fold difference between the highest and lowest A antigen intensities at the same site among the 13 type A donors and 2 type AB donors was 98 (0.98/0.01) in the renal artery, 213 (2.13/0.01) in the renal vein, 54.2 (3.25/0.06) in renal tissue, 81.5 (1.63/0.02) in the hepatic artery, 10.2 (1.53/0.06) in the hepatic vein, 11.4 (5.00/0.44) in the portal vein, and 10.2 (0.51/0.05) in hepatic tissue. The To eliminate false-positive errors, specimens from blood group O were incubated with anti-blood group A and B antibodies, and A/B antigens were not detected in type O organs. In addition, B antigen expression was not detected in blood group A specimens, and vice versa.h To eliminate false-positive errors, specimens from blood group O were incubated with anti-blood group A and B antibodies, and A/B antigens were not detected in type O organs. In addition, B antigen expression was not detected in blood group A specimens, and vice versa. The glycoprotein A and B antigen intensities at the seven sites are displayed in Fig. 1. Results h Western blot analysis of blood group antigens from partial samples is shown in Fig. 2. The mean intensities of A antigen among the 13 type A donors and 2 type AB donors were 0.25 ± 0.30 in the renal artery, 0.25 ± 0.17 in hepatic tissue, 0.52 ± 0.50 The glycoprotein A and B antigen intensities at the seven sites are displayed in Fig. 1. Western blot analysis of blood group antigens from partial samples is shown in Fig. 2. The mean intensities of A antigen among the 13 type A donors and 2 type AB donors were 0.25 ± 0.30 in the renal artery, 0.25 ± 0.17 in hepatic tissue, 0.52 ± 0.50 Wang et al. BMC Immunol (2021) 22:66 Page 4 of 9 fold difference between the highest and lowest B antigen intensities at the same site among the 6 type B donors and 2 type AB donors was 56.5 (1.13/0.02) in the renal artery, 36.2 (2.17/0.06) in the renal vein, 63.3 (8.23/0.13) ( ) median fold difference between the highest and lowest A antigen intensity at various sites in the same donor was 11.9 (range 4.15–317), while the median fold difference between the highest and lowest B antigen intensity at var- ( ) Fig. 1  Western blot results showing the relative expression of blood group A and B antigens in different tissues. The tissue samples included 88 samples from 15 blood group A donors and 49 samples from 8 blood group B donors. Research data are presented as the mean ± standard deviation. PV: portal vein, RA: renal artery; RV: renal vein; HA: hepatic artery; HV: hepatic vein; Renal: kidney tissue; Hepatica: liver tissue Fig. 2  Western blot analysis of blood group antigens from two antigen A donors and two antigen B donors. PV: portal vein; RA: renal artery; RV: renal vein; HA: hepatic artery; HV: hepatic vein; RE: kidney tissue; HE: liver tissue Fig. 1  Western blot results showing the relative expression of blood group A and B antigens in different tissues. The tissue samples included 88 samples from 15 blood group A donors and 49 samples from 8 blood group B donors. Research data are presented as the mean ± standard deviation. PV: portal vein, RA: renal artery; RV: renal vein; HA: hepatic artery; HV: hepatic vein; Renal: kidney tissue; Hepatica: liver tissue Fig. Results h 1  Western blot results showing the relative expression of blood group A and B antigens in different tissues. The tissue samples included 88 samples from 15 blood group A donors and 49 samples from 8 blood group B donors. Research data are presented as the mean ± standard deviation. PV: portal vein, RA: renal artery; RV: renal vein; HA: hepatic artery; HV: hepatic vein; Renal: kidney tissue; Hepatica: liver tissue Fig. 2  Western blot analysis of blood group antigens from two antigen A donors and two antigen B donors. PV: portal vein; RA: renal artery; RV: renal vein; HA: hepatic artery; HV: hepatic vein; RE: kidney tissue; HE: liver tissue Fig. 2  Western blot analysis of blood group antigens from two antigen A donors and two antigen B donors. PV: portal vein; RA: renal artery; RV: renal vein; HA: hepatic artery; HV: hepatic vein; RE: kidney tissue; HE: liver tissue Fig. 2  Western blot analysis of blood group antigens from two antigen A donors and two antigen B donors. PV: portal vein; RA: renal artery; RV: renal vein; HA: hepatic artery; HV: hepatic vein; RE: kidney tissue; HE: liver tissue median fold difference between the highest and lowest A antigen intensity at various sites in the same donor was 11.9 (range 4.15–317), while the median fold difference between the highest and lowest B antigen intensity at var- ious sites in the same donor was 20.1 (range 4.03–70.75). Univariate analysis revealed that blood group glyco- protein antigen expression in males was significantly fold difference between the highest and lowest B antigen intensities at the same site among the 6 type B donors and 2 type AB donors was 56.5 (1.13/0.02) in the renal artery, 36.2 (2.17/0.06) in the renal vein, 63.3 (8.23/0.13) in renal tissue, 21.7 (2.82/0.13) in the hepatic artery, 48.9 (10.26/0.21) in the hepatic vein, 9.88 (3.26/0.33) in the portal vein, and 8.7 (1.31/0.15) in hepatic tissue. The median fold difference between the highest and lowest A antigen intensity at various sites in the same donor was 11.9 (range 4.15–317), while the median fold difference between the highest and lowest B antigen intensity at var- ious sites in the same donor was 20.1 (range 4.03–70.75). g Univariate analysis revealed that blood group glyco- protein antigen expression in males was significantly Wang et al. BMC Immunol (2021) 22:66 Page 5 of 9 express A antigens on their RBCs. Results h Similarly, blood group B individuals express B antigens, group O individuals express neither A nor B antigens, and group AB individu- als express both [19]. In addition to RBCs, ABO blood group antigens are also distributed on lymphocytes, platelets, and most epithelial and endothelial cells. The targets of blood group antibodies in ABOi transplanta- tion are endothelial cells, but the antigen expression pat- terns of endothelial cells are not faithfully modelled by RBCs. Currently, there is little known about the endothe- lial expression of blood group antigens in human organs. Vascularized allografts are the targets of blood group antibodies, which, upon binding to endothelial cell sur- faces, activate the complement system, which in turn mediates AMR [20].hi higher than that in females (p = 0.048) in both the A and B groups (Table  2). Furthermore, we found that glyco- protein antigen expression was higher in young people (p = 0.038). No association was observed between anti- gen expression intensity and the BMI or transfusion his- tory of the donor (Table 2). In all IHC sections, blood group antigen is shown in red, and nuclei are represented in blue. The intensity and distribution of the A antigen showed distinctly different patterns in different tissues (Fig. 3). The renal tissue was most strongly stained, and positivity was mainly found in the glomerular and tubular capillaries. In the renal artery and renal vein, the immunostaining was relatively weaker, which was most obvious in the renal artery. In the renal vein, portal vein, hepatic artery, and hepatic vein, positive staining was mainly seen in the vascular bed, where the endothelium was stained, whereas in liver tissue, positive staining was mainly found in the venae centrales hepatis and hepatic sinusoid. The intensity and distribution of blood group antigens showed distinctly different patterns in different tissues in both WB and IHC results. The amount of antigen displayed on a specific organ may be of particular importance in ABOi transplan- tation. Gehrie et  al. performed IHC staining of blood group A antigen in tissue blocks of 18 blood type A cadaveric hearts obtained at autopsy [12]. Light micro- scopic examination found that the endothelium stained with a low intensity in 4 (22%) myocardial samples, an intermediate intensity in 5 (28%) samples, and a high intensity in 9 (50%) samples. PV portal vein; RA renal artery; RV renal vein; HA hepatic artery; HV hepatic vein; RE kidney tissue; HE liver tissue Results h The digital analysis of IHC staining intensity and percentage of the total surface area of immunoreactivity revealed a 20-fold difference between the lowest and highest expressing specimens, and immunoreactivity was positively associated with Patients were grouped and then compared by male/female, transfusion history/no transfusion history, cut-off value of median age, or cu value. P < 0.05 was regarded significantly different and marked in bold al artery; RV renal vein; HA hepatic artery; HV hepatic vein; RE kidney tissue; HE liver tissue Discussion This study also provided important experimental datato further illustrate the mechanism of ABOi AMR. However, the major limitation of these previous studies was that the IHC analysis of blood groups may be subject to intra- and interobserver variability. Meanwhile, other techniques for blood group antigen detection—such as Western blotting—could have been affected by contami- nating RBCs that are ubiquitous in autopsy and biopsy specimens [20]. RBCs made it difficult to distinguish between erythrocytic and tissue sources of blood group antigen expression. The existence of RBCs may lead to an overestimation of the relative expression in WB and IHC results. Thus, autopsy samples cannot be used to accurately quantify blood group antigens. Our study used RBC-free histidine-tryptophan-ketoglutarate solution to perfuse donor kidneys and livers to eliminate residual RBCs. Thus, there should have been few, if any, resid- ual RBCs in our tissue samples. A previous study found highly individual- and tissue-specific expression of gly- colipid group A and B blood antigens, but no studies have analysed and compared glycoprotein A/B antigens. Thus, we detected the relative expression of blood group glyco- protein antigens in kidney and liver tissues with Western blotting. Two weeks after ABOi transplantation, an antigen– antibody reaction does not occur, and the ABOi allo- grafts function normally, despite the presence of A/B antigens on the graft and the existence of antibodies directed against the corresponding antigens in the blood of the recipient [23–25]. This type of tolerance is referred to as “accommodation”, and its underlying mechanisms remain to be elucidated. Accommodation may be due to (1) a change in the antigen, leading to decreased anti- body binding; (2) a change in antibodies, reducing their cytotoxicity; or iii) a change in the graft, enabling it to resist the injury mediated by the host immune system [16, 26, 27]. During clinical transplantation accommo- dation, these processes can manifest as the inhibition of the activity of glycosyltransferase, resulting in decreased antigenic immunogenicity. On the other hand, antigen downregulation might underlie the process of accommo- dation in which a graft survives and functions despite the Our study found that the mean intensity of glycopro- tein A and B antigen was generally similar (p > 0.05). Furthermore, kidney tissue and the portal vein were the two sites with the highest average intensity, and the renal artery was the site with the lowest intensity. Discussion In the human renal vascular bed, three different A anti- gen expression patterns with a major, minor, and minimal staining distribution were observed. The major pattern showed intense A antigen expression in the endothelium of arteries, glomerular/peritubular capillaries, and veins. A minor pattern showed overall weaker antigen expres- sion, whereas minimal had faint staining of peritubular capillaries only. In all cases, the distal tubular epithelium was focally stained, whereas proximal tubules were nega- tive. The secretor gene did not influence renal A antigen expression. All B kidneys showed a B antigen pattern slightly weaker but similar to the major pattern of the A antigen. pre-transplant preconditioning than ABOi liver trans- plantation and why the incidence of AMR in ABOi kid- ney transplantation was more higher than that in ABOi liver transplantation. We also found a wide diversity of blood group glycoprotein antigen intensities at the same site from a cohort of different deceased donors as well as at different sites from the same donor. These observa- tions may explain why even when the ABO antibody titre was “safe” on the transplant day, two allografts in our case series of 48 ABOi recipients exhibited immediate failure and pathology consistent with hyperacute rejection [21]. Thus, pre-transplant evaluation of the risk and sever- ity of ABO blood group AMR may be important when performing ABOi kidney transplantation and may allow individualized preconditioning regimens based on A/B antigen intensity and diversity. For example, when the organ tissues and main vessels in a donor express a high level of blood group antigens, the risk of AMR in the cor- responding ABOi recipients may be likely to be higher, and such recipients may need more intense precondition- ing to decrease the ABO antibody titre to an even lower level [22]. Worldwide, there are currently no safe, non- invasive, and reliable methods that can be used to quan- tify and inhibit ABO blood group antigen expression in donor organs. As a result, the preconditioning regimen in ABOi organ transplantation has been limited to decreas- ing the blood group antibody titre in the recipients. Our research revealed the prominent individual diversity of glycoprotein intensity for the ABO antigen in different organs and tissues by Western blotting. These results are useful for the further study of risk stratification and preconditioning regimens based on donor blood group antigen expression levels in ABOi organ transplantation. Discussion ABO blood group antigens are carbohydrate chains expressed on the cell membrane of RBCs. The H anti- gen is the only ABO structure present in blood type O, and A/B blood group antigens contain the H antigen as a common precursor [18]. Blood group A individuals Table 2  Univariate analysis of clinical features related to blood group antigen expressionsff Feature P value PV RA RV HA HV RE HE Total Sex A 0.567 0.045 0.003 0.001 0.365 0.300 – 0.008 B – 0.738 0.749 0.832 0.958 0.718 0.543 0.739 A&B 0.920 0.238 0.027 0.130 0.598 0.295 0.568 0.048 Transfusion A 0.090 0.168 0.475 0.262 0.187 0.580 0.848 0.675 B 0.036 0.990 0.698 0.471 0.321 0.934 0.747 0.367 A&B 0.005 0.237 0.719 0.252 0.227 0.783 0.872 0.699 Age A 0.648 0.382 0.309 0.178 0.678 0.646 0.050 0.459 B 0.890 0.504 0.042 0.009 0.446 0.165 – 0.029 A&B 0.690 0.908 0.121 0.065 0.464 0.204 0.809 0.038 BMI A 0.722 0.380 0.351 0.850 0.714 0.885 – 0.874 B – 0.124 0.133 0.006 0.266 0.177 0.255 0.009 A&B 0.926 0.940 0.153 0.208 0.398 0.143 0.350 0.054 Table 2  Univariate analysis of clinical features related to blood group antigen expressions F t P l Table 2  Univariate analysis of clinical features related to blood group antigen expressions Wang et al. BMC Immunol (2021) 22:66 Page 6 of 9 Fig. 3  Immunohistochemical staining of the renal artery (A), renal vein (B), portal vein (C), hepatic tissue (D), hepatic artery (E), hepatic vein (F), renal tissue (G) of an A antigen donor and the renal tissue (H) of a blood type O donor. RA, renal artery; RV, renal vein; RE, renal tissue; HE, hepatic tissue; HA, hepatic artery; HV, hepatic vein; PV, portal vein Fig. 3  Immunohistochemical staining of the renal artery (A), renal vein (B), portal vein (C), hepatic tissue (D), hepatic artery (E), hepatic vein (F), renal tissue (G) of an A antigen donor and the renal tissue (H) of a blood type O donor. RA, renal artery; RV, renal vein; RE, renal tissue; HE, hepatic tissue; HA, hepatic artery; HV, hepatic vein; PV, portal vein Wang et al. BMC Immunol (2021) 22:66 Page 7 of 9 patient age (p = 0.004). Breimer et al. examined the A/B antigen expression of renal biopsy samples by IHC [15]. Availability of data and materials The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. This study had several limitations. First, the statistical power may have been limited due to the relatively small sample size. Second, all individuals in the A and AB blood groups had A1 subtypes because the frequency of A2 in the Chinese population is < 1%, and no A2 individ- uals were included in this study. Finally, all livers and kid- neys from the deceased donors underwent subsequent ABO-compatible but not ABOi organ transplantation. Thus, the association between A/B expression patterns and blood group AMR remains to be elucidated. A large prospective clinical trial is needed to confirm our current findings and explore the association of A/B expression patterns with AMR and graft function in ABOi organ transplant recipients. Further studies might determine whether there is a threshold of the expression of blood group antigen that is likely to trigger AMR. Abbreviations ABOi: ABO-incompatible; AMR: Antibody-mediated rejection; IHC: Immunohis- tochemistry; BMI: Body mass index; PV: Portal vein; RA: Renal artery; RV: Renal vein; HA: Hepatic artery; HV: Hepatic vein; RE: Kidney tissue; HE: Liver tissue. 3. Flint S, Walker R, Hogan C, Haeusler M, Robertson A, Francis D, Millar R, Finlay M, Landgren A, Cohney S. Successful ABO-incompatible kidney transplantation with antibody removal and standard immunosuppres- sion. Am J Transplant Off J Am Soc Transplant Am Soc Transplant Surg. 2011;11(5):1016–24. Author details 1 1 Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Number 37, Guoxue Alley, Chengdu 610041, Sichuan, China. 2 Organ Transplantation Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China. 3 Department of Urology/Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, China. 4 West China School of Clinical Medicine, Sichuan University, Chengdu, Sichuan, China. 5 Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan, China. Discussion It was not surprising that the injury in renal tissue would be more severe than that in the main renal vessels when blood group AMR occurred. The high level of blood group anti- gens in the portal vein may be related to the high inci- dence of portal vein thrombosis and portal vein stenosis after liver transplantation. Additionally, the compari- son of the intensity in kidney versus liver tissues indi- cated that there was a much higher expression level of glycoprotein antigen in renal tissue than in liver tissue from the same donor, which might partially explain why ABOi kidney transplantation requires more aggressive Wang et al. BMC Immunol (2021) 22:66 Wang et al. BMC Immunol (2021) 22:66 Page 8 of 9 [grant number 2019-YF05-00084-SN]; and 1.3.5 Project for Disciplines of Excellence-Clinical Research Incubation Project, West China Hospital, Sichuan University [grant number 2018HXFH049, ZYJC18004, ZY2016104, 2019-075, 2021HXFH007]. The funders had no role in study design, data collection or analysis, preparation of the manuscript, or the decision to publish. [grant number 2019-YF05-00084-SN]; and 1.3.5 Project for Disciplines of Excellence-Clinical Research Incubation Project, West China Hospital, Sichuan University [grant number 2018HXFH049, ZYJC18004, ZY2016104, 2019-075, 2021HXFH007]. The funders had no role in study design, data collection or analysis, preparation of the manuscript, or the decision to publish. presence of anti-donor antibodies in the circulation of the recipient. Ulfvin et al. analysed glycolipids extracted from ABO-incompatible allografts that had become accommodated and found the accommodated grafts had reduced levels of antigen, suggesting that antigen down- modulation might play a role in the long-term function of the organs [28]. The authors have none to declare. 4. Koo T, Yang J. Current progress in ABO-incompatible kidney transplanta- tion. Kidney Res Clin Pract. 2015;34(3):170–9. Conclusions Our study revealed substantial inter-individual variations in blood group A and B antigens between human livers and kidneys. These variations may explain differences in the incidence and clinical severity of AMR in ABOi kid- ney/liver transplantations and could theoretically be used to risk-stratify ABOi organ transplant procedures. Future studies may consider non-invasive detection methods for the intensity of blood group antigens in a specific donor organ, which could more accurately assess the risk of AMR in ABOi transplantation recipients and help to select more precise desensitization regimens to perform ABOi organ transplantation safely. Received: 28 October 2020 Accepted: 23 September 2021 Consent for publication Consent for publication Not applicable. Consent for publication Not applicable. Not applicable. Authors’ contributions XW, FZ and YJ wrote the main manuscript text. The clinical tisses were col- lected by ZX, XF, LL, YF, TS, YS, and ZH. Study was designed by TL and XW. The experiments were done by FZ and YJ. XW and FZ prepared Figs. 1, 2 and Tables 1, 2. All authors reviewed the manuscript. All authors read and approved the final manuscript. 5. Uchida J, Kosoku A, Naganuma T, Tanaka T, Nakatani T. Latest insights on ABO-incompatible living-donor renal transplantation. Int J Urol Off J Jpn Urol Assoc. 2020;27(1):30–8. 6. Masterson R, Hughes P, Walker RG, Hogan C, Haeusler M, Robertson AR, Millar R, Suh N, Cohney SJ. ABO incompatible renal transplantation with- out antibody removal using conventional immunosuppression alone. Am J Transplant. 2014;14(12):2807–13. Referencesf 1. Schiffer M, Kielstein J. ABO-incompatible renal transplantation: from saline flushes to antigen-specific immunoadsorption-tools to overcome the barrier. Korean J Hematol. 2011;46(3):164–8. 1. Schiffer M, Kielstein J. ABO-incompatible renal transplantation: from saline flushes to antigen-specific immunoadsorption-tools to overcome the barrier. Korean J Hematol. 2011;46(3):164–8. 2. Montgomery R, Locke J, King K, Segev D, Warren D, Kraus E, Cooper M, Simpkins C, Singer A, Stewart Z, Melancon J, Ratner L, Zachary A, Haas M. ABO incompatible renal transplantation: a paradigm ready for broad implementation. Transplantation. 2009;87(8):1246–55. Ethics approval and consent to participate Informed consent was obtained from next of kin in accordance with the Declaration of Helsinki and the Council for International Organizations of Medical Sciences. This study protocol was reviewed and approved by the Biomedical Ethics Committee, West China Hospital (No. 2019SHEN282). This study protocol was reviewed and approved by the Biomedical Ethics Commit- tee, West China Hospital (No. 2019SHEN282). All organ donation cases were conducted according to the protocols for China Categories I, II, and III donors. Written consent to participate in the study was obtained from the donor’s family. All tissues were obtained in West China Hospital, China and no tissues were obtained from prisoners. Acknowledgements The authors have none to declare. Funding Thi k Aikawa A, Hadano T, Ohara T, Yamashita M, Arai K, Hirayama N, Mori Y, Muramatsu M, Hasegawa A. Donor specific antibody suppression in ABO incompatible kidney transplantation. Transplant Proc. 2001;33(1–2):395–7 13. Jeyakanthan M, Tao K, Zou L, Meloncelli P, Lowary T, Suzuki K, Boland D, Larsen I, Burch M, Shaw N, Beddows K, Addonizio L, Zuckerman W, Afzali B, Kim D, Mengel M, Shapiro A, West L. Chemical basis for qualitative and quantitative differences between ABO blood groups and subgroups: implications for organ transplantation. Am J Transplant Off J Am Soc Transplant Am Soc Transplant Surg. 2015;15(10):2602–15. 25. Park WD, Grande JP, Ninova D, Nath KA, Platt JL, Gloor JM, Stegall MD. Accommodation in ABO-incompatible kidney allografts, a novel mechanism of self-protection against antibody-mediated injury. Am J Transplant. 2003;3(8):952–60. 26. Park W, Grande J, Ninova D, Nath K, Platt J, Gloor J, Stegall M. Accom- modation in ABO-incompatible kidney allografts, a novel mechanism of self-protection against antibody-mediated injury. Am J Transplant Off J Am Soc Transplant Am Soc Transplant Surg. 2003;3(8):952–60. 14. Jeyakanthan M, Meloncelli P, Zou L, Lowary T, Larsen I, Maier S, Tao K, Rusch J, Chinnock R, Shaw N, Burch M, Beddows K, Addonizio L, Zucker- man W, Pahl E, Rutledge J, Kanter K, Cairo C, Buriak J, Ross D, Rebeyka I, West L. ABH-glycan microarray characterizes ABO subtype antibodies: fine specificity of immune tolerance after ABO-incompatible transplanta- tion. Am J Transplant Off J Am Soc Transplant Am Soc Transplant Surg. 2016;16(5):1548–58. 27. Takahashi K, Saito K, Takahara S, Okuyama A, Tanabe K, Toma H, Uchida K, Hasegawa A, Yoshimura N, Kamiryo Y. Excellent long-term outcome of ABO-incompatible living donor kidney transplantation in Japan. Am J Transplant Off J Am Soc Transplant Am Soc Transplant Surg. 2004;4(7):1089–96. 15. Breimer ME, Mölne J, Nordén G, Rydberg L, Thiel G, Svalander CT. Blood group A and B antigen expression in human kidneys correlated to A1/ A2/B, Lewis, and secretor status. Transplantation. 2006;82(4):479–85. 28. Ogasawara K, Ueki J, Takenaka M, Furihata K. Study on the expression of ABH antigens on platelets. Blood. 1993;82(3):993–9. 28. Ogasawara K, Ueki J, Takenaka M, Furihata K. Study on the expression of ABH antigens on platelets. Blood. 1993;82(3):993–9. 28. Ogasawara K, Ueki J, Takenaka M, Furihata K. Study on the expression of ABH antigens on platelets. Blood. 1993;82(3):993–9. 16. Ulfvin A, Bäcker A, Clausen H, Hakomori S, Rydberg L, Samuelsson B, Bre- imer M. Funding Thi k This work was supported by grants from the National Natural Science Founda- tion of China [grant number 81870513]; Sichuan Science and Technology Pro- gram [grant number 2019YJ0133]; Chengdu Science and Technology Program 7. Scurt F, Ewert L, Mertens P, Haller H, Schmidt B, Chatzikyrkou C. Clinical outcomes after ABO-incompatible renal transplantation: Page 9 of 9 Wang et al. BMC Immunol (2021) 22:66 Wang et al. BMC Immunol (2021) 22:66 Wang et al. BMC Immunol (2021) 22:66 18. Milland J, Sandrin M. ABO blood group and related antigens, natural antibodies and transplantation. Tissue Antigens. 2006;68(6):459–66. a systematic review and meta-analysis. Lancet (London, England). 2019;393(10185):2059–72. a systematic review and meta-analysis. Lancet (London, England). 2019;393(10185):2059–72. a systematic review and meta-analysis. Lancet (London, England). 2019;393(10185):2059–72. 8. Fryer J, Benedetti E, Perry E, Matas A. Antibody-mediated rejection of an HLA-identical, ABO-incompatible kidney transplant after two failed cadaver transplants. Transplantation. 1994;58(6):723–5. 19. Yamamoto F, McNeill P, Hakomori S. Genomic organization of human histo-blood group ABO genes. Glycobiology. 1995;5(1):51–8. histo-blood group ABO genes. Glycobiology. 1995;5(1):51–8. 20. Garcia de Mattos Barbosa M, Cascalho M, Platt J. Accommodation in ABO- incompatible organ transplants. Xenotransplantation. 2018;25(3):e12418. cadaver transplants. Transplantation. 1994;58(6):723–5. 9. Sugiyama K, Arai K, Aikawa A, Miyagi M, Ohara T, Hasegawa A, Muramatsu M, Hirayama N, Tajima E, Kawamura T, Ogihara H, Hadano T, Nakano H. Reversibility from delayed hyperacute rejection in ABO-incompatible renal transplantation: histopathological findings of renal allograft biopsy. Transpl Proc. 2005;37(2):701–4. 21. Wang XD, Liu JP, Fan Y, Song TR, Shi YY, Li YM, Lv YH, Li XH, Huang ZL, Lin T. Individualized preconditioning for ABO-incompatible living-donor kidney transplantation: an initial report of 48 cases from China. Ann Transplant. 2020;25:e920224. 10. Warner P, Nester T. ABO-incompatible solid-organ transplantation. Am J Clin Pathol. 2006;125:S87-94. 22. Kobayashi T, Saito K. A series of surveys on assay for anti-A/B antibody by Japanese ABO-incompatible Transplantation Committee. Xenotransplan- tation. 2006;13(2):136–40. 11. Montgomery J, Berger J, Warren D, James N, Montgomery R, Segev D. Outcomes of ABO-incompatible kidney transplantation in the United States. Transplantation. 2012;93(6):603–9. 23. Shimmura H, Tanabe K, Ishikawa N, Tokumoto T, Takahashi K, Toma H. Role of anti-A/B antibody titers in results of ABO-incompatible kidney transplantation. Transplantation. 2000;70(9):1331–5. 12. Gehrie E, Cates J, Nian H, Olson S, Young P. Blood Group A antigen expres- sion on cardiac endothelium is highly individualized: possible implica- tions for transplantation. Cardiovasc Pathol. 2013;22(4):251–6. 24. Funding Thi k Expression of glycolipid blood group antigens in single human kidneys: change in antigen expression of rejected ABO incompatible kidney grafts. Kidney Int. 1993;44(6):1289–97. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in pub- lished maps and institutional affiliations. 17. Huang J, Wang H, Fan ST, Zhao B, Zhang Z, Hao L, Huo F, Liu Y. The national program for deceased organ donation in China. Transplantation. 2013;96(1):5–9. 17. Huang J, Wang H, Fan ST, Zhao B, Zhang Z, Hao L, Huo F, Liu Y. The national program for deceased organ donation in China. Transplantation. 2013;96(1):5–9. • fast, convenient online submission • thorough peer review by experienced researchers in your field • rapid publication on acceptance • support for research data, including large and complex data types • gold Open Access which fosters wider collaboration and increased citations maximum visibility for your research: over 100M website views per year • At BMC, research is always in progress. Learn more biomedcentral.com/submissions Ready to submit your research Ready to submit your research ? Choose BMC and benefit from: ? 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Supplementary Figure 1 from BRCA2 and Nucleophosmin Coregulate Centrosome Amplification and Form a Complex with the Rho Effector Kinase ROCK2
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Supplementary Figure S3 Wang et al. Wang et al. γ-Tubulin with Hoechst merge with Hoechst BRCA2 with Hoechst FLAG- R3 BRCA2 FLAG- R3 BRCA2 vector free FLAG-vector Fig. S3. NPM-BRCA2 interaction is critical for genomic stability. COS-7 cells were transfected with a FLAG-R3 BRCA2 (639–1508) expression vector or the empty one. The cells were stained for γ-tubulin (red), BRCA2 (green), and DNA (blue) Multinuclei are shown inside the white dotted line Arrows γ-Tubulin with Hoechst merge with Hoechst BRCA2 with Hoechst FLAG- R3 BRCA2 FLAG- R3 BRCA2 γ-Tubulin with Hoechst merge with Hoechst BRCA2 with Hoechst FLAG- R3 BRCA2 γ-Tubulin with Hoechst FLAG- R3 BRCA2 G- RCA2 FLAG- R3 BRCA2 R3 BRCA2 vector free FLAG-vector Fig. S3. NPM-BRCA2 interaction is critical for genomic stability. COS-7 cells were transfected with a FLAG-R3 BRCA2 (639–1508) expression vector or the empty one. The cells were stained for γ-tubulin (red), BRCA2 (green), and DNA (blue). Multinuclei are shown inside the white dotted line. Arrows, vector free FLAG-vector FLAG-vector Supplementary Figure S3 Supplementary Figure S3 vector free Fig. S3. NPM-BRCA2 interaction is critical for genomic stability. COS-7 cells were transfected with a FLAG-R3 BRCA2 (639–1508) expression vector or the empty one. The cells were stained for γ-tubulin (red), BRCA2 (green), and DNA (blue). Multinuclei are shown inside the white dotted line. Arrows, centrosomes.
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Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks
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Introduction olites, and the slower motions reflect more physiologically relevant transformations. Appreciation of this observation can result in elucidating structure from the network and simplifying the interactions. The reduction in dynamic dimensionality is based on such pooling and the analysis of pooling is focused in the underlying time scale hierarchy and its determinants. Under- standing the time scale hierarchy and pooling structure of these networks is critical to understanding network behavior and simplifying it down to the core interactions. The network of interactions that occur between biological components on a range of various spatial and temporal scales confer hierarchical functionality in living cells. In order to determine how molecular events organize themselves into coherent physiological functions, in silico approaches are needed to analyze how physiological functions emerge from the evolved temporal structure of networks. Time scale decomposition is a well-established, classical approach to dissecting network dynamics and there is a notable history of analyzing the time scale hierarchy in metabolic networks and matching the events that unfold on each time scale with a physiological function [1–6]. This approach enables the identification of the independent, characteristic time scales for a dynamic system. In particular it has been possible to decompose a cell-scale kinetic model of the human red blood cell in time to show how its key metabolic demands are met through a dynamic structure-function relationship. The underly- ing principle is one of aggregation of concentration variables into ‘pools’ of concentrations that move in tandem on slower time scales [5,7]. Top-down studies of dynamic characteristics of networks begin with fully developed kinetic models that are formal representations of large amounts of data about the chemistry and kinetics component interactions. Network properties can be studied by numerical simulations (that are condition-specific) or by analysis (that often yield general model properties) of the model equations. Since comprehensive numerical simulation studies become intractable for larger networks and the identification of general model properties are needed for the judicious simplification of models, there is a need for analysis based methods in order to characterize properties of dynamic networks. In this study we present an in silico analysis method to determine pooling of variables in complex dynamic models of biochemical reaction networks. This method is used to study metabolic network models and allows us to identify and analyze pool formation resulting from the underlying stoichiometric, thermodynamic, and kinetic properties. Abstract The study of dynamic functions of large-scale biological networks has intensified in recent years. A critical component in developing an understanding of such dynamics involves the study of their hierarchical organization. We investigate the temporal hierarchy in biochemical reaction networks focusing on: (1) the elucidation of the existence of ‘‘pools’’ (i.e., aggregate variables) formed from component concentrations and (2) the determination of their composition and interactions over different time scales. To date the identification of such pools without prior knowledge of their composition has been a challenge. A new approach is developed for the algorithmic identification of pool formation using correlations between elements of the modal matrix that correspond to a pair of concentrations and how such correlations form over the hierarchy of time scales. The analysis elucidates a temporal hierarchy of events that range from chemical equilibration events to the formation of physiologically meaningful pools, culminating in a network-scale (dynamic) structure– (physiological) function relationship. This method is validated on a model of human red blood cell metabolism and further applied to kinetic models of yeast glycolysis and human folate metabolism, enabling the simplification of these models. The understanding of temporal hierarchy and the formation of dynamic aggregates on different time scales is foundational to the study of network dynamics and has relevance in multiple areas ranging from bacterial strain design and metabolic engineering to the understanding of disease processes in humans. Citation: Jamshidi N, Palsson B (2008) Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks. PLoS Comput Biol 4(9): e1000177. doi:10.1371/journal.pcbi.1000177 Received November 26, 2007; Accepted August 4, 2008; Published September 12, 2008 ceived November 26, 2007; Accepted August 4, 2008; Published September 12, 2008 Received November 26, 2007; Accepted August 4, 2008; Published September 12, 2008 Copyright:  2008 Jamshidi, Palsson. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. nding: This work was supported in part by a National Institutes of Health Training Grant to the Department of Bioengineering, Univ ego. Competing Interests: The authors have declared that no competing interests exist. Competing Interests: The authors have declared that no competing interests exist. * E-mail: palsson@ucsd.edu * E-mail: palsson@ucsd.edu PLoS Computational Biology | www.ploscompbiol.org Neema Jamshidi, Bernhard Ø. Palsson* Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks Neema Jamshidi, Bernhard Ø. Palsson* September 2008 | Volume 4 | Issue 9 | e1000177 Citation: Jamshidi N, Palsson B (2008) Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks. PLoS Comput Biol 4(9): e1000177. doi:10.1371/journal.pcbi.1000177 Method Development Dynamic description of networks. Linearizing the mass conservation equations for a chemical reacting system around the steady state yields the linear form of the dynamic mass balances, dx0 tð Þ dt ~Jx0 tð Þ ð1Þ Defining pools from modes. A column of the modal matrix describes the participation of a concentration in each of the linearly independent modes. When two concentrations (xi and xj) become dynamically correlated beyond a particular time scale (say after the kth time constant), the entries of the modal matrix in the two corresponding columns are correlated with one another on the subsequent time scales (Figure 2). This characteristic enables the identification of the time scales that two concentrations would pool together. ð1Þ where J is the n6n Jacobian matrix, and x9 ( = x2xss) is the deviation vector of the concentration variables from the steady state (xss). J describes the dynamical characteristics of the network near the steady state. The properties of J can be analyzed using matrix decomposition methods, and it is important for these methods to capture the interactions between components across all of the time scales of the network. where J is the n6n Jacobian matrix, and x9 ( = x2xss) is the deviation vector of the concentration variables from the steady state (xss). J describes the dynamical characteristics of the network near the steady state. The properties of J can be analyzed using matrix decomposition methods, and it is important for these methods to capture the interactions between components across all of the time scales of the network. Employing a geometric interpretation for this determination, one can explicitly identify pool formation by calculating the angle between columns (M21)i of the modal matrix, Temporal decomposition. We can apply a similarity transformation (see Materials and Methods) to J, J~M1L 1M1{1 ð2Þ ð2Þ H~cos qij   ~ M{1  T i : M{1   j M{1 ð ÞT i   M{1 ð Þj   ð5Þ ð5Þ where L is a diagonal matrix with the eigenvalues, that are the negative reciprocal time constants [8]. The superscript star indicates the possible presence of imaginary components in the matrices. Complex conjugate pairs can be removed by pre-multiplying by a modified identity matrix with block diagonal ones at the rows and columns in which the matrix has imaginary components. Author Summary Furthermore, different steady states can be characterized as well, by recalculating the Jacobian at the alternate steady states. Elucidating Network Pooling Structure Elucidating Network Pooling Structure dynamically independent ‘‘aggregates’’, or pooling of metabolites into independent dynamic variables. Time scale decomposition can be successfully performed only if the eigenvalues are well separated. When J is rank deficient, it implies the presence of dynamically invariant pools reflecting chemically conserved moieties in the network, whose sum total is constant. These vectors are not included in the modal matrix. Author Summary Introduction The dynamics of biological networks characteristically span large time scales (8 to 10 orders of magnitude), which contributes to the challenge of analyzing and interpreting related models. However, there is structure in this dynamic hierarchy of events, particularly in biochemical networks in which the fastest motions generally correspond to the chemical equilibria between metab- September 2008 | Volume 4 | Issue 9 | e1000177 1 Author Summary Cellular metabolism describes the complex web of bio- chemical transformations that are necessary to build the structural components, to convert nutrients into ‘‘usable energy’’ by the cell, and to degrade or excrete the by- products. A critical aspect toward understanding metabo- lism is the set of dynamic interactions between metabolites, some of which occur very quickly while others occur more slowly. To develop a ‘‘systems’’ understanding of how networks operate dynamically we need to identify the different processes that occur on different time scales. When one moves from very fast time scales to slower ones, certain components in the network move in concert and pool together. We develop a method to elucidate the time scale hierarchy of a network and to simplify its structure by identifying these pools. This is applied to dynamic models of metabolism for the human red blood cell, human folate metabolism, and yeast glycolysis. It was possible to simplify the structure of these networks into biologically meaningful groups of variables. Because dynamics play important roles in normal and abnormal function in biology, it is expected that this work will contribute to an area of great relevance for human disease and engineering applications. The modal matrix separates the dynamics of the network into a series of dynamically independent motions [5,8], moving from the fastest (top) modes to the slowest (bottom) modes as the time scales lengthen (Figure 1B). Here we present an approach to the analysis of the modal matrix that simplifies the elucidation of notable pools without the need for intensive calculations of dynamic phase portraits and auto-correlations functions in order to identify biologically relevant interpretations of these modes as pools of metabolites being created and consumed on different time scales [2]. An illustrative ‘toy’ example of time scale decomposition is described in the supplementary material (Figure S1). Table 2 summarizes some of the trade-offs between the characterization of dynamics using the Jacobian matrix and carrying out large numbers of dynamic simulations directly. Although carrying out dynamic simulations are not restricted to a particular steady state, they are condition dependent (e.g. initial conditions) and resource intensive. Hence for larger networks, dynamic simulations are not a viable option. In contrast, characterization of the pooling structure of networks via analysis of the Jacobian requires only a single set of calculations to characterize a particular steady state and this approach can be applied to large and small networks alike. Method Development The complex conjugate pairs arise in situations in which the motions of these modes cannot be decomposed in time. The modal matrix, M21, can then be used to define the modes, m, such that, in which M{1 i   refers to the magnitude of the ith column of the modal matrix and qij refers to the angle between the ith and jth columns of the modal matrix. However, if one were to simply calculate the correlations between metabolites across all time scales, in general no pooling would be observed among the metabolites, even though there may be physiologically relevant pooling between metabolites, that characteristically occur on slower time scales. A simple illustration of this is depicted in by the modal matrix in Figure 2, which highlights the need to characterize aggregate pool formation of variables in the context of progressively slower time scales. Hence this approach analyzes progressive pooling across all of the network’s independent time scales, in contrast to simulation based methods which are dependent on a priori specification of the time scales of interest for identifying correlations between metabolites. m~M{1x ð3Þ ð3Þ which combined with Equation 1 results in, which combined with Equation 1 results in, dm dt ~Lm ð4Þ ð4Þ as described previously [5]. The rows in the modal matrix define as described previously [5]. The rows in the modal matrix define PLoS Computational Biology | www.ploscompbiol.org September 2008 | Volume 4 | Issue 9 | e1000177 September 2008 | Volume 4 | Issue 9 | e1000177 2 Elucidating Network Pooling Structure Figure 1. Subspaces of the Jacobian matrix and different approaches for decomposing it into dynamically independent interactions between metabolites. (A) The Jacobian acts as a linear operator mapping the dynamics onto the deviation variable. (B) The Modal Matrix maps network dynamics onto independent time scales. Panels C and D illustrate two approaches to understanding the interactions between metabolites on the different time scales. (C) Beginning from the fastest time scale and moving forward, components that move together on subsequent time scales are lumped into an aggregate pool variable. The pooling pictorially for three different time scales in glycolysis and the Rapoport-Leubering shunt in the red cell. The large blue dots indicate pool formation between two metabolites, signifying that these two metabolites become coupled or correlated on slower times scales. Method Development In this case, glyceraldehyde 3-phosphate and dihydroxyacetone phosphate pool together after the first time scale, the hexose phosphates pool together after the fourth time scale, and the triose phosphates pool together after the eighth time scale. (D) Each time scale is analyzed independently and the interactions are defined in terms of the coefficients in the model and their contribution to the cumulative sum of the modal coefficients. Analyzing all of the modes in this manner allows the identification of variables that are dominant across multiple modes and identifying the time scales across which they are most active. Four fundamental subspaces are associated with J and its mapping onto its time derivative. The key to temporal decomposition is the time-ordered removal of dynamic motions that lead to the step- by-step increase in the null and left null spaces of J. doi:10.1371/journal.pcbi.1000177.g001 Figure 1. Subspaces of the Jacobian matrix and different approaches for decomposing it into dynamically independent interactions between metabolites. (A) The Jacobian acts as a linear operator mapping the dynamics onto the deviation variable. (B) The Modal Matrix maps network dynamics onto independent time scales. Panels C and D illustrate two approaches to understanding the interactions between metabolites on the different time scales. (C) Beginning from the fastest time scale and moving forward, components that move together on subsequent time scales are lumped into an aggregate pool variable. The pooling pictorially for three different time scales in glycolysis and the Rapoport-Leubering shunt in the red cell. The large blue dots indicate pool formation between two metabolites, signifying that these two metabolites become coupled or correlated on slower times scales. In this case, glyceraldehyde 3-phosphate and dihydroxyacetone phosphate pool together after the first time scale, the hexose phosphates pool together after the fourth time scale, and the triose phosphates pool together after the eighth time scale. (D) Each time scale is analyzed independently and the interactions are defined in terms of the coefficients in the model and their contribution to the cumulative sum of the modal coefficients. Analyzing all of the modes in this manner allows the identification of variables that are dominant across multiple modes and identifying the time scales across which they are most active. Four fundamental subspaces are associated with J and its mapping onto its time derivative. Method Development The key to temporal decomposition is the time-ordered removal of dynamic motions that lead to the step- by-step increase in the null and left null spaces of J. doi:10.1371/journal.pcbi.1000177.g001 metabolites, in which no aggregate pools form, there will be m sets of pooling matrices. Conversely, for the extreme case in which all of the metabolites form a single aggregate pool on a single time scale there will only be a single pooling matrix. In order to identify the time scales at which pool formation occurs, we compute the angle between two columns as a function of an index k that runs from 1 to n time scales. As each row of the modal matrix is removed (k increases by one) the angle is recomputed to form a series of angles as a function of k; i.e., qij(k), k = 1, 2, …, n. If the angle qij(k) is close to zero, the two columns are correlated at and above that k value and the two corresponding concentrations will move in tandem for the subsequent time scales, thus forming an aggregate variable or a pool. The practical issue is to determine when the angle is close enough to zero to make a call on the formation of a pool. Defining dominant interactions for each mode. One can quantitatively ascertain the contribution of each metabolite to each mode by rank ordering the normalized mode and keeping only the largest weights that add up to the specified cutoff percentage. At low cut-off ranges, all metabolites with small contributions to the mode will be zeroed out. The interactions across the modes can be mapped on top of the interactions defined by the stoichiometric matrix in order to compare and contrast the topological connectivity versus the dynamic connectivity at time scales of interest. The pools can be described as a sum of matrix products over the time scales of the network: Fts i M{1Fm i ð6Þ PLoS Computational Biology | www.ploscompbiol.org Application of the Method ð6Þ The models studied here exhibit a significant span of time scales (Table 1). A hierarchy pool formation on different time scales was found in all networks based on the calculation of all pair wise qij(k) in the models (Figures 1C and 2). The results can be presented in a symmetric correlation tiled array, where each entry can be used to represent k for a pair of concentrations. Figure 3 shows the result Fts i is a binary diagonal matrix, with n2i non-zero elements on the diagonal. Fm i is a binary matrix with off-diagonal elements whenever two columns meet a specific cutoff and can be combined into an aggregate pool. Fts i and Fm i act on the modal matrix, by filtering out modes or combining variables, respectively. For a network with m PLoS Computational Biology | www.ploscompbiol.org September 2008 | Volume 4 | Issue 9 | e1000177 September 2008 | Volume 4 | Issue 9 | e1000177 3 Elucidating Network Pooling Structure Figure 2. Illustration of the progression correlation between two variables as fast time scales are removed. The set of dynamic equations are linearized about a particular steady state. Applying a similarity transformation to the Jacobian, enables the calculation of the modal matrix (depicted to the right). The rows of the matrix correspond to different time scales. When the ratios between two entries are constant, the two metabolites pool together. After the second time scale, metabolites xi and xi+1 form an aggregate pool and after the fifth time scale, xi+2 joins the pool. If the variables were compared across all time scales, no significant correlations would be observed. Hence, this simple example highlights the need for a method to analyze correlations between metabolites with consideration of the characteristic time scales of the network. doi:10.1371/journal.pcbi.1000177.g002 Figure 2. Illustration of the progression correlation between two variables as fast time scales are removed. The set of dynamic equations are linearized about a particular steady state. Applying a similarity transformation to the Jacobian, enables the calculation of the modal matrix (depicted to the right). The rows of the matrix correspond to different time scales. When the ratios between two entries are constant, the two metabolites pool together. After the second time scale, metabolites xi and xi+1 form an aggregate pool and after the fifth time scale, xi+2 joins the pool. Application of the Method If the variables were compared across all time scales, no significant correlations would be observed. Hence, this simple example highlights the need for a method to analyze correlations between metabolites with consideration of the characteristic time scales of the network. doi:10.1371/journal.pcbi.1000177.g002 Table 1. Summary of properties of the various kinetic models, particularly the Jacobian matrices of the networks. System Dimension Rank Pooling Conservation Pools Effective Dimensionality Time Scale Span RBC 34 34 Complete 0 17 1.30E+10 Folate 10 9 Complete 1 6 4.88E+04 Yeast 20 20 Fragmented 0 13 7.50E+06 Pooling of the tiled modal arrays can be classified as complete (in which all elements pools together eventually) or fragmented. The number of conservation pools is equal to the size of the left null space of the Jacobian. The effective dynamic dimensionality is the number of different time scales at which pooling occurs. The time scale span is the ratio of the largest to smallest eigenvalue for each of the networks. doi:10.1371/journal.pcbi.1000177.t001 Pooling of the tiled modal arrays can be classified as complete (in which all elements pools together eventually) or fragmented. The number of conservation pools is equal to the size of the left null space of the Jacobian. The effective dynamic dimensionality is the number of different time scales at which pooling occurs. The time scale span is the ratio of the largest to smallest eigenvalue for each of the networks. doi:10.1371/journal.pcbi.1000177.t001 Pooling of the tiled modal arrays can be classified as complete (in which all elements pools together eventually) or fragmented. The number of conservation pools is equal to the size of the left null space of the Jacobian. The effective dynamic dimensionality is the number of different time scales at which pooling occurs. The time scale span is the ratio of the largest to smallest eigenvalue for each of the networks. doi:10 1371/journal pcbi 1000177 t001 Table 2. A comparison between the trade-offs for analyzing the Jacobian around a particular steady state versus carrying out dynamic simulations. Table 2. A comparison between the trade-offs for analyzing the Jacobian around a particular steady state versus carrying out dynamic simulations. of such an array for the human red cell. Since the array is symmetric we can display both k and the modal coefficient ratio in the pool (xi/xj) for each pair of concentrations; thus Table 2. Application of the Method A comparison between the trade-offs for analyzing the Jacobian around a particular steady state versus carrying out dynamic simulations. Jacobian Analysis Dynamic Simulations Generalized results Conditions specific results Scaleable Intractable as the number of variables increase A single set of calculations will characterize a particular steady state Resource intensive, requires many simulations in order to characterize network pooling Linear regime near a particular steady state May move from one steady state to another The approach presented here for analysis of the Jacobian in order to characterize network dynamics allows generalized, comprehensive elucidation of dynamics around a particular steady state directly and in a scaleable manner. In contrast, although the approach using dynamic simulations is not restricted to a particular steady state, it is resource intensive and for larger networks it is infeasible to characterize all of the different possible initial conditions, due to combinatorial growth of the possible combinations. doi:10.1371/journal.pcbi.1000177.t002 PLoS Computational Biology | www ploscompbiol org N The lower left triangle of the tiled array indicates the time scale k beyond which pooling occurs in the network. So for example, G6P and F6P pool together after the fourth mode in the red cell metabolic model. For the highly interconnected metabolic network in the red cell, eventually, all of the metabolites pool together. N The upper right triangle of the tiled array contains plots show the ratios of the modal coefficients (xi/xj) for each of the concentration pairs at all of the time scales above k for that pair. For many of the concentration pairs, the ratio remains fairly constant (glycolytic pools, pentose phosphate pools, etc) past a certain time scale showing the relative contribution of the compounds to a pool. N The pooling structure observed in Figure 3 is consistent with the previous descriptions [2] and enable the simplification of the network into equilibrium pools on fast time scales and physiological ones on slower time scales (Figure 4). PLoS Computational Biology | www.ploscompbiol.org September 2008 | Volume 4 | Issue 9 | e1000177 September 2008 | Volume 4 | Issue 9 | e1000177 PLoS Computational Biology | www.ploscompbiol.org 4 Elucidating Network Pooling Structure Figure 3. Time scale hierarchy of metabolic pool formation in the human red blood cell. The lower left triangle indicates the modes after which pooling occurs between the corresponding metabolites (one being the fastest time scale). Application of the Method The upper right triangle are plots of the slopes between the two metabolites for the remaining time scales after pool formation (the origin is always included in these approximations of the slopes), color coded according to the time scale at which pooling occurs. Some of the metabolites such as the phosphoglycerates have fairly constant ratios once they join aggregate pools. Others, such as ATP and ADP have varying ratios. These ratios change when interactions with other pathways dominate on subsequent time scales, for example when glycolytic intermediates dominate on one time scale and nucleotide salvage metabolites dominate on another, the respective interactions between ATP and ADP are affected differently. The cutoff value for cos(h) was 0.9. Abbreviations: G6P, Glucose-6-phosphate; F6P, Fructose-6-phosphate; FDP. Fructose-1,6-bisphosphate; DHAP, Dihydroxyacetone phosphate; GAP, Glyceraldehyde-3- phosphate; DPG13. 1,3-bisphosphoglycerate; DPG23, 2,3-bisphosphoglycerate; PG3, 3-phosphoglycerate; PG2, 2-phosphoglycerate; PEP, Phosphoenolpyruvate; PYR, Pyruvate; LAC. Lactate; NADH, Nicotinamide adenine dinucleotide (reduced); GL6P. 6-Phospho-D-glucono-1,5-lactone; GO6P, 6-Phospho-D-gluconate; NADPH, Nicotinamide adenine dinucleotide phosphate (reduced); GSH, glutathione (reduced); RU5P, Ribulose-5- phosphate; R5P, Ribose-5-phosphate; X5P, Xylulose-5-phosphate; S7P, Sedoheptulose-7-phosphate; E4P, Erythrose-4-phosphate; ADO, Adenosine; AMP, Adenosine monophosphate; ADP, Adenosine diphosphate; ATP, Adenosine triphohsphate; PRPP, 5-Phospho-D-ribose 1-diphosphate; IMP, Inosine monophosphate; INO, Inosine; HX, Hypoxanthine; R1P, Ribose-1-phosphate; ADE, Adenine; NAI, Sodium; and KI, Potassium. doi:10.1371/journal.pcbi.1000177.g003 Figure 3. Time scale hierarchy of metabolic pool formation in the human red blood cell. The lower left triangle indicates the modes after which pooling occurs between the corresponding metabolites (one being the fastest time scale). The upper right triangle are plots of the slopes between the two metabolites for the remaining time scales after pool formation (the origin is always included in these approximations of the slopes), color coded according to the time scale at which pooling occurs. Some of the metabolites such as the phosphoglycerates have fairly constant ratios once they join aggregate pools. Others, such as ATP and ADP have varying ratios. These ratios change when interactions with other pathways dominate on subsequent time scales, for example when glycolytic intermediates dominate on one time scale and nucleotide salvage metabolites dominate on another, the respective interactions between ATP and ADP are affected differently. The cutoff value for cos(h) was 0.9. Abbreviations: G6P, Glucose-6-phosphate; F6P, Fructose-6-phosphate; FDP. Fructose-1,6-bisphosphate; DHAP, Dihydroxyacetone phosphate; GAP, Glyceraldehyde-3- phosphate; DPG13. 1,3-bisphosphoglycerate; DPG23, 2,3-bisphosphoglycerate; PG3, 3-phosphoglycerate; PG2, 2-phosphoglycerate; PEP, Phosphoenolpyruvate; PYR, Pyruvate; LAC. Lactate; NADH, Nicotinamide adenine dinucleotide (reduced); GL6P. Application of the Method 6-Phospho-D-glucono-1,5-lactone; GO6P, 6-Phospho-D-gluconate; NADPH, Nicotinamide adenine dinucleotide phosphate (reduced); GSH, glutathione (reduced); RU5P, Ribulose-5- phosphate; R5P, Ribose-5-phosphate; X5P, Xylulose-5-phosphate; S7P, Sedoheptulose-7-phosphate; E4P, Erythrose-4-phosphate; ADO, Adenosine; AMP, Adenosine monophosphate; ADP, Adenosine diphosphate; ATP, Adenosine triphohsphate; PRPP, 5-Phospho-D-ribose 1-diphosphate; IMP, Inosine monophosphate; INO, Inosine; HX, Hypoxanthine; R1P, Ribose-1-phosphate; ADE, Adenine; NAI, Sodium; and KI, Potassium. doi:10.1371/journal.pcbi.1000177.g003 The time scale (k) for the formation of pools and the ratio between a pair of concentrations are functions of three factors: network stoichiometry (or topology), thermodynamics, and kinetic properties of the transformations in the network. Viewing the dynamics of the network in terms of the modal matrix and the pair-wise concentration correlations on progressing time scales enables one to consider the questions of (A) the thermodynamic versus kinetic control of concentrations within the whole network and (B) the delineation of kinetic versus topological decoupling in networks. making such thermodynamically neutral events lead to reduction in effective dynamic dimensionality. Deviations from such behavior are however observed, such as with 1,3 DPG and 2,3 DPG. Although the free energy of formation of these two must are close (as approximated by the group contribution method [9]), 2,3DPG does not pool together with 1,3DPG until the 31st mode (Figure 3). Hence the kinetic and allosteric regulatory ‘‘control’’ dominates. This ‘‘control’’ has physiological significance because 2,3DPG can regulate the binding affinity of hemoglobin for oxygen and is maintained at a higher concentration than the glycolytic intermediates. Other examples in which kinetic ‘‘control’’ dominates include ATP and NADPH, ADP and NADH, and G6P and ADP. Steady state kinetic versus thermodynamic equilibrium effects. The thermodynamic equilibrium pools of the network can be seen in Figure S2. Comparison of these pools with those in Figure 1 distinguishes between the equilibrium state and the kinetically driven steady state. In many cases such comparisons show a thermodynamic basis for pool formation, such as the hexose phosphates, the pentose phosphates, and the triose phosphates. For metabolite pairs that are thermodynamically close (with regards to the Gibbs free energy of formation), the kinetics presumably have been adjusted to be fast, Kinetic and topological decoupling. Two striking features of the tiled array are (1) the pooling between the majority of the compounds occurs on the slowest time scales and (2) the slopes for many of these are horizontal or vertical lines, implying dynami- cally independent behavior. Application of the Method This dynamically independent behavior may result from a lack of connectivity (topological PLoS Computational Biology | www.ploscompbiol.org September 2008 | Volume 4 | Issue 9 | e1000177 5 Elucidating Network Pooling Structure Figure 4. Converting human red cell metabolic network map into lumped pools according to time scale decomposition (adapted from [26]). Pooling on fast time scales define the chemical equilibrium pools and on slower time scales the physiological pools. doi:10.1371/journal.pcbi.1000177.g004 Figure 4. Converting human red cell metabolic network map into lumped pools according to time scale decomposition (adapted from [26]). Pooling on fast time scales define the chemical equilibrium pools and on slower time scales the physiological pools. doi:10.1371/journal.pcbi.1000177.g004 The tiled pooling array for folate metabolism was computed (Figure 5). There were 7 independent time scales in the modal matrix and one conserved folate moiety pool from the left null space. From the array it is observed that the folate carrier branch decoupling) or from independent kinetics (e.g., kinetic decoupling resulting from a zero order rate law). Thus, if compounds are detected to be topologically decoupled in the tiling array they are expected to dominate a particular mode. A kinetic or topologically decoupled compound will undergo the largest changes in concentration and interactions with other compounds during those time scales on which it plays a dominant role the modes. After these time scales have been passed, concentration changes are likely to be less significant and the compounds could be viewed as joining an aggregate pool, but may not be in a fixed ratio as would be dictated through strictly thermodynamic or kinetic coupling. Figure 5. Tiled array of the hierarchical pool formation for human folate metabolism (same layout and color coding as in Figure 3). Abbreviations: 5MTHF, 5-methyltetrahydrofolate; THF, tetrahydrofolate; DHF, dihydrofolate; CH2F, 5,10-methylenetrahydrofo- late; CHF, 5,10-methenyltetrahydrofolate; 10FTHF, 10-formyltetrahydro- folate; MET, methionine; SAM, S-adenosylmethionine; SAH, S-adenosyl- homocysteine; and HCY, homocysteine. doi:10.1371/journal.pcbi.1000177.g005 Networks that are tightly connected in terms of stoichiometry and kinetics will result in complete pooling of all metabolites on the slowest time scales, which is seen in large part in the red cell (Figure 1). There are examples of effectively uncoupled metabo- lites in this model however. Sodium and potassium for example are uncoupled from all metabolites except for the adenosine phosphates, which results from topological decoupling, since the only metabolites these ions interact with in the model are ATP and ADP via the Na/K ATPase. PLoS Computational Biology | www.ploscompbiol.org Application of the Method On time scales slower than the minute time scales (the sixth mode corresponds to ,6 minutes) the network boils down to interactions between the folate pool and the methionine pool. So on physiologically relevant time scales, the various possible interactions depicted in Figure 7A simplify to shifting between two carrier pools. (5MTHF, THF, DHF, CH2F, CHF, 10FTHF) of the network and the methionine metabolism branch (MET, SAM, SAH, HCY) of the network act fairly independently dynamically. S-adenosylme- thionine (SAM) is the primary metabolite which joins the interactions between the two branches. In order to identify if these interactions are topologically driven, kinetically driven, or combinations of both, one can plot the modes in which these interactions are most significant (see Material and Methods). Figure 6 depicts the primary interactions on the slowest mode in the network. It can be seen that SAM is not directly topologically coupled to the folate branch, so the interactions between the two branches, mediated by SAM is driven by kinetic effects. Additionally, note that although they pool together, SAM moves in opposition to the folate carriers. The folate network is depicted in Figure 7A and the progression of pooling over time is illustrated in Figure 7B. On time scales slower than the minute time scales (the sixth mode corresponds to ,6 minutes) the network boils down to interactions between the folate pool and the methionine pool. So on physiologically relevant time scales, the various possible interactions depicted in Figure 7A simplify to shifting between two carrier pools. Figure 6. An example of a graphical overlay of topological and kinetic data for the dominant interacting metabolites for a particular mode. The slowest mode in the folate network (,30 mi- nute time scale) is shown. The green and red shaded elements reflect the dynamic interactions between the metabolites on the 30 minute time scale (the colors reflect positive and negative entries, respectively). The blue lines indicate topological connectivity (i.e. from the stoichiometric matrix). doi:10.1371/journal.pcbi.1000177.g006 The tiled pooling array for the yeast glycolytic pathway was computed (Figure 8). The pooling structure of the glycolytic pathway is very similar to pool formation in the red cell, with glycolytic intermediates aggregating together on the faster time scales. The doi:10.1371/journal.pcbi.1000177.g006 Figure 7. Human folate metabolism and hierarchical simplification into aggregate pools. (A) A map of the folate network described by [23]. Application of the Method In contrast, pyruvate and lactate are decoupled from the rest of glycolysis, even though they are topologically connected to some of them, thus the decoupling is driven by kinetic effects. Figure 5. Tiled array of the hierarchical pool formation for human folate metabolism (same layout and color coding as in Figure 3). Abbreviations: 5MTHF, 5-methyltetrahydrofolate; THF, tetrahydrofolate; DHF, dihydrofolate; CH2F, 5,10-methylenetrahydrofo- late; CHF, 5,10-methenyltetrahydrofolate; 10FTHF, 10-formyltetrahydro- folate; MET, methionine; SAM, S-adenosylmethionine; SAH, S-adenosyl- homocysteine; and HCY, homocysteine. doi:10.1371/journal.pcbi.1000177.g005 The tiled arrays can be used to define the ‘effective dynamic dimensionality’ of the models by counting the number of different time scales during which two or more variables form an aggregate pool. For the networks considered, the effective dynamic dimension- ality reduced the dimension by one-third to one-half (see Table 1). September 2008 | Volume 4 | Issue 9 | e1000177 PLoS Computational Biology | www.ploscompbiol.org 6 Elucidating Network Pooling Structure Figure 6. An example of a graphical overlay of topological and kinetic data for the dominant interacting metabolites for a particular mode. The slowest mode in the folate network (,30 mi- nute time scale) is shown. The green and red shaded elements reflect the dynamic interactions between the metabolites on the 30 minute time scale (the colors reflect positive and negative entries, respectively). The blue lines indicate topological connectivity (i.e. from the stoichiometric matrix). doi:10.1371/journal.pcbi.1000177.g006 (5MTHF, THF, DHF, CH2F, CHF, 10FTHF) of the network and the methionine metabolism branch (MET, SAM, SAH, HCY) of the network act fairly independently dynamically. S-adenosylme- thionine (SAM) is the primary metabolite which joins the interactions between the two branches. In order to identify if these interactions are topologically driven, kinetically driven, or combinations of both, one can plot the modes in which these interactions are most significant (see Material and Methods). Figure 6 depicts the primary interactions on the slowest mode in the network. It can be seen that SAM is not directly topologically coupled to the folate branch, so the interactions between the two branches, mediated by SAM is driven by kinetic effects. Additionally, note that although they pool together, SAM moves in opposition to the folate carriers. The folate network is depicted in Figure 7A and the progression of pooling over time is illustrated in Figure 7B. Application of the Method (B) An illustration of progressive pool formation across the first 4 time scales for the folate network based on the results from Figure 5. Beyond the first time scale pools form between CHF and CH2F; and 5MTHF, 10FTHF, SAM; and MET and SAH. DHF and THF form a pool beyond the second time scale. Beyond the third time scale CH2F/CHF join the 5MTHF/10FTHF/SAM pool. Beyond the fourth time scale HCY joins the MET/SAH pool. Ultimately, on time scales on the order of a minute and slower, interactions between the pools of folate carriers and methionine metabolites interact. doi:10.1371/journal.pcbi.1000177.g007 Figure 7. Human folate metabolism and hierarchical simplification into aggregate pools. (A) A map of the folate network described by [23]. (B) An illustration of progressive pool formation across the first 4 time scales for the folate network based on the results from Figure 5. Beyond the first time scale pools form between CHF and CH2F; and 5MTHF, 10FTHF, SAM; and MET and SAH. DHF and THF form a pool beyond the second time scale. Beyond the third time scale CH2F/CHF join the 5MTHF/10FTHF/SAM pool. Beyond the fourth time scale HCY joins the MET/SAH pool. Ultimately, on time scales on the order of a minute and slower, interactions between the pools of folate carriers and methionine metabolites interact. doi:10.1371/journal.pcbi.1000177.g007 September 2008 | Volume 4 | Issue 9 | e1000177 September 2008 | Volume 4 | Issue 9 | e1000177 PLoS Computational Biology | www.ploscompbiol.org PLoS Computational Biology | www.ploscompbiol.org 7 Elucidating Network Pooling Structure Figure 8. Tiled array of the hierarchical pool formation for the yeast glycolytic pathway (same layout and color coding as in Figure 3). Glycolytic intermediates and adenosine phosphates pool together on fast time scales. Fragmented pooling is also observed (i.e. there were 0 entries in the slowest mode, indicating that on the slowest time scale, all of the components in the network do not move together in a lumped pool). GLC, intracellular glucose; GLCX, extracellular glucose; G6P, glucose 6-phosphate; F6P, fructose 6-phosphate; FBP, fructose 1,6- bisphosphate; GAP, glyceraldehyde 3-phosphate; DHAP, dihydroxyacetone phosphate; GLYC, intracellular glycerol; GLYCX, extracellular glycerol; BPG, 1,3-bisphosphoglycerate; PEP, phosphoenol pyruvate; PYR, pyruvate; ACA, intracellular acetaldehyde; ACAx, extracellular acetaldehyde; EtOH, intracellular ethanol; EtOHx, extracellular ethanol; NADH, nicotinamide adenine dinucleotide (reduced form); ATP. adenosine triphosphate; ADP, adenosine diphosphate. doi:10.1371/journal.pcbi.1000177.g008 Figure 8. Application of the Method Comparing the topological versus kinetic interactions in a graphical format (not shown) illustrates that the lack of interactions by acetate (ACA) and cyanide (CNX) with the other components in the network are due to topological constraints. adenosine phosphates also pool together very quickly. A feature of the tiled array not observed with the other models considered is fragmentation of the pooling structure. This implies that unlike the other two models considered, all of the metabolites do not eventually move together in fixed ratios on the slowest time scales. These effects can be driven by topological properties or kinetic properties of the network as well. Comparing the topological versus kinetic interactions in a graphical format (not shown) illustrates that the lack of interactions by acetate (ACA) and cyanide (CNX) with the other components in the network are due to topological constraints. The fragmented pooling reflects the fact that interactions between ACA and CNX and the rest of the network can only occur during particular time scales. These constraints however dictate much of the overall behavior of the network. The fragmented pooling observed in Figure 8 result in a simplified view of the network built around the transporters, as seen in Figure 9. Figure 9. Simplified model of the yeast glycolytic pathway dictated by the fragmented pooling of the network. The glycolytic and redox potentials are similar to those in the red cell. The adenosine phosphate potential is only composed of ATP and ADP. The NADH/NAD ratio determines the redox interactions with glycolysis, glycogen, and conversion between acetaldehyde and ethanol. doi:10.1371/journal.pcbi.1000177.g009 Taken together, in this study we: (1) developed top-down approaches for the computationally driven delineation of pools, (2) showed how to distinguish between topological, kinetic and thermodynamic basis for pool formation, and (3) applied the methods to analyze the dynamic structure of metabolic network models in yeast and humans. The application of these methods enabled the simplification of the networks based on the dynamic pooling of metabolites on progressive time scales and the identification of the key metabolic interactions on the slower time scales. Figure 9. Simplified model of the yeast glycolytic pathway dictated by the fragmented pooling of the network. The glycolytic and redox potentials are similar to those in the red cell. The adenosine phosphate potential is only composed of ATP and ADP. The NADH/NAD ratio determines the redox interactions with glycolysis, glycogen, and conversion between acetaldehyde and ethanol. PLoS Computational Biology | www.ploscompbiol.org Application of the Method Tiled array of the hierarchical pool formation for the yeast glycolytic pathway (same layout and color coding as in Figure 3). Glycolytic intermediates and adenosine phosphates pool together on fast time scales. Fragmented pooling is also observed (i.e. there were 0 entries in the slowest mode, indicating that on the slowest time scale, all of the components in the network do not move together in a lumped pool). GLC, intracellular glucose; GLCX, extracellular glucose; G6P, glucose 6-phosphate; F6P, fructose 6-phosphate; FBP, fructose 1,6- bisphosphate; GAP, glyceraldehyde 3-phosphate; DHAP, dihydroxyacetone phosphate; GLYC, intracellular glycerol; GLYCX, extracellular glycerol; BPG, 1,3-bisphosphoglycerate; PEP, phosphoenol pyruvate; PYR, pyruvate; ACA, intracellular acetaldehyde; ACAx, extracellular acetaldehyde; EtOH, intracellular ethanol; EtOHx, extracellular ethanol; NADH, nicotinamide adenine dinucleotide (reduced form); ATP. adenosine triphosphate; ADP, adenosine diphosphate. doi:10 1371/journal pcbi 1000177 g008 doi:10.1371/journal.pcbi.1000177.g008 adenosine phosphates also pool together very quickly. A feature of the tiled array not observed with the other models considered is fragmentation of the pooling structure. This implies that unlike the other two models considered, all of the metabolites do not eventually move together in fixed ratios on the slowest time scales. These effects can be driven by topological properties or kinetic properties of the network as well. Comparing the topological versus kinetic interactions in a graphical format (not shown) illustrates that the lack of interactions by acetate (ACA) and cyanide (CNX) with the other components in the network are due to topological constraints. The fragmented pooling reflects the fact that interactions between ACA and CNX and the rest of the network can only occur during particular time scales. These constraints however dictate much of the overall behavior of the network. The fragmented pooling observed in Figure 8 result in a simplified view of the network built around the transporters, as seen in Figure 9. subsequent time scales. Furthermore, metabolites that are connected to multiple pathways are likely to have change ratios even after they begin pooling. This is observed for ATP and ADP adenosine phosphates also pool together very quickly. A feature of the tiled array not observed with the other models considered is fragmentation of the pooling structure. This implies that unlike the other two models considered, all of the metabolites do not eventually move together in fixed ratios on the slowest time scales. These effects can be driven by topological properties or kinetic properties of the network as well. Materials and Methods The method developed above was developed, tested, and implemented in Mathematica (Wolfram Research, Chicago, IL) version 5.2. The models analyzed herein: the model of human red cell metabolism [20–22], human folate metabolism [23], and yeast glycolysis [24] were implemented in Mathematica. For each model, a stable steady state was identified by integrating the equations over time until the concentration variables no longer changed (error ,1610210, see Table S1). The Jacobian was then calculated symbolically at that steady state condition. A growing number of large-scale kinetic models of biochemical reaction networks are becoming available (e.g. http://www.cellml. org/, http://www.siliconcell.net/). There are also growing compi- lations of information regarding enzyme kinetics (e.g., http://www. brenda-enzymes.info/, http://sabio.villa-bosch.de/SABIORK/), which portend the development and availability of more kinetic models. Since dynamics simulations are not a viable approach for the comprehensive characterization of pool formation for larger models, there is a need for analysis based approaches to identify these general characteristics in metabolic networks. Temporal decomposition was carried out as described in the Results/Discussion section. Briefly for a general case, a similarity transformation [8] of a square matrix, A, is given by A = DLD21 in which D is invertible (by definition) and L is a diagonal matrix. D is an orthogonal matrix composed of eigenvectors correspond- ing to the entries of L (the eigenvalues). When the Jacobian matrix for a first order differential equation with respect to time is decomposed in this manner, the negative reciprocals of the eigenvalues correspond to the characteristic time scales for the corresponding modes [8] (this is immediately clear upon integration of Equation 4). All three of the models considered here exhibited at least one pair of complex conjugate eigenvalues at the steady states considered, hence the corresponding complex conjugate modes were combined in order to eliminate oscillating motions. The pooling approaches developed here were based on identifying the dynamically independent times scales and their corresponding modes. The principle pooling approach considered here was based on a particular calculation given by the matrix product, M{1  T M{1 ð7Þ ð7Þ The calculations for the correlations across progressive time scales were carried out as described in Results/Discussion. Once the modal matrix, M21, was calculated, all pairwise angles between the metabolites (columns of the modal matrix) were calculated (see Equation 5). The modal matrix is rank ordered from the fastest (k = 1) to the slowest (k = n) modes. Materials and Methods The angles between the columns of the modal matrix were recalculated n21 more times, in which an additional row of the modal matrix is zeroed out at each iteration. For example at the third iteration (k = 2), the first two rows of the modal matrix have been zeroed out. The spectrum of correlation cut-off values for pooling were considered from 10% to 99%. Cut-off values in the range 85% to 95% resulted in pooling of variables most consistent with the known pooling structures of the human red cell [2,5]. A value of 90% was used as the correlation cutoff for the red cell, folate, and yeast glycolysis models. The angle between two zero vectors was classified as undefined and the angle between any zero vector and another vector with at least one non-zero element was defined as 90u. Fragmentation of the pooling structure, in the strictest sense, was identified by any 0 entry (or ,,10213) in the final row of the metabolite modal matrix. In order to identify pools of metabolites, it was necessary to sequentially eliminate rows and recalculate the product, however it is worth noting that the matrix product in Equation 7 reflects the ‘dynamic connectivity’ of the network. These collective analyses of the modal matrix allowed the subsequent identification of pools, effective dimensionality reduction, differentiation between kinetic and topological properties, and characterizing the component condition numbers and strength of interactions between compo- nents in the network. There has been an increased interest in the analysis of the intrinsic characteristics of the growing number of available large- scale kinetic biological network models [10–14]. The systematic, algorithmic approach described herein demonstrated a general approach to pool identification, thus demonstrating how top-down analyses can be used to identify the hierarchical interactions between components over the span of time scales and assist in the simplification, analysis, and interpretation of network capabilities. This type of an analysis thus helps to link the component interactions to the overall physiological functions and how such functions can be affected by genetic parameters and how they respond to environmental conditions. Values for the Gibbs standard free energies of formation for the metabolites in the human red cell model were used from [25]. Elucidating Network Pooling Structure Elucidating Network Pooling Structure in the human red blood cell (Figure 3). These metabolites interact with glycolysis, the pentose phosphates, and the nucleotide salvage pathway and these interactions vary as the time scales are dominated by the different pathways. Conversely, the ATP/ADP ratio is fairly fixed and uniform in the yeast glycolytic model. This appears to be a result of the fact that there is only one major pathway that interacts with ATP and ADP. Further investigations into when and why pooling ratios change may lead to a richer appreciation of the integrated dynamic structure of metabolic networks. Additionally it was observed that the pooling structure may changes about different steady states. For example, in the human red cell changing the magnitude of the energy load will shift the time scale of the ATPase and hence alter the pooling of the network (not shown). This is also an area in which further investigation will yield an appreciation of altered dynamics corresponding to different steady state conditions. ments of the fluxome and metabolome at various time points, under different perturbations can be analyzed in terms of overall dynamics and used to validate the model when computed and measured results agree and alternatively used to highlight areas where further revisions are needed when they disagree. This will conceivably add a new dimension to the analysis of metabolism on the genome-scale. Materials and Methods Recently, with the continued development of technologies and experimental procedures to calculate cellular fluxes using iso- topomer data and to carry out quantitative metabolomic measurements on a larger scale [15–19], a more complete biochemical characterization of cells has become possible. The approach and analysis presented herein, using the Jacobian to characterize network and cellular level dynamics will benefit from and serve to benefit the utility of these large datasets. Measure- PLoS Computational Biology | www.ploscompbiol.org Application of the Method doi:10.1371/journal.pcbi.1000177.g009 There were some observations in the results worth pointing to suggest further areas worthy of investigation. The pooling ratios between metabolites are not always constant and metabolites that pool early on are more likely to have changing ratios on September 2008 | Volume 4 | Issue 9 | e1000177 8 References 15. Bartnik BL, Hovda DA, Lee PW (2007) Glucose metabolism after traumatic brain injury: estimation of pyruvate carboxylase and pyruvate dehydrogenase flux by mass isotopomer analysis. J Neurotrauma 24: 181–194. 1. Heinrich R, Schuster S, Holzhutter HG (1991) Mathematical analysis of enzymic reaction systems using optimization principles. Eur J Biochem 201: 1–21. y p y J 16. Brauer MJ, Yuan J, Bennett BD, Lu W, Kimball E, et al. (2006) Conservation of the metabolomic response to starvation across two divergent microbes. Proc Natl Acad Sci U S A 103: 19302–19307. 2. Kauffman KJ, Pajerowski JD, Jamshidi N, Palsson BO, Edwards JS (2002) Description and analysis of metabolic connectivity and dynamics in the human red blood cell. Biophys J 83: 646–662. 17. Schaub J, Mauch K, Reuss M (2007) Metabolic flux analysis in Escherichia coli by integrating isotopic dynamic and isotopic stationary 13C labeling data. Biotechnol Bioeng 99: 1170–1185. 3. Kholodenko BN, Schuster S, Garcia J, Westerhoff HV, Cascante M (1998) Control analysis of metabolic systems involving quasi-equilibrium reactions. Biochim Biophys Acta 1379: 337–352. 18. Vo TD, Paul Lee WN, Palsson BO (2007) Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh’s syndrome. Mol Genet Metab 91: 15–22. 4. Okino MS, Mavrovouniotis ML (1998) Simplification of mathematical models of chemical reaction systems. Chem Rev 98: 391–408. 5. Palsson BO, Joshi A, Ozturk SS (1987) Reducing complexity in metabolic networks: making metabolic meshes manageable. Fed Proc 46: 2485–2489. 19. Zhao J, Baba T, Mori H, Shimizu K (2004) Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on 13C-labeling experiments and the measurement of enzyme activities. Appl Microbiol Biotechnol 64: 91–98. 6. Heinrich R, Sonntag I (1982) Dynamics of non-linear biochemical systems and the evolutionary significance of time hierarchy. Biosystems 15: 301–316. e evolutionary significance of time hierarchy. Biosystems 15: 301–316 7. Reich J, Selkov E (1981) Energy Metabolism of the Cell: A Theoretical Treatise. New York: Academic Press. 20. Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BO (2001) Dynamic simulation of the human red blood cell metabolic network. Bioinformatics 17: 286–287. 8. Strang G (2003) Introduction to Linear Algebra. Wellesley: Wellesley-Cam- bridge. 21. Joshi A, Palsson BO (1989) Metabolic dynamics in the human red cell. Part I—a comprehensive kinetic model. J Theor Biol 141: 515–528. 9. Mavrovouniotis ML (1991) Estimation of standard Gibbs energy changes of biotransformations. J Biol Chem 266: 14440–14445. Acknowledgments We thank Dr. Christopher Henry for helpful correspondence and determination of Gibbs free energy of formation calculations for various metabolites. Supporting Information Figure S1 Illustrative example of time scale decomposition. An Illustrative example of modal decomposition for a toy network. The dynamics of 3 reactions involving 6 metabolites is analyzed in terms of the Jacobian matrix. Time scale decomposition is carried PLoS Computational Biology | www.ploscompbiol.org September 2008 | Volume 4 | Issue 9 | e1000177 September 2008 | Volume 4 | Issue 9 | e1000177 9 Elucidating Network Pooling Structure out along with simulations and determination of the pooling structure for this toy example. Table S1 Steady state concentrations and fluxes for folate, yeast, and red blood cell. Found at: doi:10.1371/journal.pcbi.1000177.s003 (0.02 MB XLS) Found at: doi:10.1371/journal.pcbi.1000177.s001 (0.09 MB PDF) Found at: doi:10.1371/journal.pcbi.1000177.s001 (0.09 MB PDF) Figure S2 Standard free energy of formation ratios for metabolites in the human red blood cell. The lower left triangle of the tiled array depicts a matrix with the ratios of the Gibbs free energy of formation between the metabolites in the red blood cell metabolic network. Ratios below 0.85 or above 1.15 were filtered out and not shown. The remaining entries (blackened entries) indicate expected pools if thermodynamic considerations alone determined the behavior of the network in a closed system. Author Contributions Conceived and designed the experiments: NJ BOP. Performed the experiments: NJ. Analyzed the data: NJ. Wrote the paper: NJ BOP. Conceived and designed the experiments: NJ BOP. Performed the experiments: NJ. Analyzed the data: NJ. Wrote the paper: NJ BOP. Found at: doi:10.1371/journal.pcbi.1000177.s002 (0.06 MB PDF) PLoS Computational Biology | www.ploscompbiol.org References 22. Joshi A, Palsson BO (1990) Metabolic dynamics in the human red cell. Part III— metabolic reaction rates. J Theor Biol 142: 41–68. 10. Famili I, Mahadevan R, Palsson BO (2005) k-Cone analysis: determining all candidate values for kinetic parameters on a network scale. Biophys J 88: 1616–1625. 23. Reed MC, Nijhout HF, Neuhouser ML, Gregory JF III, Shane B, et al. (2006) A mathematical model gives insights into nutritional and genetic aspects of folate- mediated one-carbon metabolism. J Nutr 136: 2653–2661. 11. Holzhutter HG (2006) The generalized flux-minimization method and its application to metabolic networks affected by enzyme deficiencies. Biosystems 83: 98–107. 24. Teusink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC, et al. (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem 267: 5313–5329. 12. Holzhutter S, Holzhutter HG (2004) Computational design of reduced metabolic networks. ChemBioChem 5: 1401–1422. constituent enzymes? Testing biochemistry. Eur J Biochem 267: 5313 25. Henry CS, Broadbelt LJ, Hatzimanikatis V (2007) Thermodynamics-based metabolic flux analysis. Biophys J 92: 1792–1805. 13. Klipp E (2007) Modelling dynamic processes in yeast. Yeast 24: 943–959. 14. Steuer R, Gross T, Selbig J, Blasius B (2006) Structural kinetic modeling of metabolic networks. Proc Natl Acad Sci U S A 103: 11868–11873. 26. Jamshidi N (2000) A Model of the Human Red Blood Cell Metabolism: The In Silico Erythrocyte. La Jolla: University of California San Diego. PLoS Computational Biology | www.ploscompbiol.org September 2008 | Volume 4 | Issue 9 | e1000177 10
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FOXO3a-mediated suppression of the self-renewal capacity of sphere-forming cells derived from the ovarian cancer SKOV3 cell line by 7-difluoromethoxyl-5,4′-di-n-octyl genistein
Molecular Medicine Reports
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Mol Med Rep 9: 1982‑1988, 2014; DOI: 10.3892/mmr.2014.2012 Mol Med Rep 9: 1982‑1988, 2014; DOI: 10.3892/mmr.2014.2012 Subsequently to the publication of this paper, an interested reader drew to the authors’ attention that strikingly similar western blot data were shown in Fig. 2 (to portray the Nagon data in Fig. 2A and the CD133 data in Fig. 2B), and the same data also appeared to have been included in Fig. 4 (to show the p‑FOXO3a data). After having examined their original data, the authors have realized that these figures were inadvertently assembled incorrectly Figure 2. SKOV3 cell‑line‑derived SFCs possess properties of OCSLCs. (A) Western immunoblot analysis demonstrated that BMI1, Nagon and SOX2 were highly expressed in SFCs derived from SKOV3 cells compared with the PC. (B) Western immunoblot analysis demonstrated that CD133, CD44 and ADLH1 were highly expressed in SFCs derived from SKOV3 cells compared with the PC. (C) H&E staining revealed that the histological features of SFC‑derived xenografted tumors were similar to those identified for parental SKOV3 cells (magnification, x100). SFCs, sphere‑forming cells; OCSLCs, ovarian cancer stem‑like cells; PC, parental cells. The corrected versions of Figs. 2 and 4, showing the correct data for the CD133 experiment in Fig. 2B and the p‑FOXO3a experiment in Fig. 4, are shown opposite. Note that these errors did not significantly affect the results or the conclusions reported in this paper, and all the authors agree to this Corrigendum. Furthermore, the authors apologize to the readership for any inconvenience caused. Figure 4. DFOG reduces FOXO3a phosphorylation and CSC marker expression of OCSLCs derived from SKOV3 cells. (A) The phosphorylated form of the FOXO3a protein was highly expressed in SFCs derived from SKOV3 cells compared with corresponding PCs. (B) Treatment with DFOG downregulated the expression of phosphorylated FOXO3a in SFCs derived from SKOV3 cells. (C) Treatment with DFOG downregulated the expression of the self‑renewal associated proteins, including BMI1, Nagon and SOX2 in SFCs derived from SKOV3 cells. (D) Treatment with DFOG downregulated the expression of CSC markers, including CD133, CD44 and ALDH1 in SFCs derived from SKOV3 cells. DFOG, 7‑difluoromethoxyl‑5,4’‑di‑n‑octyl genistein; CSC, cancer stem cell; OCSLCs, ovarian cancer stem‑like cells; SFCs, sphere‑forming cells; PCs, parental cells. Figure 4. DFOG reduces FOXO3a phosphorylation and CSC marker expression of OCSLCs derived from SKOV3 cells. (A) The phosphorylated form of the FOXO3a protein was highly expressed in SFCs derived from SKOV3 cells compared with corresponding PCs. This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) License. CORRIGENDUM DOI: 10.3892/mmr.2021.12449 DOI: 10.3892/mmr.2021.12449 FOXO3a‑mediated suppression of the self‑renewal capacity of sphere‑forming cells derived from the ovarian cancer SKOV3 cell line by 7‑difluoromethoxyl‑5,4’‑di‑n‑octyl genistein MOLECULAR MEDICINE REPORTS 24: 809, 2021 MOLECULAR MEDICINE REPORTS 24: 809, 2021 Figure 2. SKOV3 cell‑line‑derived SFCs possess properties of OCSLCs. (A) Western immunoblot analysis demonstrated that BMI1, Nagon and SOX2 were highly expressed in SFCs derived from SKOV3 cells compared with the PC. (B) Western immunoblot analysis demonstrated that CD133, CD44 and ADLH1 were highly expressed in SFCs derived from SKOV3 cells compared with the PC. (C) H&E staining revealed that the histological features of SFC‑derived xenografted tumors were similar to those identified for parental SKOV3 cells (magnification, x100). SFCs, sphere‑forming cells; OCSLCs, ovarian cancer stem‑like cells; PC, parental cells. Mol Med Rep 9: 1982‑1988, 2014; DOI: 10.3892/mmr.2014.2012 (B) Treatment with DFOG downregulated the expression of phosphorylated FOXO3a in SFCs derived from SKOV3 cells. (C) Treatment with DFOG downregulated the expression of the self‑renewal associated proteins, including BMI1, Nagon and SOX2 in SFCs derived from SKOV3 cells. (D) Treatment with DFOG downregulated the expression of CSC markers, including CD133, CD44 and ALDH1 in SFCs derived from SKOV3 cells. DFOG, 7‑difluoromethoxyl‑5,4’‑di‑n‑octyl genistein; CSC, cancer stem cell; OCSLCs, ovarian cancer stem‑like cells; SFCs, sphere‑forming cells; PCs, parental cells.
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Implementation of WHO multimodal strategy for improvement of hand hygiene: a quasi-experimental study in a Traditional Chinese Medicine hospital in Xi’an, China
Antimicrobial resistance and infection control
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* Correspondence: w.xq1123@163.com 1Department of Infection Control, Xi’an Hospital of Traditional Chinese Medicine, No.69 Feng Cheng 8th Road, Weiyang District, Xi’an 710021, China Full list of author information is available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Implementation of WHO multimodal strategy for improvement of hand hygiene: a quasi-experimental study in a Traditional Chinese Medicine hospital in Xi’an, China Li Shen1, Xiaoqing Wang1* , Junming An2, Jialu An3, Ning Zhou1, Lu Sun1, Hong Chen1, Lin Feng4, Jing Han3 and Xiaorong Liu3 RESEARCH Open Access Implementation of WHO multimodal strategy for improvement of hand hygiene: a quasi-experimental study in a Traditional Chinese Medicine hospital in Xi’an, China Li Shen1, Xiaoqing Wang1* , Junming An2, Jialu An3, Ning Zhou1, Lu Sun1, Hong Chen1, Lin Feng4, Jing Han3 and Xiaorong Liu3 Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 DOI 10.1186/s13756-017-0254-4 RESEARCH Open Access Implementation of WHO multimodal strategy for improvement of hand hygiene: a quasi-experimental study in a Traditional Chinese Medicine hospital in Xi’an, China Li Shen1, Xiaoqing Wang1* , Junming An2, Jialu An3, Ning Zhou1, Lu Sun1, Hong Chen1, Lin Feng4, Jing Han3 and Xiaorong Liu3 Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 DOI 10.1186/s13756-017-0254-4 Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 DOI 10.1186/s13756-017-0254-4 Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 DOI 10.1186/s13756-017-0254-4 Part II: Observation of compliance and correctness before and after intervention Part II: Observation of compliance and correctness before and after intervention Part II: Observation of compliance and correctness before and after intervention g Healthcare-associated infection (HAI) represents a major burden and safety issue for patients in the developing countries, with severe and greatly underestimated effect on patients and health care systems [1]. According to the survey of National HAI Surveillance System, in 2014, at least 26,972 cases of HAI arose in patients admitted to hospital in China [2]. HAI resulted in prolonged length of hospital stay, direct economic loss, morbidity and mortal- ity among hospitalized patients [3]. A recent study in China identified that the average cost of hospitalization in- creased ¥13,839.16(€1792.64) due to HAI [4]. The hands of healthcare workers (HCWs) can be a major mode of transmission of microbial pathogens by touching the en- vironment or patients’ skin during healthcare delivery, which supports that hand hygiene (HH) is a critical com- ponent of a bundle approaches for preventing and con- trolling HAIs [5–9]. The World Health Organization (WHO) launched a multimodal strategy in 2009 to im- prove HH practice worldwide, which includes 5 important components: (1) system change, (2) training and educa- tion, (3) evaluation and feedback, (4) reminders in the workplace (5) institutional safety climate [10]. It has been demonstrated the implementation of WHO HH strategy is feasible and effective to enhance hand hygiene compli- ance, which leads to a reduction of HAI [11–14]. However, there have been few data on the implementation of the WHO multimodal HH strategy in China. We initi- ated this study of implementation of WHO multimodal HH strategy in order to improve awareness of HAI and enhance HH compliance and correctness among HCWs. In this part, detailed intervention measures were drawn up and then implemented according to the multimodal improvement strategy acquired from the results of ques- tionnaire survey. We collected observational data on compliance and correctness with HH before and after intervention respectively. Observation sessions were performed by 9 trained stu- dent nurses. The training course included HH indica- tions and correct HH techniques recommended by WHO. A standard form was used to record the HH compliance and correctness. Observers were taught how to complete the form and record the number of HH ac- tions and HH opportunities. We defined an opportunity as the occurrence of any indication during the observed care sequences. Part I: Questionnaire survey In this part, we did a questionnaire survey on pos- sible factors affecting HH behaviors of HCWs. Each participant voted those factors contributing to HH noncompliance from the questionnaire. On the basis of the reasons for HH noncompliance summarized in the questionnaire, multimodal improvement strategy was developed accordingly. Part II: Observation of compliance and correctness before and after intervention We recorded actions, either handwash- ing or hand rubbing based on WHO “My Five Moments for Hand Hygiene”: before touching a patient, before clean/aseptic procedure, after body fluid exposure risk, after touching a patient, and after touching patient sur- roundings [15]. Since an indication for HH was related to the risk of pathogen transmission from one surface to another, we added two more WHO recommended indi- cations in our study: if moving from a contaminated body site to a clean body site during patient care, after removing gloves [16]. An action with correct HH tech- niques must satisfy three criteria: (1) rub hands with 6- step HH techniques; (2) duration of the rub procedure lasts 15 s at least; (3) dry hands with disposable paper towels. Each observer monitored the HH practice of HCWs for 45–60 min. Abstract Background: Hand hygiene (HH) is an essential component for preventing and controlling of healthcare-associated infection (HAI), whereas compliance with HH among health care workers (HCWs) is frequently poor. This study aimed to assess compliance and correctness with HH before and after the implementation of a multimodal HH improvement strategy launched by the World Health Organization (WHO). Methods: A quasi-experimental study design including questionnaire survey generalizing possible factors affecting HH behaviors of HCWs and direct observation method was used to evaluate the effectiveness of WHO multimodal HH strategy in a hospital of Traditional Chinese Medicine. Multimodal HH improvement strategy was drawn up according to the results of questionnaire survey. Compliance and correctness with HH among HCWs were compared before and after intervention. Also HH practices for different indications based on WHO “My Five Moments for Hand Hygiene” were recorded. Results: In total, 553 HCWs participated in the questionnaire survey and multimodal HH improvement strategy was developed based on individual, environment and management levels. A total of 5044 observations in 23 wards were recorded in this investigation. The rate of compliance and correctness with HH improved from 66.27% and 47.75% at baseline to 80.53% and 88.35% after intervention. Doctors seemed to have better compliance with HH after intervention (84.04%) than nurses and other HCWs (81.07% and 69.42%, respectively). When stratified by indication, compliance with HH improved for all indications after intervention (P < 0.05) except for “after body fluid exposure risk” and “after touching patient surroundings”. Conclusion: Implementing the WHO multimodal HH strategy can significantly improve HH compliance and correctness among HCWs. Keywords: Hand hygiene, Compliance, Correctness, Healthcare-associated infection Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Page 2 of 7 Page 2 of 7 Page 2 of 7 Methods Compliance and correctness with HH were compared before and after the implementation. HCWs including doctors, nurses, technicians, interns and cleaners were observed for HH actions and HH opportunities. Data of technicians, interns and cleaners was combined as other HCWs. We expressed HH compliance as the proportion of predefined opportunities met by HH actions. And HH correctness was regarded as the proportion of all HH ac- tions met by HH actions with correct techniques. All the data was analyzed with SPSS version 16.0. The Chi square test was applied to test the statistical difference in HH compliance and correctness before and after the implementation. Also HH compliance stratified by pro- fessional category and indication was calculated. Results with P < 0.05 were considered statistically significant. The study was conducted in Xi’an Hospital of Traditional Chinese Medicine (TCM), Xi’an, China, between September 2015 and August 2016. It is the largest public hospital in north Xi’an, which is the capital city of Shaanxi Province. This hospital has 1001 beds in 27 clinical departments including acupuncture and moxibustion, intensive care, emergency, surgical and TCM subspecialties with 1377 HCWs. We performed this two-part quasi-experimental study including questionnaire survey of factors affecting HH behaviors of HCWs and direct observation of compliance and correctness with HH before and after intervention. Part I: Questionnaire survey Part I: Questionnaire survey A total of 558 HCWs from 37 departments participated in this survey. Of these, 553 (99.10%) completed the baseline questionnaire. The general information of all participants was summarized in Table 1. Each participant Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Page 3 of 7 Page 3 of 7 Table 1 The general information of 553 participants in the survey N (cases) Percentage (%) Mean (±s) Age 553 31.78 ± 8.120 Gender Female 433 78.30 Male 120 21.70 Work experience <1 year 104 18.81 1 ~ 5 years 139 25.13 5 ~ 10 years 155 28.03 ≥10 years 155 28.03 Education level Senior high school 14 2.53 Junior college 181 32.73 College 273 49.37 Post graduate 85 15.37 Profession Doctors 191 34.54 Nurses 300 54.25 Technicians 35 6.33 Interns 23 4.16 Cleaners 4 0.72 Table 1 The general information of 553 participants in the survey N (cases) Percentage (%) Mean (±s) Age 553 31.78 ± 8.120 For the individual reasons such as poor HH awareness, full training campaign on HH techniques among HCWs was carried out. Our management of infection control department first participated in the training of WHO “My Five Moments for Hand Hygiene” provided by Xi’an Quality Control Center of Nosocomial Infection. Then we shoot instructional videos on five key moments for HH and correct HH techniques in our hospital wards with our HCWs. After that they were called together to study HH knowledge via videos and PPT (based on WHO training slides). All the HCWs including doctors, nurses, interns, student nurses, lab technicians and cleaners should attend educational courses on HH every year. A posttest format was used to assess training effi- cacy after each course. Inadequate HH supplies and inconvenient HH facil- ities was another cause for noncompliance with HH in our hospital. We took a series of measures to improve HH facilities: increasing supplies of pocket alcohol-based hand rub (ABHR) and disposable paper towels; making sure every wash basin equipped with disposable paper towels and poster for correct handwashing techniques; replacing water tap in nurse station with automatic elec- tronic sensor tap; distributing skin care products to HCWs. Colorful HH posters were placed in the doctor’s office in each ward with WHO “My Five Moments for Hand Hygiene”. A little tip for HH was placed at the edge of the computer screen of nurse station. HH compliance by indication The rate of compliance with HH was statistically ele- vated after intervention for all indications (P < 0.05) ex- cept for “after body fluid exposure risk” and “after touching patient surroundings”. The highest relative im- provement appeared to be indication “if moving from a contaminated body site to a clean body site during pa- tient care”, from 30.61% to 59.82% (shown in Table 4). Part II: Observation of compliance and correctness before and after intervention HH compliance In our study, a total of 5044 opportunities for HH were recorded in 23 wards before and after intervention. The rate of compliance with HH improved from 66.27% at baseline to 80.53% after intervention (shown in Table 2). After implementing the improvement strategy, doctors had better HH compliance (84.04%) than nurses and other HCWs (81.07% and 69.42%, respectively). The rate Part I: Questionnaire survey Visible re- minders for HH were also set at the entrance of each ward. To create a better environment for HH, we offered large-scale HH improvement campaign to both HCWs voted those factors contributing to HH noncompliance from the questionnaire. All the possible factors affecting HH behaviors of HCWs were arranged in descending order according to the number of votes (Fig. 1). The main reasons for HH noncompliance were classified into indi- vidual, environment and management levels. Multimodal improvement strategy was drafted accordingly (Fig. 2) and detailed intervention measures were drawn up at the same time. Fig. 1 Possible factors affecting HH behaviors of HCWs in the questionnaire survey Fig. 1 Possible factors affecting HH behaviors of HCWs in the questionnaire survey Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Page 4 of 7 Fig. 2 Main reasons for HH noncompliance and corresponding improvement measures Fig. 2 Main reasons for HH noncompliance and corresponding improvement measures of compliance with HH was statistically increased after intervention for each professional category (P < 0.05). of compliance with HH was statistically increased after intervention for each professional category (P < 0.05). and patients with knowledge contest, visible display boards, and live performance. In order to strengthen the supervision of HH practice among HCWs, a seasonal feedback and evaluation sys- tem was established. Management of infection control department regularly reported HH compliance and HH products consumption in the meeting of Nosocomial Infection Control Management Committee, which in- cluded hospital management, department heads, head nurses and focal persons. Also HH compliance and HH products consumption was directly related to the scores of quality control of each department through HH re- wards and punishment mechanism. Department with noncompliant HCWs had to pay a fine. HH correctness A total of 2927 actions with correct HH techniques were recorded. The rate of correctness with HH im- proved from 47.75% to 88.35% after intervention (shown in Table 3). The increase of correctness ap- plied for all professional categories, which was statis- tically significant (P < 0.05). Discussion We recog- nized that compliance rates were above 70% for these two indications before intervention, which suggested that our HCWs intended to perform HH when they thought there might be microbial contamination and in- fection risk. In addition, compliance rates for “before” related indications were promoted after intervention, such as “before touching a patient” and “before clean/ aseptic procedures”. These findings revealed that HCWs were inclined to wash their hands to protect themselves rather than protect patients from potential infection, which was noted in previous studies [31, 32]. As for in- dication “after touching patient surroundings”, HH op- portunities with this indication were most commonly associated with lower levels of compliance than follow- ing direct patient contact [33]. Traditional Chinese Medicine treatments such as acupuncture and moxibus- tion are often combined with diathermy machine and herb fumigation device to get better curative effect. Most of our HCWs could perform HH after therapy devices were turned off. But when there was need to adjust the setting of therapy devices, required HH practices were not performed according to our observers. Multiple studies indicated that HAI could be caused by many pathogenic organisms present in the hospital environ- ment and objects frequently touched by patients’ hands, such as bed side rail, door knob, patient record, nurse call button [34, 35]. Moreover, it was of vital import- ance to strengthen the effectiveness of cleaning and in order to prevent the transmission of pathogens from patient surrounding environment to HCWs and patients [36, 37]. T ll k l d h th HCW t d Epidemiological evidence have shown that hand con- tamination of nurses could cause cross-infection in a direct or indirect way, especially in intensive care unit and hemodialysis unit where nurses have many patient contact opportunities [26, 27]. In our study, HH compli- ance of doctors seemed superior to nurses when strati- fied by professional category. There were far more opportunities of HH for nurses in most departments than for doctors. Then overcrowding workload of nurses made them provide clinical care to multiple patients without HH to finish their tasks faster. HH compliance in other HCWs was generally lower than doctors and nurses. Poor HH compliance was witnessed among tech- nicians during physiotherapy [28]. Gloves were often used during cleaning work to replace HH by cleaners, which might increase the risk of transmission of bacteria via contaminated gloved hands [29, 30]. Discussion Antimicrobial Resistance and Infection Control (2017) 6:98 Page 5 of 7 Table 4 Comparison of HH compliance before and after intervention of HCWs by indication HH compliance before intervention (%) HH compliance after intervention (%) χ2 P Before touching a patient 263/489 (53.78) 766/944 (81.14) 119.121 <0.001 After touching a patient 374/489 (76.48) 737/897 (82.16) 6.420 0.011 If moving from a contaminated body site to a clean body site during patient care 15/49 (30.61) 134/224 (59.82) 13.837 <0.001 After body fluid exposure risk 65/84 (77.38) 172/209 (82.30) 0.937 0.333 Before clean/aseptic procedures 160/254 (62.99) 460/552 (83.33) 40.547 <0.001 After touching patient surroundings 150/190 (78.95) 339/415 (81.69) 0.631 0.427 After removing gloves 83/120 (69.17) 105/128 (82.03) 5.589 0.018 Table 4 Comparison of HH compliance before and after intervention of HCWs by indication irritation and dryness, which was a vital cause for non- compliance with HH. In addition, irritated hands might be more vulnerable to be colonized with pathogens [17]. Since cleaning hands frequently is essential for every health care worker, it is important for health care set- tings to provide proper HH products. Compared with detergent and soap, ABHR has been reported to cause less skin irritation, especially those with emollient prop- erties [18, 19]. The application of skin care products can preserve unimpaired skin, reduce the incidence of skin irritation and dryness and ensure effective hand hygiene [20]. In the last decades, there were concerns that skin care products might pose a negative influence on the ef- ficacy of hand disinfection [21, 22]. With the wide re- search of well-formulated disinfectants with emollients in recent years, it seems that the efficacy of disinfectants would not be impaired when they are applied with se- lected, compatible skin care products [23, 24]. In our study, we provided skin care products to our HCWs to minimize the influence on HH compliance due to skin irritation and dryness. Moreover, we encourage our HCWs to use skin care products before work, cleaning and after work under recommendations [25]. to accomplish full training on HH. All in all, HH com- pliance was improved in different professional categories after intervention. Data of compliance by different HH indication was also investigated in the present study. Compliance with HH improved after intervention across all indications except for “after body fluid exposure” and “after touch- ing patient surroundings” in the observation. Discussion Our study identified that implementation of WHO multimodal HH improvement strategy was effective to enhance HH compliance and correctness among HCWs. In the questionnaire survey, over 50% of the participants thought frequently washing hands led to hand skin Table 3 Comparison of HH correctness of HCWs before and after intervention by professional category HH correctness before intervention (%) HH correctness after intervention (%) χ2 P Doctors 169/342 (49.42) 201/279 (72.04) 32.669 <0.001 Nurses 349/747 (46.72) 2030/2266 (89.59) 621.30 <0.001 Other HCWs 12/21 (57.14) 166/168 (98.81) 59.123 <0.001 Overall 530/1110 (47.75) 2397/2713 (88.35) 723.76 <0.001 Table 2 Comparison of HH compliance of HCWs before and after intervention by professional category HH compliance before intervention (%) HH compliance after intervention (%) χ2 P Doctors 342/459 (74.51) 279/332 (84.04) 10.362 0.001 Nurses 747/1081 (69.10) 2266/2795 (81.07) 64.538 <0.001 Other HCWs 21/135 (15.56) 168/242 (69.42) 100.58 <0.001 Overall 1110/1675 (66.27) 2713/3369 (80.53) 123.99 <0.001 Table 3 Comparison of HH correctness of HCWs before and after intervention by professional category HH correctness before intervention (%) HH correctness after intervention (%) χ2 P Doctors 169/342 (49.42) 201/279 (72.04) 32.669 <0.001 Nurses 349/747 (46.72) 2030/2266 (89.59) 621.30 <0.001 Other HCWs 12/21 (57.14) 166/168 (98.81) 59.123 <0.001 Overall 530/1110 (47.75) 2397/2713 (88.35) 723.76 <0.001 Table 2 Comparison of HH compliance of HCWs before and after intervention by professional category HH compliance before intervention (%) HH compliance after intervention (%) χ2 P Doctors 342/459 (74.51) 279/332 (84.04) 10.362 0.001 Nurses 747/1081 (69.10) 2266/2795 (81.07) 64.538 <0.001 Other HCWs 21/135 (15.56) 168/242 (69.42) 100.58 <0.001 Overall 1110/1675 (66.27) 2713/3369 (80.53) 123.99 <0.001 Table 3 Comparison of HH correctness of HCWs before and after intervention by professional category Table 2 Comparison of HH compliance of HCWs before and after intervention by professional category Shen et al. Competing interests Th h d l h p g The authors declare that they have no competing interests. p g The authors declare that they have no competing interests. Funding g Project supported by Key Science and Technology R & D Program of Shaanxi Province, China (Grant No.2016SF-213). Discussion Besides, the growing mobility of cleaners and interns made it difficult To well acknowledge whether our HCWs mastered the standard handwashing techniques, HH correctness Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Page 6 of 7 Page 6 of 7 Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Availability of data and materials The raw data supporting the results of this study are included within the article and its additional files. Additional file 1, Additional file 2 and Additional file 3. Authors’ contributions LS carried out the study and drafted the manuscript. XW conceived of the study, participated in its design and coordination. JA contributed to the design of the study. JA participated in the literature review and performed statistical analysis. NZ, LS and HC provided training of hand hygiene indications and correct hand hygiene techniques for observers and collected data. LF organized workers to improve hand hygiene products and facilities. JH and XL contributed to check and enter data. All authors read and approved the final manuscript. Conclusions was investigated at the same time. In general, correct- ness rate was far below our standards before interven- tion. During the period of investigation, we found two most commonly reasons for low HH correctness rate in our hospital. Most of our HCWs knew the right HH technique procedures but the duration of rubbing hands did not meet our requirement (15 s at least). Inadequate disposable paper towel was another cause for unpleasant HH correctness rate. Therefore our infection control staff took steps to promote correct HH techniques, which included correct HH techniques training, increas- ing supplies of pocket ABHR and disposable paper towels. As a result, our HCWs’ HH correctness rates were elevated after intervention. In conclusion, this intervention study has shown that implementation of WHO multimodal improvement strategy could significantly increase compliance and cor- rectness with HH in our hospital. Further investigations with sufficient sample size and larger multicenter series are needed to validate the effectiveness of long-term per- sistence of HH compliance improvement strategy. Consent for publication Not applicable. Consent for publication Not applicable. Additional files Additional file 1: HH raw data. (SAV 12 kb) Additional file 2: Possible factors. (SAV 2 kb) Additional file 3: Questionnaire survey raw data. (SAV 25 kb) Additional file 1: HH raw data. (SAV 12 kb) Additional file 2: Possible factors. (SAV 2 kb) Additional file 3: Questionnaire survey raw data. (SAV 25 kb) Additional file 1: HH raw data. (SAV 12 kb) Additional file 2: Possible factors. (SAV 2 kb) Additional file 3: Questionnaire survey raw data. (SAV 25 kb) In the last few years, domestic researches on im- proving HH practice have been reported in succession [38–44]. It is noteworthy that our study is the first observational before-and-after intervention study on improving HH compliance in Xi’an, Shaanxi province. Meanwhile it is the first study implementing WHO multimodal strategy to promote HH practice in a hospital of Traditional Chinese Medicine. HCWs have many patient contact opportunities in the process of Traditional Chinese Medicine treatments such as acu- puncture and moxibustion, massage, cupping and other physical therapies. If standard HH practice were not performed, it might increase the risk of cross- infection. Our study summarized the reasons for non- compliance with HH and provided scientific evidence to promote HH practice for other hospitals of Trad- itional Chinese Medicine. Nevertheless, this study also had certain limitations. The entire observation of HH compliance and correctness were only carried out in general inpatient wards. We planned to observe HH practice in critical departments for infection control management such as emergency, intensive care unit and hemodialysis unit. These places are characterized by high patient volume, critically ill patients and more invasive operations. Improving HH compliance in such places would be meaningful for better infection control. Furthermore, using student nurses as ob- servers might have an impact on observation process. These student nurses observed HH practice of HCWs in clinical wards during their clinical clerkships. Some students told us they recognized their former teaching nurses and classmates in the observation process and thus we concerned that this covert investigation might present the Hawthorn effect. In order to lessen the influence of the Hawthorn effect on HH compli- ance of HCWs, we plan to train every HCW in our hospital to become a competent observer for HH compliance of their co-workers. In this way every HCW could be our covert observer and we could col- lect reliable data of HH practice. Ethics approval and consent to participate Our study was approved by the Ethics Committee of Xi’an Hospital of Traditional Chinese Medicine (No.XAZYYLS2015–05). The need for consent to participate was waived as no individual person’s data were collected in any form. Our study was approved by the Ethics Committee of Xi’an Hospital of Traditional Chinese Medicine (No.XAZYYLS2015–05). The need for consent to participate was waived as no individual person’s data were collected in any form. Abbreviations ABHR: Alcohol-based hand rub; HAI: Healthcare-associated infection; HCWs: Health care workers; HH: Hand hygiene; TCM: Traditional Chinese Medicine; WHO: World Health Organization References Role of hand hygiene in healthcare-associated infection prevention. J Hosp Infect. 2009;73:305–15. 7. Allegranzi B, Pittet D. Role of hand hygiene in healthcare-associated infection prevention. J Hosp Infect. 2009;73:305–15. 8. Dancer SJ. The role of environmental cleaning in the control of hospital- acquired infection. J Hosp Infect. 2009;73:378–85. 32. Patel B, Engelbrecht H, McDonald H, Morris V, Smythe W. A multifaceted hospital-wide intervention increases hand hygiene compliance. S Afr Med J. 2016;106:32–5. 9. Weber DJ, Anderson D, Rutala WA. The role of the surface environment in healthcare-associated infections. Curr Opin Infect Dis. 2013;26:338–44. 33. FitzGerald G, Moore G, Wilson AP. Hand hygiene after touching a patient's surroundings: the opportunities most commonly missed. J Hosp Infect. 2013;84:27–31. 10. WHO. Guide to implementation: a guide to the implementation of the WHO Multimodal Hand Hygiene Improvement Strategy. 2009. http://www. who.int/gpsc/5may/Guide_to_Implementation.pdf (Accessd Feb 7,2017). 34. Donskey CJ. Does improving surface cleaning and disinfection reduce health care-associated infections? Am J Infect Control. 2013;41:S12–9. g y 11. Allegranzi B, Gayet-Ageron A, Damani N, Bengaly L, McLaws ML, Moro ML, et al. Global implementation of WHO's multimodal strategy for improvement of hand hygiene: a quasi-experimental study. Lancet Infect Dis. 2013;13:843–51. 35. Weber DJ, Rutala WA, Miller MB, Huslage K, Sickbert-Bennett E. Role of hospital surfaces in the transmission of emerging health care-associated pathogens: norovirus, Clostridium Difficile, and Acinetobacter species. Am J Infect Control. 2010;38:S25–33. 12. Arntz PR, Hopman J, Nillesen M, Yalcin E, Bleeker-Rovers CP, Voss A, et al. Effectiveness of a multimodal hand hygiene improvement strategy in the emergency department. Am J Infect Control. 2016;44:1203–7. 36. Ramphal L, Suzuki S, McCracken IM, Addai A. Improving hospital staff compliance with environmental cleaning behavior. Proc (Bayl Univ Med Cent). 2014;27:88–91. 13. Farhoudi F, Sanaei Dashti A, Hoshangi Davani M, Ghalebi N, Sajadi G, Taghizadeh R. Impact of WHO hand hygiene improvement program implementation: a quasi-experimental trial. Biomed Res Int. 2016;2016: 7026169. 37. Kurashige EJ, Oie S, Furukawa H. Contamination of environmental surfaces by methicillin-resistant Staphylococcus Aureus (MRSA) in rooms of inpatients with MRSA-positive body sites. Braz J Microbiol. 2016;47:703–5. 14. Pfafflin F, Tufa TB, Getachew M, Nigussie T, Schonfeld A, Haussinger D, et al. Implementation of the WHO multimodal Hand Hygiene Improvement Strategy in a University Hospital in Central Ethiopia. Antimicrob Resist Infect Control. 2017;6:3. 38. Ji G, Yin H, Chen Y. Author details 1 1Department of Infection Control, Xi’an Hospital of Traditional Chinese Medicine, No.69 Feng Cheng 8th Road, Weiyang District, Xi’an 710021, China. 2Department of Acupuncture and Moxibustion, Xi’an Hospital of Traditional Chinese Medicine, No.69 Feng Cheng 8th Road, Weiyang District, Xi’an 710021, China. 3Department of Information Consultation, Library of Xi’an Jiaotong University, No.76 Yan Ta West Road, Yanta District, Xi’an 710061, China. 4Department of Cadre Health Care, Xi’an Hospital of Traditional Chinese Medicine, No.69 Feng Cheng 8th Road, Weiyang District, Xi’an 710021, China. Page 7 of 7 Page 7 of 7 Page 7 of 7 Shen et al. Antimicrobial Resistance and Infection Control (2017) 6:98 Received: 1 June 2017 Accepted: 4 September 2017 Received: 1 June 2017 Accepted: 4 September 2017 the efficacy of surgical hand disinfection and surgical glove perforation. BMC Infect Dis. 2014;14:315. the efficacy of surgical hand disinfection and surgical glove perforation. BMC Infect Dis. 2014;14:315. 25. Kampf G, Loffler H. Prevention of irritant contact dermatitis among health care workers by using evidence-based hand hygiene practices: a review. Ind Health. 2007;45:645–52. References 26. Duong MC, McLaws ML. Dangerous practices in a hemodialysis unit in Vietnam identify from mixed methods. BMC Infect Dis. 2017;17:181. 1. Allegranzi B, Bagheri Nejad S, Combescure C, Graafmans W, Attar H, Donaldson L, et al. Burden of endemic health-care-associated infection in developing countries: systematic review and meta-analysis. Lancet. 2011;377:228–41. 27. Ghorbani A, Sadeghi L, Shahrokhi A, Mohammadpour A, Addo M, Khodadadi E. Hand hygiene compliance before and after wearing gloves among intensive care unit nurses in Iran. Am J Infect Control. 2016;44:e279–e81. 2. Ren N, Wen X, Wu A. Nationwide cross-sectional survey on healthcare-associated infection in 2014. Chinese Journal of Infection Control. 2016;15:83–7. 2. Ren N, Wen X, Wu A. Nationwide cross-sectional survey on healthcare-associated infection in 2014. Chinese Journal of Infection Control. 2016;15:83–7. 28. O'Donoghue M, Ng SH, Suen LK, Boost M. A quasi-experimental study to determine the effects of a multifaceted educational intervention on hand hygiene compliance in a radiography unit. Antimicrob Resist Infect Control. 2016;5:36. 3. Graves N, Weinhold D, Tong E, Birrell F, Doidge S, Ramritu P, et al. Effect of healthcare-acquired infection on length of hospital stay and cost. Infect Control Hosp Epidemiol. 2007;28:280–92. 3. Graves N, Weinhold D, Tong E, Birrell F, Doidge S, Ramritu P, et al. Effect of healthcare-acquired infection on length of hospital stay and cost. Infect Control Hosp Epidemiol. 2007;28:280–92. 29. McBryde ES, Bradley LC, Whitby M, McElwain DL. An investigation of contact transmission of methicillin-resistant Staphylococcus Aureus. J Hosp Infect. 2004; 58:104–8. 4. Jia H, Hou T, Li W, Ma Q, Liu W, Yang Y, et al. Economic loss due to healthcare- associated infection in 68 general hospitals in China. Chinese Journal of Infection Control. 2016;15:637–41. 30. Snyder GM, Thom KA, Furuno JP, Perencevich EN, Roghmann MC, Strauss SM, et al. Detection of methicillin-resistant Staphylococcus Aureus and vancomycin-resistant enterococci on the gowns and gloves of healthcare workers. Infect Control Hosp Epidemiol. 2008;29:583–9. 5. Allegranzi B, Pittet D. Preventing infections acquired during health-care delivery. Lancet. 2008;372:1719–20. 6. Chen P, Liu D. Epidemiological characteristics and preventive strategies of nosocomial infection outbreak incidents in China in recent 30 years. Chinese Journal of Infection Control. 2010;9:387–92,99. 31. Lee A, Chalfine A, Daikos GL, Garilli S, Jovanovic B, Lemmen S, et al. Hand hygiene practices and adherence determinants in surgical wards across Europe and Israel: a multicenter observational study. Am J Infect Control. 2011;39:517–20. 7. Allegranzi B, Pittet D. References Prevalence of and risk factors for non-compliance with glove utilization and hand hygiene among obstetrics and gynaecology workers in rural China. J Hosp Infect. 2005;59:235–41. 15. WHO. About SAVE LIVES: Clean Your Hands. 2009. http://www.who.int/gpsc/ 5may/background/5moments/en/ (Accessd Feb 7,2017). 39. Li LY, Zhao YC, Jia JX, Zhao XL, Jia HX. Investigation on compliance of hand hygiene of healthcare workers. Zhongguo Yi Xue Ke Xue Yuan Xue Bao. 2008;30:546–9. 16. WHO. WHO guidelines on hand hygiene in health care: a summary. 2009. http://www.who.int/gpsc/information_centre/hand-hygiene-summary/en/ (Accessd Feb 7,2017). 40. Chau JP, Thompson DR, Twinn S, Lee DT, Pang SW. An evaluation of hospital hand hygiene practice and glove use in Hong Kong. J Clin Nurs. 2011;20:1319–28. 17. Visscher MO, Randall WR. Hand hygiene compliance and irritant dermatitis: a juxtaposition of healthcare issues. Int J Cosmet Sci. 2012;34:402–15. 41. Su D, Hu B, Rosenthal VD, Li R, Hao C, Pan W, et al. Impact of the international nosocomial infection control consortium (INICC) multidimensional hand hygiene approach in five intensive care units in three cities of China. Public Health. 2015;129:979–88. 18. Boyce JM, Kelliher S, Vallande N. Skin irritation and dryness associated with two hand-hygiene regimens: soap-and-water hand washing versus hand antisepsis with an alcoholic hand gel. Infect Control Hosp Epidemiol. 2000; 21:442–8. 42. Mu X, Xu Y, Yang T, Zhang J, Wang C, Liu W, et al. Improving hand hygiene compliance among healthcare workers: an intervention study in a Hospital in Guizhou Province. China Braz J Infect Dis. 2016;20:413–8. 19. Larson E, Girard R, Pessoa-Silva CL, Boyce J, Donaldson L, Pittet D. Skin reactions related to hand hygiene and selection of hand hygiene products. Am J Infect Control. 2006;34:627–35. 43. Chen P, Yuan T, Sun Q, Jiang L, Jiang H, Zhu Z, et al. Role of quality control circle in sustained improvement of hand hygiene compliance: an observational study in a stomatology hospital in Shandong. China Antimicrob Resist Infect Control. 2016;5:54. 20. Bissett L. Skin care: an essential component of hand hygiene and infection control. Br J Nurs. 2007;16:976–81. 21. Walsh B, Blakemore PH, Drabu YJ. The effect of handcream on the antibacterial activity of chlorhexidine gluconate. J Hosp Infect. 1987;9:30–3. 44. Cheng VC, Tai JW, Li WS, Chau PH, So SY, Wong LM, et al. Implementation of directly observed patient hand hygiene for hospitalized patients by hand hygiene ambassadors in Hong Kong. Am J Infect Control. 2016;44:621–4. activity of chlorhexidine gluconate. References J Hosp Infect. 1987;9:30–3. 22. Benson L, LeBlanc D, Bush L, White J. The effects of surfactant systems and moisturizing products on the residual activity of a chlorhexidine gluconate handwash using a pigskin substrate. Infect Control Hosp Epidemiol. 1990;11: 67–70. 23. Heeg P. Does hand care ruin hand disinfection? J Hosp Infect. 2001;48(Suppl A): S37–9. 24. Harnoss JC, Brune L, Ansorg J, Heidecke CD, Assadian O, Kramer A. Practice of skin protection and skin care among German surgeons and influence on
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Propaganda, Presumed Influence, and Collective Protest
Political behavior
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cc-by
12,032
Abstract Political propaganda can reduce citizens’ inclinations to protest by directly influenc- ing their preferences or beliefs about the government. However, given that protest is risky in authoritarian societies and requires collective participation, propaganda can also reduce citizens’ inclination to protest by making them think that other citi- zens, rather than themselves, may have been influenced by propaganda and are, as a result, unwilling to protest. We test this indirect mechanism of propaganda using a survey experiment with Chinese internet users from diverse backgrounds and find that they do believe propaganda affects other citizens’ support for and beliefs about the government more than their own support and beliefs. Moreover, they believe that propaganda reduces other citizens’ willingness to protest, which in turn reduces their own willingness to protest. Therefore, the power of propaganda may sometimes lie more in the social perceptions and uncertainty it creates than in its direct indi- vidual effects. Keywords  Propaganda · Protest · Presumed influence · Third-person effect Accepted: 21 January 2021 / Published online: 8 February 2021 © The Author(s) 2021 Accepted: 21 January 2021 / Published online: 8 February 2021 © The Author(s) 2021 Accepted: 21 January 2021 / Published online: 8 February 2021 © The Author(s) 2021 Political Behavior (2022) 44:1789–1812 https://doi.org/10.1007/s11109-021-09683-0 Political Behavior (2022) 44:1789–1812 https://doi.org/10.1007/s11109-021-09683-0 ORIGINAL PAPER NAL PAPER Haifeng Huang1   · Nicholas Cruz1 Haifeng Huang1   · Nicholas Cruz1 1 Department of Political Science, University of California at Merced, CA, USA Introduction How does political propaganda affect citizen behavior, particularly protest, in an authoritarian society? Standard research on this question focuses on how propa- ganda directly affects individuals’ political preferences or beliefs. For example, most existing studies regard propaganda as persuasion and argue that propaganda works by persuading citizens about the merits of the government or its policies, thereby increasing citizens’ support of the regime and reducing their inclination to dissent (Adena et  al. 2015; Cantoni et  al. 2017; Gehlbach and Sonin 2014; * Haifeng Huang hhuang24@ucmerced.edu https://www.hhuang.org/ Nicholas Cruz ncruz5@ucmerced.edu 1 Department of Political Science, University of California at Merced, CA, USA (0123456789) 1 3 456789) 3 456789) 3 Political Behavior (2022) 44:1789–1812 1790 Guriev and Treisman 2020; Peisakhin and Rozenas 2018; Rozenas and Stukal 2019). Other works treat propaganda as signaling and suggest that propaganda does not necessarily affect individuals’ political support, but instead signals the power and capacity of the government through the act of propaganda itself, thereby intimidating citizens and dampening their inclination to protest (Huang 2015b; Svolik 2012; Wedeen 1999). Both propaganda as persuasion and propaganda as signaling are direct and individual-based mechanisms. Mass protests, however, are inherently collective actions. Given that protest is risky under an authoritarian regime and that partici- pants of a failed protest are subject to potentially severe punishment, most indi- viduals’ decisions about whether to protest depend not only on their own prefer- ences or beliefs about the government but also on their perceptions of whether or how many other people will turn out to protest, which then determines how likely the protest will be to succeed (Chwe 2003; Egorov et al. 2009; Lohmann 1994). In other words, protest is a game of complementarity in which individuals will be more (less) willing to participate the more (less) likely they think other people will participate (e.g., Gehlbach et al. 2016; Bueno De Mesquita 2010; Edmond 2013). Introduction Incorporating the logic of collective protest into theories of propaganda thus introduces an alternative channel by which regimes can manipulate citizen behavior: Even if propaganda does not directly persuade individuals about the merits of government or influence their beliefs about its power and capacity, it can still make them less willing to protest if they believe that propaganda has suc- cessfully persuaded or intimidated other people not to protest.l In other words, propaganda can sometimes work not by influencing individ- uals’ own preferences or beliefs but by making them think that other people’s preferences or beliefs may have been influenced. This mechanism of propaganda hinges on its indirect effect at the collective level rather than its direct effect at the individual level. We build our theory on the “influence of presumed influ- ence” model in communication studies, which argues that the effects of media are often indirect and occur through the channel of presumed media influence on other people (Gunther and Storey 2003; Tal-Or et al. 2009). A closely related idea, the “third-person effect,” which can be considered a special case of the “influence of presumed influence” model, makes an even more specific predic- tion: Individuals tend to believe that media and communications have a stronger effect on others than on themselves, and then they react to the presumed effect on others (Davison 1983; Perloff 2009; Sun et al. 2008). Curiously, although prop- aganda is a key motivating example in Davison ’s (1983) original formulation of the third person effect hypothesis, there have been few empirical investiga- tions of propaganda’s indirect effect, especially in the authoritarian setting. Most studies of the influence of presumed influence instead focus on media effects in democratic societies. This study provides such an investigation in the case of contemporary China to enrich theories of political propaganda. In addition, most existing studies under the influence of presumed media influence framework, par- ticularly those on the third-person effect, use surveys and ask people directly how they think media affects themselves and others. In contrast, we experimentally 1 3 Political Behavior (2022) 44:1789–1812 1791 compare propaganda’s presumed effect on others with its actual effect on oneself, and how the former may affect individuals’ participation in protest more than the latter. compare propaganda’s presumed effect on others with its actual effect on oneself, and how the former may affect individuals’ participation in protest more than the latter. Introduction Using an online survey experiment featuring real propaganda messages from Chi- na’s state media, we find that propaganda exposure has a greater effect on respond- ents’ beliefs about other citizens’ support for the regime than on their own support for the regime. Propaganda exposure also has a greater effect on the respondents’ beliefs about other citizens’ assessments of the power and stability of the regime than their own assessment. In addition, propaganda reduces the respondents’ beliefs about other people’s willingness to protest, which in turn has a negative effect on their own willingness to protest.i Our findings suggest that, due to the nature of collective protest, authoritarian propaganda can work not (just) by manipulating what individual citizens think about the regime or their own propensity to protest against the regime, but (also) by manipulating the information and perceptions that citizens have about each other, creating social uncertainty. In other words, political authorities can use their vantage point as an agenda setter to create a mirage surrounding propaganda; citizens’ con- cern that other citizens could have been influenced by propaganda can sometimes be sufficient to deter them from challenging the authorities. Our results are consistent with the classic game-theoretic argument about the critical role of common knowl- edge in shaping social interactions. They not only provide micro-level empirical support for the ideas of pluralistic ignorance and preference falsification sustaining authoritarian rule (Chwe 2003; Havel 1985; Kuran 1991) but also explicate a spe- cific and critical mechanism for the phenomenon. i The next section lays out our theory and hypotheses. Section  3 explains the experimental design and data. Section 4 presents the results on both the perceptual and behavioral components of the influence of presumed influence of propaganda. The last section discusses our results and concludes. 1  For similar definitions, see Huang (2018) and Jowett and O’Donnell (2018). 2  We focus attention on the typical repressive authoritarian setting rather than on settings where there is a high degree of civil liberty and where punishment for protest participation is traditionally rare, as in Cantoni et al. ’s (2019) study. 3  The process can even go one step further. Given the complementarity of collective protest, both “all people protest” and “no one protests” are potential equilibria. Propaganda may simply serve as a coordi- nation device and make the “no one protests” outcome the focal point and thus the resulting equilibrium, even if people’s preferences and beliefs about the regime are not influenced by propaganda and they do not think other people are influenced. This possibility can be examined in future research. Influence of the Presumed Influence of Propaganda Propaganda is the deliberate dissemination of inaccurate, exaggerated, or fabricated information that favors a political cause or player.1 Our theoretical framework about authoritarian propaganda posits that it operates on both the individual and collec- tive levels. At the individual level, propaganda can manipulate the preferences of individuals directly, by persuading them about the merits of the regime, its lead- ers, or its policies and thus increasing their support of the regime; this is the stand- ard theory of propaganda as persuasion (Adena et al. 2015; Cantoni et al. 2017; Gehlbach and Sonin 2014; Guriev and Treisman 2020; Peisakhin and Rozenas 2018; Rozenas and Stukal 2019). At the same time, some propaganda is not persuasive but heavy-handed and even ridiculous, but by demonstrating the state’s ability to com- mand great resources and the organizational capacity to impose such (unpersuasive 1 3 1792 Political Behavior (2022) 44:1789–1812 and unpopular) propaganda messages on the society, the regime can signal its power and capacity in social control, and thus deter the public from challenging it. In other words, instead of shaping individuals’ political preferences, propaganda can work by influencing their beliefs about the power of the state; this is the theory of propa- ganda as signaling (Huang 2015b, 2018). At the collective level, regardless of whether propaganda can change individu- als’ own support of the regime or beliefs about the regime’s power, it may affect their perceptions of other people’s support for the regime or their beliefs about the regime’s power, since it is possible that other people have been influenced by propa- ganda. Because a single person’s protest can be easily defeated by the regime, effec- tive protest almost necessarily requires collective participation. In particular, strate- gic complementarity “characterizes mass protests” (Gehlbach et al. 2016, p. 579); the fewer people who participate in a protest, the less likely it will succeed (Bueno De Mesquita 2010; Chwe 2003; Edmond 2013). Influence of the Presumed Influence of Propaganda The literature has examined a variety of explanations for the prevalent self-other perceptual gap: motivational explanations that center on people’s motivations for self-enhancement and the feeling that they are better and less gullible than others, and cognitive explanations in which people act as naive social scientists and create simple theories about the effects of media on society (see Tal-Or et al. 2009, for a review of the literature). Regardless of the specific sources of self-other perceptual gaps, it should be emphasized that the existence of the per- ceptual component of the presumed media influence model enjoys robust empirical support. This study does not consider the cognitive or psychological sources of the perception that media and communications may have stronger effects on others than oneself, only that the effect can exist in some form and be exploited by propaganda. f Drawing on individual-level theories of propaganda and the perceptual compo- nent of the influence of presumed influence framework, we offer two hypotheses about the presumed influence of propaganda. Given that propaganda is traditionally understood as efforts by regimes to increase citizen support through persuasion, our first hypothesis (H1) is that individuals believe that propaganda would increase other people’s support of the regime; in fact, propaganda’s presumed influence on others’ support for the regime will be stronger than its effects on one’s own support for the regime. Note that here we compare individuals’ perceptions of propaganda’s effect on others with its actual effect on oneself. In the traditional third-person effect litera- ture, the comparison is between individuals’ perceptions of media’s effects on others and their perceptions of media’s effects on themselves (but see Cohen et al. 1988). Since people’s perceptions of media’s effects on themselves may not be accurate, it is more useful to use the actual effect as a comparison. This difference will be reflected in our research design, to be discussed in the next section. l Our second hypothesis (H2) is based on the more recent literature on propaganda as signaling, and it posits that propaganda will make individuals believe that propa- ganda would increase other people’s assessment of the regime’s power and capac- ity to maintain social stability; in fact, propaganda’s presumed influence on others’ assessment of the regime’s capacity to maintain stability will be stronger than its effect on their own assessment of the regime’s capacity. Influence of the Presumed Influence of Propaganda Therefore, given the risk and poten- tially severe negative consequences of participating in a failed protest against an authoritarian government, people will be less likely to protest the less they think other people will participate in protest.2 Propaganda can thus reduce citizens’ protest inclination by making them think that other people (may) have been influenced by propaganda (and consequently support the government or believe the government is too powerful to oppose), even if the effect of propaganda on themselves is limited.3 Our focus in this study is on this indirect, collective-level effect of propaganda, i.e., the influence of presumed influence of propaganda (IPIP). It is important to note that IPIP does not deny that propaganda can influence individuals directly. It argues, however, that even if there is little individual-level direct effect, propaganda may still work through its indirect effect at the collective level.ll f We build our theory of IPIP on the “influence of presumed influence” frame- work of media effects (Gunther and Storey 2003), including the third-person effect hypothesis (Davison 1983), which has been one of the most influential theoretical frameworks in communication studies (Perloff 2009). The influence of presumed influence model has two components. First, people perceive some influence of a message on others, and this presumed influence on others may well be stronger than the message’s perceived effect on themselves (the perceptual component); Second, people react to their perceptions of the message’s influence on others (the behavioral component). In other words, a media message can have indirect influences on indi- viduals’ behavior through their perceptions of its effect on other people. f The literature in communication studies and social psychology has found robust evidence for the perceptual component of the indirect media influence framework 1 3 Political Behavior (2022) 44:1789–1812 1793 across a wide variety of contexts, such as media violence and pornography, adver- tising, news coverage, and entertainment, as well as across various study designs (e.g., Cohen et al. 1988; Mutz 1989; Perloff 1999; Peiser and Peter 2000; Price and Tewksbury 1996; Sun et al. 2008). Recent work has extended the research to new areas, such as fake news, polling, social media, and international news, and similarly found that individuals often perceive others to be more influenced than themselves by such messaging and platforms (e.g., Chung et al. 2017; Jang and Kim 2018; Tsay- Vogel 2016; Wei et al. 2017). Influence of the Presumed Influence of Propaganda Note again, here we are comparing individuals’ perceptions of propaganda’s effect on others with its actual effect on themselves.f f Our third and perhaps most important hypothesis is about the behavioral effects of propaganda’s presumed influence. While earlier research in the third-person effect literature using the self-other perceptual gap to predict individuals’ behavior has yielded mixed results (Perloff 1999; Xu and Gonzenbach 2008), the influence of presumed influence model emphasizes media’s presumed influence on others rather 1 3 Political Behavior (2022) 44:1789–1812 1794 than perceptual differences between self and others (Gunther and Storey 2003),4 and here the evidence has been considerably stronger (Chung and Moon 2016; Dohle et al. 2017; Tal-Or et al. 2009; Wei et al. 2017). But existing research on the influ- ence of presumed media influence has focused on individuals’ support for censor- ship and restrictions of media content that are perceived to have a negative influence on others, e.g., hate speech, fake news, and pornography. Even in other contexts, such as voting and online political discussion, the behavioral consequence of the third-person effect is usually thought to be that individuals take actions to correct or balance the perceived negative effect of media messaging on others (Golan et al. 2008; Rojas 2010).fl We study the effect of the presumed influence of propaganda on collective protest in the authoritarian setting, where the consequence of government messaging is that individuals may take actions to conform to the expected behavior of others who are thought to have been influenced by the messaging rather than to counterbalance the effect of the messaging on others. In addition, dealing with collective action rather than individual behavior, our focus is not just on how the presumed influence of propaganda on other people’s attitudes affects individuals’ behavior, as is commonly the case in existing studies of the influence of presumed influence and third-per- son effects, but on how the expected behavior of other people, due to propaganda, affects individuals’ own behavior. In other words, given the complementarity of pro- test behavior, we focus on how propaganda affects individuals’ coordination motives rather than their correction or counterbalance motives (Little 2017; Tal-Or et  al. 2009). We therefore hypothesize that propaganda exposure will create the expectation that propaganda has made other citizens less willing to protest (H3a), and this expec- tation will negatively affect individuals’ own willingness to protest (H3b). 4  Even in Davison ’s (1983) original thesis about third-person effects, for the behavioral component he emphasized the presumed influence on others rather than the self-other perceptual gap (Chung and Moon 2016). Influence of the Presumed Influence of Propaganda In other words, we propose an indirect channel through which propaganda reduces protest: by affecting how individuals perceive their peers’ willingness to protest, thereby inhibiting their own willingness to participate in collective action. Here, perceptions of other citizens’ willingness to protest serves as a mediating variable between prop- aganda exposure and individuals’ willingness to protest.fl Our analysis of the behavioral effect of the presumed influence of propaganda is related to a few recent studies of media effects. Jin et al. (2018) study how blog posts about the Fukushima nuclear accident’s contamination risks affected people’s seafood consumption behavior and their perceptions of others’ behavior, and how their own behavior and others’ behavior affected each other. Similarly, Tewksbury et  al. (2004) study how anxieties about the Y2K computer problem and percep- tions of other people’s overreactions to it (e.g., bank withdrawals and food hoard- ing) influenced individuals’ own protective behavior. These studies, however, do not explain the theoretical foundations of the interaction between self-behavior and other-behavior, e.g., why in the individualistic consumption (as opposed collective 1 3 3 Political Behavior (2022) 44:1789–1812 1795 action) setting, after controlling for anxiety levels, people would reduce eating sea- food in response to other people’s reduced seafood consumption, or why other peo- ple’s over-hoarding of cash and food would reduce one’s own protective behavior. Little (2017) provides a game-theoretic model in which some citizens are credulous, and informed citizens who know the government is lying would nevertheless behave as if they believe its propaganda since they want to coordinate their behavior with credulous citizens. The coordination motive is also essential in our collective protest setting, but, in our setting, citizens can be homogeneous (and all disbelieve propa- ganda) rather than having divergent information capacity. Our theory is consistent with the classic formal-theoretic literature about the crucial roles of common knowledge, preference falsification, and pluralistic igno- rance in affecting regime stability. Propaganda breaks down public communications, without which it will be hard to form common knowledge about citizens’ politi- cal attitudes (Chwe 2003). More specifically, in accordance with Kuran ’s (1991) account of preference falsification, propaganda (together with repression) makes citizens hide their true and private preferences and leads to a public discourse that prevents citizens from knowing the real distribution of anti-government sentiments in the society (see also Havel 1985). Such pluralistic ignorance is the wellspring of authoritarian stability. Influence of the Presumed Influence of Propaganda In the more recent global game literature, Edmond (2013) has shown that even though citizens are aware of propaganda, they cannot completely discount the government’s exaggeration of its strength when neither the govern- ment’s actual level of strength nor the amount of propaganda is perfectly observed. Further, since citizen actions are strategic complements, information manipulation will reduce every citizens’ incentive to participate in anti-government collective actions if it reduces some citizens’ incentive. Our study provides micro-level empiri- cal evidence in support of these theoretical insights and explicates a specific and critical mechanism, the influence of the presumed influence of propaganda, which leads to preference falsification, pluralistic ignorance, and the breakdown of com- mon knowledge. Study Design To test the above hypotheses, we conducted a survey experiment in July-August 2018 with 895 Chinese internet users from diverse backgrounds (see more below). The experiment proceeded as follows. Participants were first asked a battery of background questions about their social and political attitudes, including life satis- faction, national pride, political interest, pro-Western orientation, and evaluation of China’s current political system. See Online Appendix 1 for question wording. They were then randomly assigned into one of five groups: a control group that did not receive any propaganda treatment and four treatment groups that each received a dif- ferent propaganda message (see below). The experiment was designed to compare individuals who were exposed to propaganda with individuals who were not. We use four different propaganda treatments simply because there exists a wide variety of 1 3 3 1796 Political Behavior (2022) 44:1789–1812 propaganda, and we do not want to unnecessarily limit our analysis to a particular message.i propaganda, and we do not want to unnecessarily limit our analysis to a particular message.i Afterwards, all respondents were asked two sets of outcome questions, the first about their own opinions about China’s current overall current situation, China’s future prospects, the government’s ability in governing the country, its responsive- ness to citizen demands, its ability to maintain social and political stability, and, finally, their willingness to participate in protest against government malfeasance and injustice in their region. Due to the political sensitivity of the last question, we used the term “collective walk,” a widely understood codeword on the Chinese internet, to refer to protest. The questions on China’s overall current situation, the Chinese government’s governance, its responsiveness, and China’s future prospects were all intended to measure respondents’ support for the government, so they were summed into an aggregate variable regime support to avoid the issue of multiple hypothesis testing.5 The question on the Chinese government’s ability to maintain stability was intended to measure its perceived power and capacity, in light of the signaling theory of propaganda. The last question on “collective walk” simply measures willingness to protest.6 The second set of outcome questions asked the respondents how they thought an average person (“yiban ren”) in the society would answer the above questions if they had been exposed to the same materials during the survey. 5  Cronbach’s alpha for the index is 0.796, indicating fairly good inter-item reliability. Cronbach’s alpha for the index when measuring the respondents’ perceptions of other people’s support for the government (see below) is even higher: 0.848. 6  The topics of willingness to protest and the regime’s stability-maintaining capacity were potentially more politically sensitive than other questions. To increase the respondents’ willingness to complete the survey and reduce their wariness, the survey only asked one question for each of the two topics. Study Design (For the control group, participants were simply asked how they thought an average person would answer the questions they had just answered). For example, in the first set of ques- tions, respondents were asked about their willingness to protest, and, in the second set, respondents were asked what they believed an average citizen’s willingness to protest was. To avoid priming, the set of questions on the respondents’ own attitudes and beliefs was asked before any questions on their perceptions of other people’s attitudes and beliefs began. Finally, demographic information was collected. Given the between-subject experimental design, in the analysis below we will compare answers to the self questions between the treatment and control groups to obtain the “self effect” of propaganda (see Cohen et al. 1988, for a similar approach). This is the actual effect of propaganda on oneself rather than its perceived effect on oneself. We will also compare answers to the other questions between the treat- ment and control groups to obtain the “other effect” of propaganda. This is the pre- sumed effect of propaganda on others. Naturally, individuals do not know the actual effect of propaganda on others, and therefore we measure their perceptions of propa- ganda’s effect on others. To examine the potentially different effects of propaganda on individuals’ self attitudes and their perceptions of other people’s attitudes, we will compare the differences between answers to the self and other questions in the 1 3 Political Behavior (2022) 44:1789–1812 1797 treatment groups and the differences in the control group, in addition to comparing the self and other effects of propaganda.f treatment groups and the differences in the control group, in addition to comparing the self and other effects of propaganda.f f This approach differs from how most existing studies measure the self-other perceptual differences. Existing studies typically use surveys, and respondents are directly asked how they think a particular media message would respectively affect themselves and others. But people might not have an accurate perception of a mes- sage’s effect on themselves; for example, they sometimes under-report the amount of actual change in their own opinions produced by media messages (Chung et al. 2017). In addition, direct questioning may have a social desirability problem. 7  The video can be viewed at http://www.china​news.com/gn/shipi​n/2018/03-12/news7​60210​.shtml​ (last accessed December 30, 2020). 8  See http://world​.huanq​iu.com/artic​le/2018-05/12116​405.html (last accessed December 30, 2020) for the article in Chinese. 9  See http://www.qsthe​ory.cn/dukan​/qs/2017-11/15/c_11219​47684​.htm (last accessed December 30, 2020) for the article in Chinese. Data The participants in the experiment were recruited through a market survey company, with each unique user and IP address allowed only once in a survey to prevent repet- itive participation. The respondents were directed to a US-based survey website to take the survey anonymously, which also allowed us to maintain full control over the survey, and the survey company did not have access to the data. There are several reasons why conducting the survey experiment with an online sample is appropriate for this study. First, online anonymity can make the respondents more truthful with their answers than face-to-face or telephone surveys, which is crucial here, given the sensitivity of our survey questions. Second, over half of China’s population are now online, and the internet has become the center of activism and collective action in the country, with the middle class broadly preferring digital forms of engagement over traditional forms of political participation (Huang 2015a; Yang 2009). Under- standing the internet population’s political attitudes and potential behavior is there- fore particularly important. As shown in Online Appendix 1, the participants had diverse sociodemographic backgrounds: They came from all walks of life, from var- ious education backgrounds and age groups, and from all over China. In fact, their gender, regional, urban/rural, and occupational distributions are broadly comparable to China’s general internet population. They were younger and better educated on average than the general population, but such characteristics may also be particularly important for our topic: protest. Table 1 shows the summary statistics of the independent and dependent variables across the experimental groups. With regards to the pre-treatment independent vari- ables, all the demographic variables are balanced across the groups. Most of the pre- treatment dispositional variables are also well balanced, with national pride being the main exception. In the statistical regressions below, we control the demographic and other pre-treatment covariates.i As for the dependent variables, Table 1 indicates that there are no significant dif- ferences in the mean values of the self variables between the groups, but there are significant differences in the mean values of the other regime support and other sta- bility. This is mainly driven by the differences between the self variables and other variables in the control group, as their differences in the treatment groups are much smaller. 10  See http://media​.peopl​e.com.cn/n1/2018/0129/c4060​6-29791​511.html (last accessed December 30, 2020) for the article in Chinese. Study Design They should all feel ashamed,” which lauds the achievements of China’s space program and its willingness to share the use of Chi- na’s planned space station with foreign countries, in contrast to some other coun- tries’ refusal to allow China to participate in the International Space Station project, with some vivid examples (space treatment).8 The third treatment was an article from the Seeking Truth magazine, titled “China is the world’s largest democracy,” which argues that China actually has a democratic system and is the world’s largest democracy due to its population (democracy treatment).9 The final treatment was 1 3 Political Behavior (2022) 44:1789–1812 1798 an article from the People’s Daily titled “The Whole World is Reading this Book: Xi Jinping on Governance in China,” which touts the alleged popularity of said book around the world (book treatment).10 Again, it is important to note that we are not interested in comparing the effects of different treatments; rather, our goal is to understand the differences between the treatment and the control conditions. an article from the People’s Daily titled “The Whole World is Reading this Book: Xi Jinping on Governance in China,” which touts the alleged popularity of said book around the world (book treatment).10 Again, it is important to note that we are not interested in comparing the effects of different treatments; rather, our goal is to understand the differences between the treatment and the control conditions. Study Design Indeed, studies have shown that messages viewed as socially desirable often elicit a first-person effect: Respondents state that the positive messages have greater effects on themselves than on others (e.g., Duck et al. 1995; Gunther and Thorson 1992). The social desirability problem may be particularly acute in an authoritarian coun- try, where it is undesirable and even risky to directly reveal the lack of effect of government messages—on themselves or others. Similarly, people’s reports of their own level of support for the regime cannot be taken at face value. Indeed, some recent studies on Chinese public opinion have shown that people often misrepresent their true opinions on politically sensitive questions when asked directly (Jiang and Yang 2016; Li et al. 2018). Our approach did not ask respondents directly how they think propaganda affected themselves or others; rather, it measures propaganda’s effects indirectly and unobtrusively through inter-group comparisons of political attitudes and perceptions. Similarly, when analyzing self-other differences in politi- cal attitudes, we do not focus on within-subject differences, since either self attitudes or other attitudes (but particularly the former) may be misrepresented. Instead, we focus on the inter-group differences in the self-other differences. ff The four treatments were selected to cover the breadth of state media propaganda in contemporary China. The first treatment was a short and artistically appealing video, titled “China in One Minute,” made by China’s premier official newspaper People’s Daily, that describes the country’s recent economic and social achieve- ments (video treatment).7 The second treatment was an article from Global Times, titled “China is just generous. Entries are group means for each variable. Standard deviations in parentheses Data For example, the difference between self regime support and other regime support in the control group is about 0.27 on a five-point scale ( p < 0.001 ), but they are at most around 0.1 in the treatment groups (specifically, in the case of the 1 3 Political Behavior (2022) 44:1789–1812 1799 Table 1   Summary statistics Table 1   Summary statistics Entries are group means for each variable. Standard deviations in parentheses Control Video Book Democracy Space Min Max F Prob > F N = 175 N = 169 N = 204 N = 180 N = 167 Independent vari- ables  Female 0.589 0.538 0.539 0.539 0.509 0 1 0.57 0.686 (0.493) (0.500) (0.500) (0.500) (0.501)  Age group 2.983 2.947 3.088 3.100 3.222 1 10 0.95 0.432 (1.603) (1.436) (1.314) (1.506) (1.335)  Education 4.343 4.420 4.407 4.239 4.521 1 6 1.96 0.099 (1.1015) (1.078) (0.929) (0.982) (0.904)  Income level 4.394 4.426 4.588 4.639 4.563 1 7 1.68 0.153 (1.055) (1.100) (1.021) (1.181) (1.117)  CCP member 0.117 0.207 0.240 0.150 0.174 0 1 1.50 0.201 (0.383) (0.406) (0.428) (0.358) (0.380)  Urban 0.617 0.609 0.598 0.606 0.605 0 1 0.04 0.997 (0.487) (0.489) (0.492) (0.490) (0.490)  Life satisfaction 3.549 3.621 3.721 3.456 3.437 0 5 2.18 0.070 (1.107) (1.112) (1.048) (1.115) (1.090)  Political interest 2.863 2.769 2.887 2.828 2.784 1 4 0.75 0.555 (0.776) (0.845) (0.724) (0.746) (0.807)  National pride 3.726 3.553 3.681 3.556 3.593 1 4 2.82 0.024 (0.508) (0.724) (0.613) (0.749) (0.678)  Pro-west orienta- tion 2.837 2.926 2.870 2.917 2.916 1 4 0.61 0.653 (0.626) (0.658) (0.621) (0.688) (0.644)  System evaluation 3.474 3.361 3.466 3.372 3.365 1 4 1.07 0.369 (0.702) (0.752) (0.690) (0.784) (0.779) Dependent variables  Self regime sup- port 3.124 3.178 3.290 3.204 3.204 0.5 4 1.44 0.217 (0.681) (0.737) (0.645) (0.695) (0.681)  Other regime support 2.840 3.249 3.199 3.083 3.207 0 4 8.64 <0.001 (0.826) (0.673) (0.701) (0.775) (0.752)  Self regime stabil- ity 4.274 4.337 4.324 4.344 4.347 1 5 0.30 0.878 (0.761) (0.723) (0.752) (0.663) (0.711)  Other regime stability 3.989 4.302 4.230 4.222 4.311 1 5 5.10 0.001 (0.864) (0.662) (0.756) (0.706) (0.806)  Self protest 2.377 2.337 2.441 2.350 2.473 1 4 0.65 0.624 (0.968) (0.925) (1.023) (0.948) (0.943)  Other protest 2.749 2.509 2.578 2.550 2.515 1 4 1.93 0.104 (0.919) (0.901) (0.962) (0.923) (0.950) 3 1800 Political Behavior (2022) 44:1789–1812 Fig. 1   Treatment effects on regime support. 11  It is also interesting that in the baseline (control) condition, the respondents’ self-reported regime sup- port and assessment of regime stability are higher than their perception of other people’s regime sup- port and assessment of regime stability, and their self-reported willingness to protest is lower than their perception of other people’s protest willingness. However, due to the political desirability of overstating one’s support for the regime and understating willingness to dissent, we do not take this self-reported self-other difference within each group at face value. Instead, we focus on the inter-group differences. Data These are regression coefficients of the treatments, showing their effects on the respondents’ own regime support (left), their perceptions of other people’s regime support (middle), and the differences between their perceptions of other people’s regime support and their own regime support (right). “TREATED” represents a separate model where all treatment groups were pooled as the “treated” group. Regime support is re-scaled to range from 0 to 1. The horizontal lines represent 95% confidence intervals Fig. 1   Treatment effects on regime support. These are regression coefficients of the treatments, showing their effects on the respondents’ own regime support (left), their perceptions of other people’s regime support (middle), and the differences between their perceptions of other people’s regime support and their own regime support (right). “TREATED” represents a separate model where all treatment groups were pooled as the “treated” group. Regime support is re-scaled to range from 0 to 1. The horizontal lines represent 95% confidence intervals democracy group, p = 0.009 ). Essentially, it appears the treatments increased the values of the other variables, without similarly increasingly the values of the self variables.11 The next section will take a closer look into the differences. Presumed Influence of Propaganda We first report the results about propaganda’s effects on individuals’ preferences and beliefs about the government, their perceptions of propaganda’s effects on other peo- ple’s preferences and beliefs, and the self-other differences. Figure 1 plots the effects 1 3 Political Behavior (2022) 44:1789–1812 1801 of the treatments on regime support, with and without controlling for demographic and attitudinal covariates (see Tables S2 and S3 in Online Appendix for numerical regression results). The left panel of Fig. 1 shows that, without controlling for the covariates, only the treatment about Xi Jinping’s book significantly increased the respondents’ self regime support relative to the control condition, while the other three treatments did not change self regime support. When the covariates are con- trolled, all four treatments increased the respondents’ self regime support. Using the omnibus variable “TREATED,” which indicates whether a respondent received any treatment, the effect size of the treatments on self regime support was 3.9 percentage points (with covariates controlled, see Table S2). The middle panel of Fig. 1 shows that, whether controlling for the covariates or not, all four treatments significantly increased the respondents’ perceptions of other people’s regime support. The effect size of the TREATED variable for other regime support when the covariates are controlled was 9.2 percentage points, more than twice as large as the effect size for self regime support.if This suggests the treatments had a significantly greater effect on the respond- ents’ assessment of other people’s regime support than on their own regime sup- port. The right panel of Fig. 1 shows this is indeed the case. Here the estimand is the difference between the respondents’ perceptions of other people’s regime sup- port and their own regime support. The panel shows that the other-self discrepancies are significantly larger in all treatment groups except the democracy group than in the control group. In other words, not only did the respondents believe propaganda increased other people’s support for the regime, but the messages had a stronger effect on their perceptions of other citizens’ regime support than on their own sup- port, consistent with H1.f Figure  2 plots the effects of the treatments on the respondents’ assessment of regime stability (see Tables S4 and S5 in Online Appendix for numerical regression results). Presumed Influence of Propaganda The left panel shows that, none of the four propaganda treatments increased the respondents’ own assessment of regime stability relative to the control condi- tion, whether controlling for the covariates or not. The middle panel, on the other hand, shows that all four propaganda messages increased their perceptions of other people’s assessment of regime stability. The effect size of the omnibus TREATED variable for other regime stability is 6.7 percentage points. This suggests that propa- ganda has stronger effects on the respondents’ perceptions of other people’s assess- ment of regime stability than on their own assessment of regime stability. The right panel of Fig. 2 shows that this is indeed the case. Here the estimand is the difference between the respondents’ perceptions of other people’s assessment of regime stabil- ity and their own assessment of regime stability. The panel shows that the other-self discrepancies are larger in all treatment groups except the democracy group, where the difference misses the .05 significance level, than in the control group. This is because propaganda increased the respondents’ perceptions of other people’s assess- ment of regime stability without similarly increasing their own assessment of regime stability. The results are consistent with H2.ff To further test the difference between the treatments’ effects on self attitudes and on other attitudes, we conduct coefficient equality tests for regime support and assessment of regime stability using seemingly unrelated regressions (SUR), 1 3 3 3 Political Behavior (2022) 44:1789–1812 1802 Fig. 2   Treatment effects on assessment of regime stability. These are regression coefficients of the treat- ments, showing their effects on the respondents’ own assessment of regime stability (left), their per- ceptions of other people’s assessment of regime stability (middle), and the differences between their perceptions of other people’s assessment of regime stability and their own assessment of regime sta- bility (right). “TREATED” represents a separate model where all treatment groups were pooled as the “treated” group. Assessment of regime stability is re-scaled to range from 0 to 1. The horizontal lines represent 95% confidence intervals Fig. 2   Treatment effects on assessment of regime stability. These are regression coefficients of the treat- ments, showing their effects on the respondents’ own assessment of regime stability (left), their per- ceptions of other people’s assessment of regime stability (middle), and the differences between their perceptions of other people’s assessment of regime stability and their own assessment of regime sta- bility (right). Presumed Influence of Propaganda “TREATED” represents a separate model where all treatment groups were pooled as the “treated” group. Assessment of regime stability is re-scaled to range from 0 to 1. The horizontal lines represent 95% confidence intervals which estimate self attitudes and other attitudes as a system of equations and allow the errors in different equations to be correlated. The top panel of Table 2 shows that except for the democracy treatment, the coefficients of all other treat- ments as well as the omnibus TREATED variable are larger for other regime sup- port than for self regime support. The bottom panel shows that the coefficients of all treatments are larger for other regime stability than for self regime stability, although the difference is only significant at .1 percent level for the democracy treatment. The results are consistent with Figs. 1 and 2 and once more indicate that propaganda has differential effects on the respondents’ own regime support and assessment of regime stability than on their perceptions of others. The results above lend strong support to both H1 and H2. Propaganda makes the respondents perceive that other people are now more supportive of the regime and that the regime’s ability to maintain stability is now stronger in other peo- ple’s assessment. This presumed influence on other peoples’ regime support and assessment of regime stability is stronger than propaganda’s influence on the respondents’ own regime support and assessment of regime stability. 1 3 Political Behavior (2022) 44:1789–1812 1803 Table 2   Coefficient equality tests for regime support and assessment of regime stability Table 2   Coefficient equality tests for regime support and assessment of regime stability Equality of coefficient tests with seemingly unrelated regressions, controlling for demographic and pre-treatment attitudinal covariates. “TREATED” represents a separate model where all treatment groups were pooled together as the “treated” group Treatment Coefficient Standard error P Other regime support – self regime support  Video 0.080 0.017 0.000  Democracy 0.026 0.017 0.129  Book 0.047 0.016 0.004  Space 0.062 0.017 <0.001  TREATED 0.053 0.014 <0.001 Other regime stability – self regime stability  Video 0.059 0.019 0.002  Democracy 0.035 0.019 0.070  Book 0.047 0.018 0.010  Space 0.058 0.019 0.003  TREATED 0.049 0.015 0.001 Treatment Coefficient Standard error P Equality of coefficient tests with seemingly unrelated regressions, controlling for demographic and pre-treatment attitudinal covariates. Presumed Influence of Propaganda “TREATED” represents a separate model where all treatment groups were pooled together as the “treated” group One potential concern about our results is that since our sample is not representa- tive of Chinese society, when the respondents answered questions about what an average person (“yiban ren”) in the society would think about the government, they might have in mind someone different from themselves. In particular, the average person in the society may be less well educated and have lower income than our sample. Indeed, while most of the self-other perceptual gaps in the third person effect literature can be interpreted as biases, Shen et al. (2018) argue that some self- other perceptual gaps may reflect accurate differences, rather than biases, because the individuals in question are comparing themselves to a different group of people. f One way to address the issue is to recognize that because people tend to interact more with and live among people who are like themselves, they tend to overestimate their own representativeness in the population. As a result, when they think about “an average person in the society,” the person they have in mind would be more sim- ilar to themselves than an actual average person in the society. In that sense, what the actual average person is like is not as crucial as people’s perception of what an average person is like. Nevertheless, to mitigate the concern that our respondents might be thinking about people very different from themselves in demographic characteristics when answering questions about the “average person,” we divided the participants into those with college education and those without, and those with high income and those with low income (based on the median values). We then interact the treat- ments with both education and income, and regress the outcome variables on the interaction terms. As Tables S8–S11 in Online Appendix show, the coefficients of the interaction terms were never statistically significant, meaning that the college- educated did not react to the treatments differently from the non-college-educated, and that the high-income people did not react to the treatments differently from 1 3 3 3 1804 Political Behavior (2022) 44:1789–1812 Fig. 3   Treatment effects on willingness to protest. Presumed Influence of Propaganda These are regression coefficients of the treatments, showing their effects on the respondents’ willingness to protest (left), their perceptions of other people’s willingness to protest (middle), and the differences between other people’s presumed willingness to pro- test and the respondents’ own willingness to protest (right). “TREATED” represents a separate model where all treatment groups were pooled as the “treated” group. Willingness to support is re-scaled to range from 0 to 1. The horizontal lines represent 95% confidence intervals Fig. 3   Treatment effects on willingness to protest. These are regression coefficients of the treatments, showing their effects on the respondents’ willingness to protest (left), their perceptions of other people’s willingness to protest (middle), and the differences between other people’s presumed willingness to pro- test and the respondents’ own willingness to protest (right). “TREATED” represents a separate model where all treatment groups were pooled as the “treated” group. Willingness to support is re-scaled to range from 0 to 1. The horizontal lines represent 95% confidence intervals the low-income people, with regards to either self attitudes or perceptions of other attitudes. This suggests that responses to the “average person” questions were not affected by the lack of representativeness of the online sample. 12  In line with much of the literature on the third-person effect and influence of presumed influence, we use behavioral intentions or attitudes toward behavior to measure behavioral effects. Behavioral Effects of Propaganda’s Presumed Influence We now examine propaganda’s effect on individuals’ willingness to protest, their perceptions of other citizens’ willingness to protest, and how the latter may affect the former.12 Corresponding to Figs. 1, 2, and 3 plots the effects of the treatments on the respondents’ own willingness to protest and their perceptions of others’ willingness to protest (see Tables S6 and S7 for numerical regression results). The left and middle panels show that the propaganda treatments did not affect the respondents’ willingness to protest relative to the control condition, but they did reduce their perceptions of other people’s willingness to protest, which is natural, 1 3 Political Behavior (2022) 44:1789–1812 1805 Table 3   Coefficient equality tests for protest willingness Table 3   Coefficient equality tests for protest willingness Equality of coefficient tests with seemingly unrelated regressions. “TREATED” represents a separate model where all treatment groups were pooled as the “treated” group Treatment Coefficient Standard error P Other protest willingness – self protest willingness  Video − 0.052 0.023 0.024  Democracy − 0.037 0.023 0.100  Book − 0.060 0.022 0.006  Space − 0.082 0.023 <0.001  TREATED − 0.058 0.018 0.001 Coefficient Standard error P Equality of coefficient tests with seemingly unrelated regressions. “TREATED” represents a separate model where all treatment groups were pooled as the “treated” group Fig. 4   Direct and indirect effects of propaganda on willingness to protest Fig. 4   Direct and indirect effects of propaganda on willingness to protest given propaganda’s presumed influence on other people’s regime support and assessment of regime stability, and consistent with H3a. The right panel of Fig. 3 and the coefficient equality tests in Table 3 indicate that the treatments indeed have differential effects on self protest willingness and other protest willingness.i ff While the above result confirms H3a, it does not address a critical part of our third hypothesis, namely whether individuals’ perceptions of other citizens’ will- ingness to protest would affect their own willingness to protest (H3b). In particu- lar, the null total effects of propaganda on the respondents’ self protest willing- ness, shown in Fig. 3, is a combination of the direct effect of propaganda on their own protest willingness and the indirect effect of propaganda on their willingness to protest through its impact on other citizens’ presumed willingness to protest (the mediator), as illustrated in Fig. 4. Behavioral Effects of Propaganda’s Presumed Influence We need to separate the two effects to understand how changes in other people’s presumed willingness to protest affect individuals’ own willingness to protest.f Therefore, to test H3b and unpack the indirect effect of propaganda on individu- als’ protest willingness through its effect on their perceptions of other people’s pro- test willingness, we employ mediation analysis (Imai et al. 2010, 2011). This method 1 3 Political Behavior (2022) 44:1789–1812 1806 Table 4   Mediation analysis: propaganda’s effect on self protest with other protest as the mediator ACE is average causal mediation effect, and ADE is average direct effect. Robust standard errors in parentheses. ***p < 0.001 , **p < 0.01 , * p < 0.05 Video Democracy Book Space TREATED ACME − 0.036* − 0.030* − 0.029* − 0.031* − 0.032** (0.015) (0.014) (0.029) (0.015) (0.012) ADE 0.029 0.008 0.041* 0.061** 0.034* (0.020) (0.023) (0.021) (0.022) (0.017) Total effect − 0.007 − 0.022 0.013 0.030 0.002 (0.025) (0.026) (0.025) (0.026) (0.021) separates the average treatment effect (total effect) into two components: the Aver- age Causal Mediation Effect (ACME) and the Average Direct Effect (ADE). The former represents the indirect effect of the treatment on the outcome through the mediator, while the latter represents the direct effect of the treatment on the outcome with no mediator. The method is intended to ascertain if the treatment explains any variation in the mediator and if that variation in turn explains any variation in the outcome. separates the average treatment effect (total effect) into two components: the Aver- age Causal Mediation Effect (ACME) and the Average Direct Effect (ADE). The former represents the indirect effect of the treatment on the outcome through the mediator, while the latter represents the direct effect of the treatment on the outcome with no mediator. The method is intended to ascertain if the treatment explains any variation in the mediator and if that variation in turn explains any variation in the outcome. Our mediation model has propaganda exposure as the treatment, individuals’ perceptions of other people’s protest willingness as the mediator, and individuals’ own protest willingness as the outcome. Table 4 presents the results of the mediation analysis. The ACMEs of the Video, Democracy, Book, and Space propaganda treat- ments as well as the omnibus TREATED variable are all negative and significant. 13  The result also suggests that the perceived self-other discrepancy in media and propaganda effects may reflect not just magnitude but also direction. Behavioral Effects of Propaganda’s Presumed Influence This essentially translates to assuming that there are no unmeasured pre-treatment or post-treatment covariates that confound the relationship between the mediator and outcome. It is this latter component of the mediation model that potentially poses a threat to our inference.i Recall that the survey experiment first exposed participants to propaganda mes- sages, then asked them about their own willingness to protest, and later asked them about their perceptions of others’ willingness to protest. Because the outcome is measured before the mediator, this raises the potential that a question ordering effect is creating endogeneity between the outcome and mediator. In other words, it could be the case that a correlation between self protest and other protest is a causal effect of the former on the latter via a priming effect. However, in our survey, the question measuring the respondents’ own willingness to protest (self protest) did not immedi- ately precede the question measuring their perceptions of other people’s willingness to protest (other protest). The set of questions on the respondent’s own attitudes and behavior was asked before the set of questions on others began, so there was consid- erable space between the questions measuring self protest and other protest. There- fore, any question ordering effects are likely to be minimal.f f Nevertheless, to offer evidence about the appropriateness of the mediation analy- sis, we conduct a sensitivity analysis and analyze additional, re-specified, media- tion models. Figure 5 presents the sensitivity analysis for the mediation models of Table 4. The sensitivity analysis tests for the degree to which the confidence interval for an indirect effect is sensitive to the correlation between the residuals of the medi- ator and outcome regressions, which is defined as 휌 . In other words, this test esti- mates the degree of correlation between these two sets of residuals that is necessary to make the confidence interval around the indirect effect contain zero. In effect, this tests for how sensitive the ACME is to a confounding variable. For our models, the sensitivity analysis estimates a 휌 of approximately 0.6, which indicates that the estimates of our mediation model are relatively robust to the presence of a potential confounding variable. For further robustness, we estimated additional mediation models, but this time the mediating and outcome variables were swapped. Behavioral Effects of Propaganda’s Presumed Influence This provides strong evidence that propaganda exposure indirectly reduces individu- als’ protest willingness by reducing their perceptions of others’ protest willingness, as stated in H3b. The ADEs of the Video and Democracy treatments cannot be dis- tinguished from zero, but interestingly the Book and Space treatments have posi- tive direct effects on protest willingness, suggesting that propaganda messages may sometimes unwittingly cause citizens to want to protest, a kind of backfire effect. In our experiment, this is perhaps because the propaganda messages about the great- ness of China and its leader encourage the respondents to express willingness to dis- sent against injustice and government malfeasance, which are holding China back.13 But regardless of propaganda’s direct effect, people’s concern about other citizens’ interpretation of and reactions to propaganda pulled them back and reduced their desire to protest to the null condition, as reflected in the insignificant total effect of propaganda on protest willingness.i The finding of the mediation model does come with one important caveat, however. As Imai et al. (2011) show, use of a mediation model to infer causality must satisfy one key assumption: sequential ignorability. This assumption has two components. First, given the observed pre−  treatment confounders, the treatment 1 3 1 3 Political Behavior (2022) 44:1789–1812 1807 assignment is statistically independent of potential outcomes and potential media- tors. In other words, we are assuming that there are no omitted variables confound- ing the relationship between the treatment and the mediator and the relationship between the treatment and the outcome. This first component of the assumption holds because treatment assignment is randomized. Second, the observed mediator is ignorable given the actual treatment status and pre-treatment confounders. This essentially translates to assuming that there are no unmeasured pre-treatment or post-treatment covariates that confound the relationship between the mediator and outcome. It is this latter component of the mediation model that potentially poses a threat to our inference.i assignment is statistically independent of potential outcomes and potential media- tors. In other words, we are assuming that there are no omitted variables confound- ing the relationship between the treatment and the mediator and the relationship between the treatment and the outcome. This first component of the assumption holds because treatment assignment is randomized. Second, the observed mediator is ignorable given the actual treatment status and pre-treatment confounders. Discussion and Conclusion This study experimentally shows that people often believe that propaganda increases other people’s support for a regime or their beliefs about a regime’s capacity to maintain stability. In fact, the presumed influence of propaganda on other people’s support for and beliefs about a regime are usually stronger than propaganda’s actual influence on oneself. Consequently, propaganda can reduce people’s perceptions of other people’s willingness to protest, which in turn dilutes their own propensity to protest due to its risky nature under authoritarian regimes. Thus, propaganda can stave off dissent not by directly changing individuals’ own attitudes and intentions but, instead indirectly, by altering people’s perceptions of other people’s attitudes and behavioral intentions.i These findings imply that, due to the complementarity of participation in mass protest, authoritarian regimes have a special advantage by being the agenda setters in the propaganda game. Propaganda does not have to directly change individuals’ own willingness to protest to be effective. As long as propaganda reduces individu- als’ perceptions of other people’s willingness to protest, or just makes them uncer- tain if other citizens have been influenced by it, they will be more timid in challeng- ing the regime. Propaganda can achieve much of its function for the regime simply by sowing uncertainty among citizens about what they think others think and will do. Different from what conventional wisdom often assumes, the power of propa- ganda may sometimes lie more in the social perception and uncertainty it creates than in changes it induces in individuals’ own political attitudes and beliefs. The study thus enriches theories of authoritarian propaganda, which have so far focused on propaganda’s direct effect on individuals’ themselves. The results also contrast with findings in the existing literature that in democratic and semi-dem- ocratic societies, where basic rights of expression and association are guaranteed, stronger perception of other people’s willingness to participate in protest or voting, or perceptions of protest news’s effects on other people, are associated with a lower willingness to participate (Banning 2006; Cantoni et al. 2019; Lo et al. 2017). In these societies, participation is more of a public good that demands a threshold level of contribution: Perception of other people’s participation reduces the need for one- self to participate in order to meet the threshold and, thus, could drive down one’s own willingness to participate. In other words, these are games of substitutes. Behavioral Effects of Propaganda’s Presumed Influence If it is indeed the case that indi- viduals’ own willingness to protest is driving their perceptions of others’ willingness to protest, then it should be the case that the propaganda exposure explains some variation in self willingness to protest, and that variation in turn explains some vari- ation in others’ presumed willingness to protest. However, these alternative mod- els failed to identify a significant ACME. As Table 5 shows, the ACME is consist- ently indistinguishable from zero for all treatment conditions, suggesting that the variations in self protest that were caused by treatment exposure did not explain the variations in other protest. Additionally, consistent with our earlier finding that treat- ment exposure caused a reduction in other protest, the ADE and total effect of these 1 3 3 3 1808 Political Behavior (2022) 44:1789–1812 Fig. 5   Protest mediation sensitivity Fig. 5   Protest mediation sensitivity Table 5   Alternative mediation analysis: propaganda’s effect on other protest with self protest as the mediator Table 5   Alternative mediation analysis: propaganda’s effect on other protest with self protest as th mediator ACE is average causal mediation effect, and ADE is average direct effect. Robust standard errors in parentheses. ***p < 0.001 , **p < 0.01 , * p < 0.05 Video Democracy Book Space TREATED ACME − 0.004 − 0.012 0.007 0.016 0.001 (0.017) (0.014) (0.013) (0.014) (0.011) ADE − 0.058** − 0.044* − 0.058** − 0.073*** − 0.056*** (0.020) (0.021) (0.020) (0.022) (0.017) Total effect − 0.062* − 0.056* − 0.051* − 0.057* − 0.055** (0.025) (0.025) (0.024) (0.026) (0.021) ACE is average causal mediation effect, and ADE is average direct effect. Robust standard errors in parentheses. ***p < 0.001 , **p < 0.01 , * p < 0.05 alternative mediation models are significantly negative in all cases. These results suggest that the possibility of a confounding priming effect is negligible. Our initial mediation analysis results are therefore fairly robust: Perceptions of others’ reduced 1 Political Behavior (2022) 44:1789–1812 1809 willingness to protest due to propaganda would drive down people’s own willing- ness to protest. willingness to protest due to propaganda would drive down people’s own willing- ness to protest. Discussion and Conclusion Col- lective protests in authoritarian settings, however, are strategic games of comple- ments (Chwe 2003; Edmond 2013; Gehlbach et  al. 2016): The more/less willing other people are to participate, the more/less willing are individuals themselves. It is in this strategic setting that propaganda can inhibit people’s willingness to protest by reducing their perceptions of other people’s willingness to protest. And it is this mechanism that contributes to preference falsification, pluralistic ignorance, and the breakdown of common knowledge (Chwe 2003; Havel 1985; Kuran 1991). 1 3 1810 Political Behavior (2022) 44:1789–1812 Besides enriching our understanding of authoritarian propaganda, this study also contributes to the literature on the influence of presumed media influence. The standard literature on the influence of presumed influence focuses on people’s per- ceptions of media’s influence on others, without comparing the influence on others with influence on oneself. The third-person effect literature, on the other hand, focus on the discrepancy between media’s presumed influence on oneself and on others, without considering wither the presumed effect on oneself is accurate, or whether the presumed influence of media is really stronger than its actual influence on one- self. We show that propaganda’s presumed effects on others can be stronger than its actual effects on oneself, not just stronger than its presumed effects on oneself. It is this “real” presumed influence of propaganda that leads to one’s perceptions of propaganda’s influence on other people’s behavior, which in turn affects one’s own behavior.f One limitation of the study is that the propaganda messages had negative effects on the respondents’ perceptions of other people’s protest willingness, hence nega- tive indirect effects on their own protest willingness, but the messages had either null or positive direct effects on the respondents’ protest willingness. As discussed above, the positive direct effect is likely because the propaganda messages about the greatness of China and its leader encouraged the respondents to express willingness to dissent against injustice and government malfeasance, which were holding China back. Self-other perceptual discrepancies have always been recognized in the third- person effect literature as a kind of inconsistency or bias. Our study suggests the self-other discrepancies may be larger than typically understood: A media message’s self and other effects may differ not just in magnitude but also in direction. Acknowledgements  The authors would like to thank Zhaotian Luo, Arturas Rozenas, Minh Trinh, audi- ence members at APSA and MPSA, and several anonymous reviewers for helpful comments. Replication data are available at https​://doi.org/10.7910/DVN/ZEYLM​H Open Access  This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Com- mons licence, and indicate if changes were made. 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Supplementary Information Supplemental Table 1. Primers used in this study. Name Direction Sequence 5' to 3' iNOS forward reverse CAAGCTGAACTTGAGCGAGGA TTTACTCAGTGCCAGAAGCTGGA IRF8 forward reverse CTGCTCAGGCAGGTGTCAGAAG AGGCCAGCCATTAGTGGTGAAG IL-12p40 forward reverse ACTCACATCTGCTGCTCCACAAG CACGTGAACCGTCCGGAGTA Arg-1 forward reverse AGCTCTGGGAATCTGCATGG ATGTACACGATGTCTTTGGCAGATA Ym1 forward reverse GATGGCCTCAACCTGGACTG CGTCAATGATTCCTGCTCCTG Fizz1 forward reverse CAGCTGATGGTCCCAGTGAA CAAGCACACCCAGTAGCAGTC PD-L1 forward reverse TGTGTCCGTCGTGGATCTGA TTGCTGTTGAAGTCGCAGGAG TIM-3 forward reverse AGCTCTGGGAATCTGCATGG ATGTACACGATGTCTTTGGCAGATA PD-1 forward reverse GATGGCCTCAACCTGGACTG CGTCAATGATTCCTGCTCCTG TGF-β1 forward reverse CAGCTGATGGTCCCAGTGAA CAAGCACACCCAGTAGCAGTC GAPDH forward reverse TGTGTCCGTCGTGGATCTGA TTGCTGTTGAAGTCGCAGGAG Supplementary Information Supplemental Table 1. Primers used in this study. Name Direction Sequence 5' to 3' iNOS forward reverse CAAGCTGAACTTGAGCGAGGA TTTACTCAGTGCCAGAAGCTGGA IRF8 forward reverse CTGCTCAGGCAGGTGTCAGAAG AGGCCAGCCATTAGTGGTGAAG IL-12p40 forward reverse ACTCACATCTGCTGCTCCACAAG CACGTGAACCGTCCGGAGTA Arg-1 forward reverse AGCTCTGGGAATCTGCATGG ATGTACACGATGTCTTTGGCAGATA Ym1 forward reverse GATGGCCTCAACCTGGACTG CGTCAATGATTCCTGCTCCTG Fizz1 forward reverse CAGCTGATGGTCCCAGTGAA CAAGCACACCCAGTAGCAGTC PD-L1 forward reverse TGTGTCCGTCGTGGATCTGA TTGCTGTTGAAGTCGCAGGAG TIM-3 forward reverse AGCTCTGGGAATCTGCATGG ATGTACACGATGTCTTTGGCAGATA PD-1 forward reverse GATGGCCTCAACCTGGACTG CGTCAATGATTCCTGCTCCTG TGF-β1 forward reverse CAGCTGATGGTCCCAGTGAA CAAGCACACCCAGTAGCAGTC GAPDH forward reverse TGTGTCCGTCGTGGATCTGA TTGCTGTTGAAGTCGCAGGAG Supplementary Information 1 1 Supplementary Figure Legends Supplementary Figure S1. Gating strategy in flow cytometry analysis of mast cells, basophils, neutrophils, and macrophages together with M1 and M2 macrophages. On day 19 after tumor implantation, the LSK cell population in the BM was purified (A) and their multipotency was examined under in vitro myeloid cell differentiation conditions into mast cells and basophils (B), and neutrophils and macrophages (C). Supplementary Figure S2. IL-27 augments the infiltration of CD11b+ myeloid cells into MC38 tumor. MC38-IL-27 or MC38-Vector tumor was implanted and tumor growth was monitored (A). Data are shown as mean ± SEM (n = 3 or 4) and are representative of more than three independent experiments. On day 20, tumor was harvested, single-cell suspension was prepared and subjected to flow cytometer analysis. Representative dot plots of macrophage population are shown (B), and the cell numbers of individual populations were counted (C). Data are shown as mean ± SEM (n = 3 or 4) and are representative of more than two independent experiments. *P < 0.05, **P < 0.01, ***P < 0.001. Supplementary Figure S3. IL-27 promotes the differentiation into M1 macrophages in MC38 tumor-bearing mice. Single-cell suspensions prepared from tumor on day 20 after tumor implantation were analyzed by flow cytometry. Representative dot plots of Gr-MDSCs, Mo-MDSCs, and macrophages are shown, and their cell numbers were counted (A and B). (C) Representative dot plots of M1 and M2 macrophages are shown, their cell numbers were counted, and ratio of M1/M2 macrophages was calculated. Data are shown as mean ± SEM (n = 3 or 4) and are representative of more than two independent experiments. (D) mRNA expression of markers for M1 and M2 macrophages in purified CD11b+ myeloid cells was analyzed by real-time RT-PCR. Data are shown as mean ± SEM (n = 4) and are representative of more than four independent experiments. *P < 0.05, **P < 0.01, ***P < 0.001. 2 2 Supplementary Figure S4. IL-27 much less but significantly augments the infiltration of M1 macrophages into B16F10 tumor when the tumor size in B16F10-IL-27 tumor-bearing mice reaches the similar tumor size to that in control tumor-bearing mice. B16F10-IL-27 tumor (2 × 107 cells/mouse) or B16F10-Vector tumor (5 × 104 cells/mouse) was implanted and tumor growth was monitored. When the tumor size reached the same size 13 days after tumor implantation, the tumor-infiltrating cells were analyzed by flow cytometry. Supplementary Figure Legends Representative dot plots of macrophages (A) and M1/M2 macrophages (B) are shown. Their cell numbers were counted per tumor volume, and ratio of M1/M2 macrophages was calculated (C-F). Their cell numbers were also counted per tumor weight, and ratio of M1/M2 macrophages was calculated (G-J). Data are shown as mean ± SEM (n = 5) and are representative of two independent experiments. *P < 0.05, **P < 0.01. Supplementary Figure S5. IL-27 inhibits the differentiation into immunosuppressive macrophages in MC38 tumor-bearing mice. On day 20 after tumor implantation, mononuclear cells were purified from tumor masses, and CD11b+ myeloid cells were further purified and subjected to immunosuppressive activity, which was assessed by the ability to inhibit OVA-specific CD8+ T-cell proliferation. Data are shown as mean ± SEM (n = 3) and are representative of more than three independent experiments. *P < 0.05, **P < 0.01, ***P < 0.001. Supplementary Figure S6. Therapeutic potential of the CD11b+ myeloid cells purified from tumors of B16F10-IL-27 tumor-bearing mice on pre-existing tumor model. Mice were implanted with B16F10-IL-27 tumor (2 × 107 cells/mouse) or B16F10-Vector tumor (5 × 105 cells/mouse), and CD11b+ myeloid cells were purified from their tumors 8 days after implantation. When mice were implanted with parental B16F10 tumor (5 × 3 3 105 cells/mouse) and their tumor size reached 5 mm in diameter on day 5, these CD11b+ myeloid cells (5 × 105 cells/50 µl/mouse) were both intravenously and intratumorally injected into these mice with the pre-existing tumor. Tumor growth was monitored with time course. Data are shown as mean ± SEM (n = 5) and are representative of two independent experiments. *P < 0.05. Supplementary Figure S7. IL-27-induced MC38 tumor-infiltrating myeloid cells exert direct antitumor effects by killing tumor through NO. (A) CD11b+ myeloid cells purified from tumor of MC38-IL-27 or MC38-Vector tumor-bearing mice were admixed with parental MC38 tumor, and tumor growth was monitored with time course. Data are shown as mean ± SEM (n = 4 or 5) and are representative of more than two independent experiments. On day 20 after tumor implantation, killing activity of CD11b+ myeloid cells against parental MC38 tumor was measured by 51Cr release assay (B), and NO production in the culture supernatant was measured in the presence or absence of NOS inhibitor, L-NMMA (C). (D) The effects of inhibition of NOS activity by L-NMMA on the killing activity were examined. Supplementary Figure Legends Data are shown as mean ± SEM (n = 4 or 5) and are representative of more than four independent experiments. *P < 0.05, **P < 0.01, ***P < 0.001. Supplementary Figure S8. Enhanced mRNA expression of immune checkpoint molecules and TGF-β1 in CD11b+ myeloid cells in IL-27-expressing tumor-bearing mice. B16F10-IL-27 and B16F10-Vector tumor or MC38-IL-27 and MC38-Vector tumor were implanted and tumor growth was monitored. On day 18, tumor was harvested, and CD11b+ myeloid cells were purified from tumor and subjected to real-time RT-PCR. Blood was also collected and its serum TGF-β1 level was determined by its specific ELISA. Data are shown as mean ± SEM (n = 4) and are representative of three independent experiments. *P < 0.05, ***P < 0.001. 4
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Susceptibility Profiles of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) to Deltamethrin Reveal a Contrast between the Northern and the Southern Benin
International journal of environmental research and public health/International journal of environmental research and public health
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Susceptibility Profiles of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) to Deltamethrin Reveal a Contrast between the Northern and the Southern Benin Eric Tossou 1,2,*, Ghislain Tepa-Yotto 1,3, Ouorou K. Douro Kpindou 1, Ruth Sandeu 4, Benjamin Datinon 1, Francis Zeukeng 4 , Romaric Akoton 1,2, Généviève M. Tchigossou 1,2, Innocent Djègbè 5, John Vontas 6,7, Thibaud Martin 8,9, Charles Wondji 10, Manuele Tamò 1 , Aimé H. Bokonon-Ganta 2 and Rousseau Djouaka 1,* 1 International Institute of Tropical Agriculture (IITA), 08 P.O. Tri-Postal, Box 0932 Cotonou, Benin; g.tepa-yotto@cgiar.org (G.T.-Y.); d.kpindou@cgiar.org (O.K.D.K.); b.datinon@cgiar.org (B.D.); romaricakoton88@gmail.com (R.A.); tchigossougenevieve@yahoo.fr (G.M.T.); m.tamo@cgiar.org (M.T.) 1 International Institute of Tropical Agriculture (IITA), 08 P.O. Tri-Postal, Box 0932 Cotonou, Benin; g.tepa-yotto@cgiar.org (G.T.-Y.); d.kpindou@cgiar.org (O.K.D.K.); b.datinon@cgiar.org (B.D.); 2 Direction of Plant Production, University of Abomey-Calavi, P.O. Box 526 Abomey-Calavi, Benin; aimehbg@gmail.com g g 3 School of Crop and Seed Production, National University of Agriculture (UNA-Benin), P.O. Box 43 Kétou, Benin Faculty of Science, Department of Biochemistry, University of Yaoundé I, P.O. Box 812 Yaoundé, Cameroon d 2009@ h (R S ) f k07@ h (F Z ) 4 Faculty of Science, Department of Biochemistry, University of Yaoundé I, P.O. Box 812 Yaoundé, Cam sandeu2009@yahoo.com (R.S.); zeusfranck07@yahoo.com (F.Z.) 4 Faculty of Science, Department of Biochemistry, University of Ya sandeu2009@yahoo.com (R.S.); zeusfranck07@yahoo.com (F.Z.) 5 Life And Earth Sciences, National University of Science, Technology, Engineering and Mathematics, P.O. Box 2282 Abomey, Benin; djegbe1@yahoo.fr 6 Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, N Plastira 100, 70013 Crete, Greece; vontas@imbb.forth.gr g 7 Pesticide Science, Agricultural University of Athens, Ieraodos 75, 11855 Athens, Greece 7 Pesticide Science, Agricultural University of Athens, Ieraodos 75, 11855 Athens, Greece 8 Cirad UR Hortsys, Université Montpellier, Campus international de Baillarguet, 34 398 Montpellier, France; thibaud.martin@cirad.fr 8 Cirad UR Hortsys, Université Montpellier, Campus international de Baillarguet, 34 398 Montpellier, Fra thibaud.martin@cirad.fr 9 Biosciences Unit, University Houphouet Boigny, Cocody 01 BP 6483Abidjan, Côte d’Ivoire 10 Vector group, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; charles.wondji@lstmed.ac.uk * Correspondence: eric.tossou82@gmail.com (E.T.); r.djouaka@cgiar.org (R.D.); * Correspondence: eric.tossou82@gmail.com (E.T.); r.djouaka@cgiar.org (R.D.); Tel.: +229-9563-4911 (E.T.); +229-9620-4924 (R.D.) * Correspondence: eric.tossou82@gmail.com (E.T.); r.djouaka@cgiar.org Tel.: +229-9563-4911 (E.T.); +229-9620-4924 (R.D.) p g j g g Tel.: +229-9563-4911 (E.T.); +229-9620-4924 (R.D.)   International Journal of Environmental Research and Public Health International Journal of Environmental Research and Public Health www.mdpi.com/journal/ijerph Int. J. Environ. Res. Public Health 2019, 16, 1882; doi:10.3390/ijerph16111882 1. Introduction The cotton bollworm, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) is a key polyphagous pest infesting several crops such as cotton, tomato, maize, sorghum, chickpea, pigeon pea, pulses, vegetables and tomato crops worldwide [1]. This pest causes an estimated loss of over US$ 5 billion annually in Africa despite application of pesticides [2]. In contrast to many other arthropod pests, H. armigera has a wide geographical range of host plants and can adapt to new environments [3]. New publications on H. armigera in South America [4,5] created suspicions of the presence of other species of Helicoverpa in Africa given the proximity between the two continents. Species identification remains complex with possibilities of misidentification due to morphological similarities between H. armigera and Heliothinae species (such as Helicoverpa zea (Boddie)) [6]. The restriction fragment length polymorphism (RFLP)-PCR method is used to determine a genetic variation between the populations. PCR-RFLP amplifies specific partial regions of the mitochondrial DNA (mtDNA) genome followed by the digestion of PCR products with specific endonucleases to distinguish between combining patterns of partial regions of the mitochondrial gene [7]. This technique has been optimised for confirming H. armigera [7]. Economic damage caused by H. armigera is very significant worldwide [2]. Over the past decades, management of H. armigera has become increasingly difficult due to its high reproductive and damage potentials [8]. The strong tendency of H. armigera to move from one fruit to another without consuming it completely, explains why this pest causes extensive damages to crops even when the number of larvae is relatively low [9]. y Synthetic insecticides have shown promising control of chewing and sucking insect pests in the early 1980s, these compounds are applicable to Helicoverpa pests. Cotton and tomato, the main Helicoverpa host plants, are generally protected from pest damage by application of insecticides such as carbamates, organophosphates and synthetic pyrethroids [10,11]. In comparison to carbamates and organophosphates, synthetic pyrethroids are effective at low dosages for controlling H. armigera at extremely low cost [10,12]. Excessive and continuous applications of pyrethroid insecticides for H. armigera control initiated since the mid-1980s in most countries have led to resistance selection pressure in several field populations of this insect [10,13,14]. With this development of insecticide resistance, the control of H. armigera has become critical in many regions worldwide [8,15]. Recent studies have reported the increased resistance of H. Received: 4 March 2019; Accepted: 3 May 2019; Published: 28 May 2019 Abstract: Helicoverpa armigera is an indigenous species in Africa and has been reported in the destruction of several crops in Benin. Management of H. armigera pest is mainly focused on the use of synthetic pyrethroids, which may contribute to resistance selection. This study aimed to screen the susceptibility pattern of field populations of H. armigera to deltamethrin in Benin. Relevant information on the type of pesticides used by farmers were gathered through surveys. Collected samples of Helicoverpa (F0) were reared to F1. F0 were subjected to morphological speciation followed by a confirmation using restriction fragment length polymorphism coupled with a polymerase chain reaction (RFLP-PCR). F1 (larvae) were used for insecticide susceptibility with deltamethrin alone and in the presence of the P450 inhibitor Piperonyl Butoxide (PBO). Deltamethrin and lambda-cyhalothrin were the most used pyrethroids in tomato and cotton farms respectively. All field-sampled Helicoverpa were found to be H. armigera. Susceptibility assays of H. armigera to deltamethrin revealed a high resistance pattern in cowpea (resistance factor (RF) = 2340), cotton (RF varying from 12 to 516) and tomato (RF=85) farms which is a concern for the control of this major polyphagous agricultural pest. There was a significant increase of mortality when deltamethrin insecticide was combined with piperonyl butoxide (PBO), suggesting the possible involvement of detoxification enzymes such as oxidase. This study highlights the presence of P450 induced metabolic resistance in H. armigera populations from diverse cropping systems in Benin. The recorded high levels of deltamethrin Int. J. Environ. Res. Public Health 2019, 16, 1882; doi:10.3390/ijerph16111882 2 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 resistance in H. armigera is a concern for the control of this major agricultural pest in Benin as the country is currently embarking into economical expansion of cotton, vegetables and grain-legumes cropping systems. resistance in H. armigera is a concern for the control of this major agricultural pest in Benin as the country is currently embarking into economical expansion of cotton, vegetables and grain-legumes cropping systems. Keywords: H. armigera; pyrethroid resistance; Benin 1. Introduction armigera control in different host crops and in different localities in Benin. 2.3. Insects Sampling, Molecular Speciation and Insecticide Susceptibility Testing 2.3. Insects Sampling, Molecular Speciation and Insecticide Susceptibility Testing 2.1. Study Sites Benin is located between the Equator and the Tropic of Cancer at latitudes ranging from 6◦30’ N to 12◦30’ N and longitude ranging from 1◦E to 3◦40’ E. This country shares boundaries with Togo in the West, Burkina Faso and Niger in the North, and Nigeria in the East. Four main agro-ecological zones are found in the country. The North-Sudanese, the Atacorian, the Sub-Sudanese and the Sub-Equatorial climatic zones. A total of 6 agricultural settings were surveyed in these agro-ecosystems. Field populations of Helicoverpa spp. were sampled in the following 6 localities. Kassakou in the North-Sudanese area, characterized by one long dry season and a short rainy season, with relatively low humidity and rainfall (800 to 1000 mm per year), and high temperatures (up to 45◦C during dry seasons). The localities of Yarra and Zaffé both in the Sub-Sudanese area with a long rainy season and a short dry season. Rainfalls ranging between 900 and 1200 mm, less hilly localities with wet savanna vegetation types. Finally, three localities (Djidja, Kokrokinho, Abomey-Calavi) in the Sub-Equatorial area that spans the southern part of the country and extends up to coastal areas of Benin. Two rainy and two dry seasons are recorded in these localities. The relative humidity is high, temperatures are relatively low, and the vegetation is a mosaic of coastal wetlands, forest, and wet savanna (Figure 1). 1. Introduction armigera to pyrethroids in Pakistan [16], South India [17], Spain [18] and West Africa [19]. Durigan et al. [20] pointed to metabolic resistance mechanisms and showed that the quantities of cytochrome P450 (CYP337B1, CYP337B2 and CYP337B3) are greater in resistant strains compare to susceptible strains after exposure to deltamethrin. Furthermore, Martin et al. [21] also demonstrated that P450 enzymes contribute to deltamethrin resistance in H. armigera populations from West Africa. These results were further confirmed by Brun-Barale et al. [19] who identified the modified P450 genes. Insecticide resistance development usually occurs with the appearance of genetic mutations and/ or increased enzymatic detoxification [20,22]. Recent studies indicate that metabolic resistance is primarily responsible for pyrethroid resistance in H. armigera. Elevated oxidative detoxification (P450-based resistance) was confirmed as the major resistance mechanism to pyrethroids in Australia and Asia [20,23,24]. Very little is known about the susceptibility profiles of H. armigera to the commonly used agricultural insecticide deltamethrin across agro-ecological areas in Benin. Although many studies 3 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 have been conducted worldwide on H. armigera [1,12,17,19,24], very few of these research works have been carried out in the western part of Africa [11,19,21]. In Benin for example, no study had extensively and simultaneously mapped the insecticide resistance profiles of this pest on several cropping systems such as cotton, vegetable and grain legumes currently under intensification. In addition to this lack of information on resistance mapping in Benin, no research had attempted to provide information on potential mechanisms conferring observed phenotypic resistance profiles in several cropping systems. Taking into account the current nationwide economic options made by the Benin government to promote the development of cotton, vegetables and grain legumes farming, there is a great need to regularly document and update information on insecticide resistance profiles and related resistance mechanisms developed by H. armigera nationwide. Data from this research will support strategic policies on the selection of cost-effective insecticides for better control of this polyphagous pest. This research documents on the control of H. armigera pest in various host plants, provides information on the extent of H. armigera resistance to deltamethrin in the South-North transect of Benin, investigates possible role of detoxifiers (P450 enzymes) in recorded phenotypic resistances. Information generated will help to improve decision making on the type of insecticides to be used for H. 2.2. Insecticide Utilisation by Farmers in Surveyed Localities 2.2. Insecticide Utilisation by Farmers in Surveyed Localities The knowledge of farmers on the use of chemical pesticides for H. armigera control was assessed in surveyed tomato, cotton, and cowpea farms from November 2016 to November 2017. Relevant information on the use of chemical pesticides for H. armigera control were gathered through focus group discussions, direct field observations and in-depth interviews. Information collected included: the types of pesticides used by farmers, the concentrations/doses applied and the application frequencies. Based on the number of farmers in each farm, we determined the minimal acceptable size of farmers to be interviewed in each locality. A total of 180 volunteer farmers consented this survey in the six studied localities. 2.3.1. Laboratory Strain A susceptible strain of H. armigera (SoucheVrac Sensible, SVS) was obtained from the Entomology laboratory of the Agricultural Research Institute for Development in Cameroon (IRAD-Garoua, 4 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 Cameroon). SVS was transferred to the International Institute of Tropical Agriculture (IITA-Benin) insectary at pupae stage, and was reared following laboratory conditions and steps described by Nibouche [25]. This strain was used as the standard susceptible colony during insecticide susceptibility assays. Figure 1. Map of Benin showing localities where H. armigera populations were found. ld Sampling of Wild Populations of Helicoverpa Figure 1. Map of Benin showing localities where H. armigera populations were found. 2.3.2. Field Sampling of Wild Populations of Helicoverpa 2.3.2. Field Sampling of Wild Populations of Helicoverpa Field populations of Helicoverpawere collected during rainy seasons in 6 agricultural localities namely (Kassakou, Yarra, Zaffé, Djidja, Kokrokinho and Abomey-Calavi) (Table 1; Figure 1). Collected samples of Helicoverpa (F0) were reared to F1. The parents (F0) were preserved in suitable containers filled with ethanol (100%), and stored at −20◦C. These samples (F0) were later subjected to molecular speciation using RFLP-PCR [7]. F0 progenies (third instar larvae) were used for insecticide susceptibility assays (topical assays) with deltamethrin alone and in the presence of the P450 inhibitor piperonyl butoxide (PBO). Insects collected in the field were introduced into cylindrical plastic cups (4cm diameter; Field populations of Helicoverpawere collected during rainy seasons in 6 agricultural localities namely (Kassakou, Yarra, Zaffé, Djidja, Kokrokinho and Abomey-Calavi) (Table 1; Figure 1). Collected samples of Helicoverpa (F0) were reared to F1. The parents (F0) were preserved in suitable containers filled with ethanol (100%), and stored at −20◦C. These samples (F0) were later subjected to molecular speciation using RFLP-PCR [7]. F0 progenies (third instar larvae) were used for insecticide susceptibility assays (topical assays) with deltamethrin alone and in the presence of the P450 inhibitor piperonyl butoxide (PBO). Insects collected in the field were introduced into cylindrical plastic cups (4cm diameter; 5 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 5cm height) with a cover punched with holes to allow ventilation for breathing of larvae. Each cup was filled with 4g of solid agar media for feeding larvae throughout their transportation from the field to the IITA-Benin insectary. Table 1. Geolocalization of surveyed localities for H. armigera sampling. 2.3.3. Laboratory Rearing of H. Armigera Both laboratory and field strains of H. armigera were reared at 25±1◦C, 75% Relative Humidity (RH), and a photoperiod of 12:12 Light:Darkness (L:D) in the insectary as described by Nibouche [25]. Briefly, larvae were reared on an artificial diet composed of maize flour (120 g/L), brewer yeast (40 g/L), white cowpea flour (172 g/L), honey (20 g/L), sorbic acid (2 g/L), ascorbic acid (6 g/L), agar (25 g/L), 40% formaldehyde (2 mL/L), erythrocin (0.05g/L) and acyclovir (1.2g/L). The fourth instar larvae were obtained and individualized into cylindrical plastic cups containing artificial diet (4g) to avoid cannibalism. Pupae were collected, disinfected and, morphological identifications were carried out before emergence of adults. Emerging adult males and females from F0 larvae were pooled for matting. Eggs from this matting were incubated for hatching and, larvae (F1) from hatched eggs were placed on artificial diet and reared to L3-larva stage; the developmental stage used for insecticide susceptibility assays (Topical assays) with deltamethrin insecticide. 2.3.4. Molecular Speciation of Sampled Helicoverpa spp. 2.3.1. Laboratory Strain Collection Site Region (Agro Ecosystem) Host Plant Latitude Longitude Sample Strains Zaffé Central (Sub-Sudanese) Cotton 07◦55.343’ ZAF.16 002◦15.256’ Kokrokinho South (Sub-equatorial) Tomato 06◦57.377’ KOK.16 002◦37.868’ Abomey-Calavi South (Sub-equatorial) Cowpea 06◦25.260’ AB-C.16 002◦19.684’ Kassakou North (North-Sudanese) Cotton 11◦4.520’ KAS.17 002◦54.127’ Yarra North (Sub-Sudanese) Cotton 10◦30.447’ YAR.17 002◦28.569’ Djidja Central (Sub-equatorial) Cotton 07◦19.495’ DJI.17 001◦56.393′ Benoue and Mayo Rey North Cotton - ‘SVS’ - Table 1. Geolocalization of surveyed localities for H. armigera sampling. 2.3.3. Laboratory Rearing of H. Armigera 2.4. Synergist Test with Piperonyl Butoxide (PBO) For this assay, 135 to 233 larvae of H. armigera from each locality were pre-exposed to the P450 inhibitor piperonyl butoxide 90% (PBO) (20 µg/µL) for one hour and immediately after, these larvae were exposed to deltamethrin at five concentrations thrice replicated of the technical grade (0.01DD, 0.1DD, DD, 10DD, and 100DD) so as to cover the full dose range bioassay. Acetone solution was added to serve as the control solution. The diagnostic concentration was used for plotting the graph showing the effect of the PBO synergist on larvae. Larval mortality was monitored every 24 h after exposure until 72 h. 2.3.5. Insecticide Susceptibility Assays (Topical Assays) 2.3.5. Insecticide Susceptibility Assays (Topical Assays) As documented in most published papers, this assay was conducted on larval stages as they are the most cropsdamaging stages [9]. The selection of larvae for insecticide susceptibility analysis was supported by several published papers and standards [17,27]. Technical grade of deltamethrin 99% (Sigma-Aldrich, Taufkirchen, Germany) was used in this assay. Susceptibility of third instar larvae of H. armigera (F1 offspring) to deltamethrin was tested using topical application technique [10,27]. Two-fold serial dilutions were prepared in pure acetone according to Kranthi [28] and the following concentrations were obtained for bioassays with the susceptible strain: (0.01454; 0.02908; 0.05816; 0.1163; 0.2326; 0.4653; 0.9306 µg/g). A log-probit dose (dose-mortality) curve was drawn from this strain and a diagnostic dose (DD) of 2181µg/g was obtained. Five concentrations thrice replicated of the technical grade (0.01DD, 0.1DD, DD, 10DD, and 100DD) and a control with no insecticide (0DD) were then prepared for bioassays with the field strains of H. armigera (144 to 349 larvae). Each exposed larva had a body weight between 30–40 mg. One microliter of deltamethrin was applied topically to the pro-thoraxic dorsum of the pest. Larvae were tested individually in plastic cups (4cm diameter; 5cm height) containing 4g of artificial diet and punched at the top. Pure acetone was used as control. The mortality was assessed every 24 h post exposure and was monitored for a total of 72 h for both test and control samples. Larvae were considered dead when unable to move if prodded with a blunt probe or brush [10,27]. 2.3.4. Molecular Speciation of Sampled Helicoverpa spp. PCR-RFLP was used in this speciation. Total genomic DNA was extracted from sampled F0 individuals (parents) after they had produced their progenies (F1). Samples (F0) were analysed for molecular speciation and for predicting the species profiles of offspring to be submitted to insecticide susceptibility tests. Total DNA was obtained after crushing the whole insect and following the extraction protocoldescribed by Livak [26]. Extracted DNA was quantified using a nanodrop 8000 (Thermo Scientific, Mississauga, ON, Canada) and a working DNA solution of 40–50 ng/µL was prepared for amplification. Amplifications were carried out in 50µL reaction containing cytochrome oxidase I (COI) and cytochrome b (Cytb) (Table 2) according to Behere et al. [7]. DNA amplification was confirmed by running 5µL of the post-PCR products on 1.5% agarose gel stained with 1% Midori green. Two restriction enzymes (BstZ17I and HphI) were used for discriminating H. armigera species. The pattern of product sizes on the agarose gel was used for identifying H. armigera species following Behere et al. protocol [7] (Table 3). 6 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 Table 2. Primers used for amplifying H. armigerasequences. Primers Primer Sequences COI COI-F02 5′CTC AAA TTA ATT ACT CCC CAT C′3′ COI-R02 5′GGA GGT AAG TTT TGG TAT CAT T3′ Cytb Cytb-F02 5′GAA TCC TTT AAT TTA AAA TAT AC3′ Cytb-R02 5′AAA TAT GGG TTA GTT AAA GTT AA3′ Table 2. Primers used for amplifying H. armigerasequences. Table 3. Expected sizes of digested PCR products for H. armigera identification. Extraction Amplifications Digestion Enzymes Digestion Products (pb) Helicoverpa spp. DNA Amplified product (COI) BstZ17I 318 + 193 Amplified product (CYTB) HphI 280 + 154 Table 3. Expected sizes of digested PCR products for H. armigera identification. 3.1. Insecticides Used for Cotton and Tomato Farming in Benin We conducted interviews and group discussions with a total of one hundred and eighty farmers (140 for interviews and 40 for group discussions) from tomato and cotton farms to identify insecticide families used for H. armigera control. Different classes of insecticides were identified namely: pyrethroids, organophosphates, carbamates and biopesticides (Bacillus thuringiensis, Neem) (Figure 2). Figure 2. Insecticide use in cotton and tomato farming in Benin. Figure 2. Insecticide use in cotton and tomato farming in Benin. Synthetic pyrethroids (deltamethrin, lambda-cyhalothrin and cypermethrin) were identified as the main insecticides (60%) used against H. armigera. Deltamethrin and lambda-cyhalothrin were the most used pyrethroids in tomatoes farming (50.9%) and cotton farming (28.7%) respectively. Organophosphates (chlorpyrifos and dimethoate) were also mentioned by farmers and used either as single or in combinations with pyrethroids. Information provided by farmers revealed that tomato farms are sprayed once every 10 days, whereas cotton farms are treated two times per month. Despite the use of these insecticides, cases of plants and fruits attack by insects were still reported by cotton and tomato farmers, raising the failure of these synthetic insecticides for tomato and cotton plants protection. 2.5. Data Analysis Mortality curves for different tested concentrations of deltamethrin were computed using probit analysis (WinDL50software; CIRAD, Montpellier, France). Results were expressed as percentage mortalities. Abbott’s formula was used for correcting the recorded mortalities. Resistance factors (RFs) were determined as the ratio of the lethal dose for 50% (LD50) of field collected populations of insects and the susceptible strain. RFs were used to classify levels of insecticide resistance as: susceptible (RF = 0–1), low resistance (RF = 2–10), moderate resistance (RF = 11–30), high resistance (RF = 31–100), 7 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 very high resistance (RF > 100) following descriptions made by Torres-Vila et al. [18]. The level of significance was set at p < 0.05. very high resistance (RF > 100) following descriptions made by Torres-Vila et al. [18]. The level of significance was set at p < 0.05. 3.2. Molecular Validation of Morphologically Identification of Helicoverpaarmigera. COI and Cytb genes fragments were successfully amplified in one hundred and twenty Helicoverpa samples. 20 samples of F0 adult were analysed from each surveyed agricultural setting. Following digestions of amplified PCR products with restriction endonucleases (BstZ17I and HphI). All analysed samples from the 6 surveyed localities were identified using molecular techniques as H. armigera (Table 3 and Figure 3). 8 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 Figure 3. Agarose gel electrophoresis of PCR products digested with BstZ17I and HphI restriction enzymes, showing different restriction fragment length polymorphism (RFLP) patterns of analysed samples of H. armigera. M: molecular weight markers. Lanes 1-2, 3-4, 5-6, 7-8, 9-10 and 11-12:H. armigera specimens from Kassakou, Zaffé, Kokrokinho, Djidja, Abomey-calavi and Yarra respectively. 3. Bioassays Figure 3. Agarose gel electrophoresis of PCR products digested with BstZ17I and HphI restriction enzymes, showing different restriction fragment length polymorphism (RFLP) patterns of analysed samples of H. armigera. M: molecular weight markers. Lanes 1-2, 3-4, 5-6, 7-8, 9-10 and 11-12:H. armigera specimens from Kassakou, Zaffé, Kokrokinho, Djidja, Abomey-calavi and Yarra respectively. Figure 3. Agarose gel electrophoresis of PCR products digested with BstZ17I and HphI restriction enzymes, showing different restriction fragment length polymorphism (RFLP) patterns of analysed samples of H. armigera. M: molecular weight markers. Lanes 1-2, 3-4, 5-6, 7-8, 9-10 and 11-12:H. armigera specimens from Kassakou, Zaffé, Kokrokinho, Djidja, Abomey-calavi and Yarra respectively. Bioassays 3.3.1. Susceptibility of H. armigera to Deltamethrin Following susceptibility assays conducted with deltamethrin, the LD50 of the susceptible strain of H. armigera (SVS) was 0.064 µg/g (Table 4), while the diagnostic dose (DD: LD99.9) was 2.181 µg/g. When field samples (L3 from the F1) were exposed to same serial dilutions of deltamethrin, lower mortality rates which correspond to high levels of resistance were observed. Mortality rates of 9.7% and a LD50 = 149.780 µg/g were recorded with H. armigera from the Abomey-calavi farms; mortality rates of 14.36% and LD50 = 20.378 µg/g recorded with H. armigera from the Zaffé farms; mortality rates of 31.77% and LD50 = 36.16 µg/g for samples from Djidja; mortality rates of 34.35% and LD50 = 5.428 µg/g for samples from Kokrokinho; mortality rates of 43.3% and LD50 = 2.105 µg/g for samples from Yarra; mortality rates 52.9% and DL50 = 0.800 µg/g for H. armigera from the Kassakou farm (Table 4). Table 4. Recorded LD50 with laboratory and field samples of H.armigera when exposed to Deltamethrin. Strain Host Plant Region (Agro Ecosystem) n LD50 (µg/g) (95% FL) Slope ± SE ‘SVS’ Cotton North 668 0.064 (0.035–0.064) 1.91 ± 2.29 KOK.16 (Kokrokinho) Tomato South (Sub-equatorial) 248 5.428 * (2.62–8.81) 1.02 ± 0.75 ZAF.16 (Zaffe) Cotton Central (Sub-Sudanese) South (Sub-equatorial) 240 20.378 * (12.88–34.07) 1.10 ± 1.44 KAS.17 (Kassakou) Cotton North (North-Sudanese) 150 0.800 * (0.132–4.85) 0.61 ± 0.06 YAR.17 (Yarra) Cotton North (Sub-Sudanese) 150 2.105 * (0.236–18.7) 0.56 ± 0.181 AB-C.16 (Abomey-Calavi) Cowpea South (Sub-equatorial) 349 149.780 * (31.12–720.84) 0.76 ± 1.65 DJI.17 (Djidja) Cotton Central (Sub- equatorial) 144 36.16 * (1.23–181.16) 0.32 ± 0.48 N = number of tested larvae (third instar), LD50 = dose that kills 50% of the tested sample, * = LD50 significantly different from that of the susceptible ‘SVS’ strain; 95% FL = Fidicial limits (95%). Table 4. Recorded LD50 with laboratory and field samples of H.armigera when exposed to Deltamethrin. Determined Resistance Factors (RF) from recorded mortalities were 12.5; 32.89; 318.41; and 565 folds higher for Kassakou, Yarra, Zaffé and Djidja cotton farms respectively, as compared to the susceptible laboratory strain SVS (Figure 4). For H. armigera collected in tomato farms, RF was 84.81 9 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 folds higher (samples from Kokrokinho) than the susceptible strain “SVS”. 4.2. Molecular Identification of H. armigera Molecular speciation using COI and Cytb targets coupled with digestion by BstZ17I and HphI respectively helped confirming the presence of H. armigerain the 6 surveyed sites in Benin. Previous studies based on morphological characters such as forewings of noctuid moths have shown several limitations for differentiating some members of Helicoverpa family. In this research, we have used for the first time in Benin a published DNA based protocol [7] for confirming the presence of H. armigera in different host plants in the North-South transect of the country. This molecular based identification of H. armigera in addition to traditional morphological methods described by Matthews [31] constitute effective combinations for improved speciation of H. armigera and better control of this polyphagous pest. 4.1. The Use of Insecticide for H. armigera Control This study revealed that up to 60% of tomato and cotton producers in Benin use pyrethroids to control H. armigera in their farms. Deltamethrin and lambda-cyhalothrin are the main insecticides used against H. armigera in tomato and cotton production respectively. In cotton farming systems, Lambda-cyhalothrin is most often combined with Chlorpyriphos- ethyl for H. armigera control. Data from this survey also revealed that despite the newly approved national Integrated Pest Management (IPM) strategy which replaces the use of deltamethrin by either lambda cyhalothrin (pyrethrinoid) or chlorpyriphos-ethyl (organophosphate) [29], many farmers continue to actively use deltamethrin for fighting H. armigera in cotton fields. As recorded in tomato farming, Decis 12,5 CE (deltamethrin) is also intensively used by cowpea farmers (Frequency: 6 days/1L/ha) [30]; this could explain high resistance profiles observed in H. armigera populations harvested in cowpea farms. 3.3.1. Susceptibility of H. armigera to Deltamethrin As for samples from cowpea farms of Abomey-Calavi, we recorded a RF of 2340.31 folds higher than the susceptible strain “SVS” (Figure 4). Overall, the results of this research revealed higher levels of deltamethrin resistance in cowpea farms. We also recorded an increased resistance pattern as we move down from the North to the southern part of Benin (Figure 4). Figure 4. Map of Benin showing the resistance profile of H. armigerapopulations to deltamethrin in the North-South transect. The resistance profile is expressed in term of resistance factor (RF) calculated from the DL50. 3 2 Mortality Rates of H armigera When Exposed to Combinations of PBO Synergist and Figure 4. Map of Benin showing the resistance profile of H. armigerapopulations to deltamethrin in the North-South transect. The resistance profile is expressed in term of resistance factor (RF) calculated from the DL50. 3.3.2. Mortality Rates of H. armigera When Exposed to Combinations of PBO Synergist and Deltamethrin 3.3.2. Mortality Rates of H. armigera When Exposed to Combinations of PBO Synergist and Deltamethrin When PBO was combined with deltamethrin insecticide, the recovery of susceptibility was observed for all H. armigera tested (Table S1). The susceptibility was total for H. armigera populations from cotton farms of Kassakou and Yarra with mortality rates reaching 100% (Figure 5). With populations from the cotton farm of Djidja, 81.2% mortality was recorded with the combination PBO and deltamethrin whereas, 76.2% mortality was observed with H. armigera populations from the surveyed cowpea farm of Abomey-Calavi (Figure 5). Resistance profiles recorded in cotton farms (North of Benin) were mostly metabolic whereas in cowpea and tomato farms (South of Benin) several mechanisms which include increase activities of oxidase detoxification were observed. No synergist test was performed on H. armigera from Zaffé and Kokrokinho farms due to the low number of larvae collected in these localities. 10 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 10 of 15 Figure 5. Recorded mortalities of H. armigera populations following exposures to diagnostic dose of deltamethrin in the presence or absence of piperonyl butoxide (PBO) synergist. n = number of tested larvae (third instar), NT = No tested. Figure 5. Recorded mortalities of H. armigera populations following exposures to diagnostic dose of deltamethrin in the presence or absence of piperonyl butoxide (PBO) synergist. n = number of tested larvae (third instar), NT = No tested. 4.3. Susceptibility of Helicoverpa armigera to Deltamethrin in Benin IPM strategies implemented in most cropping systems in Benin are mainly based on the use of synthetic chemicals such as pyrethroids, organochlorines and organophosphates [11]. Of these insecticide families, two pyrethroids (deltamethrin and lambda-cyhalothrin) are mostly used for protecting tomato and cotton crops against the polyphagous H. armigera as reported in Benin and other West African countries [32–35]. This regular use of pyrethroids by farmers against this pest of high economic interest has less been backed by a constant monitoring of their susceptibility patterns to insecticides. This research revealed that farmers are continuing to use deltamethrin for H. armigera control despite the fact that this insect has already developed high resistance levels to this insecticide. 11 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 This study highlights the need to provide evidence-based information to farmers on the resistance profiles of the main agricultural pests to guide their insecticide usage. Data generated revealed a high resistance of H. armigera to deltamethrin in cowpea farms (RF = 2340) followed by tomato farms (RF = 84.81) and finally cotton farms (RF ranged 12.5 to 515.94). This high resistance to deltamethrin could be attributed to the overuse and miss-use of this insecticide during many decades in vegetable (tomato), grain legumes (cowpea) and cotton fields across the country [14,33,34]. In addition to the misuse and overuse of insecticides by farmers, the poor quality of pesticides used for pest control has also been documented as favouring the selection of resistance in wild population of pests [36,37]. Resistance levels of H. armigera populations from cotton fields was lower than previously reported in other localities of Benin [11,19] and, in some west African countries such as: Burkina Faso and Ivory Coast [29]. The relatively low resistance recorded in cotton farms could be related to recent modifications made nationwide on IPM strategies such as the alternative use of insecticide families for cotton pest control [29]. In Benin for example, the treatment of cotton plants starts with two spraying of organophosphate followed by a combination of pyrethroids and organophosphate during the last four spraying passages. Such alternative use of different families of insecticides make difficult the development of high resistance levels in surveyed cotton farms. In Contrast, alternative treatments are neither conducted in tomato farms nor in cowpea cropping systems hence, the relatively high resistance profiles recorded with Helicoverpa populations from these two commodities. 4.3. Susceptibility of Helicoverpa armigera to Deltamethrin in Benin In tomato and cowpea farms, deltamethrin remains the insecticide of choice for H. armigera control [30,35]. Resistance selection observed could be primarily due to the permanent use of this insecticide by farmers or, through use of poor quality deltamethrin for pests control as documented by some authors [33,34]. Very surprisingly, we recorded high resistance levels in the cotton farms of Djidja and Zaffé in the South Benin; contradicting data from the surveyed cotton farms of Kassakou and Yarra in the North Benin. As a matter of fact, both cotton farms of Djidja and Zaffé are surrounded by tomato, and cowpea farms which are regularly under pyrethroid treatments. It is possible that Helicoverpa populations of Djidja/Zaffé cotton farms in addition to receiving insecticides residues from cotton treatments also get exposed to pyrethroid insecticides leaching from surrounding tomato and cowpea farms during rainfalls. This combined selection pressure from cotton insecticides and leached insecticides from neighbouring tomato and cowpea farms could explain the higher resistance levels recorded in cotton farms of Djidja and Zaffé contrary to other cotton farms surveyed in the northern Benin (Figure 4). High resistance profiles were globally recorded in the Southern part of Benin compare to North. These high resistance profiles of insects in the Southern Benin had also been documented by Djouaka et al. [38] and other scientists working on insecticide resistance in malaria mosquitoes [36,37,39]. These high resistance levels recorded in southern Benin, compared to northern part of the country, could be associated to combinations of resistance selection factors such as the wide range of agrochemicals misused and overused by farmers, and other environmental pollutants (xenobiotics) which are still to be well identified. The overuse and misuse of pyrethroids lead to a loss of effectiveness of this insecticide as most pests will gradually develop resistance to the selection pressure; this will further increase the financial cost of pests treatment. This misuse of insecticides also leads to environmental pollution causing the imbalance of ecosystems [40]. The importance of conducting insecticide resistance studies on H. armigera resides on the current nationwide need of boosting cotton, vegetables and grain legumes production for increased communities income in Benin. Maps on insecticide resistance spread generated will support strategic policies on the selection of more effective insecticides for better control of this polyphagous pest on different cropping systems and in d ff l l 5. Conclusions This research focused on the use of synthetic chemicals in diverseagro-ecosystems forimproved pest control strategies. Results from this study revealed high levels of pyrethroid resistance in several populations of H. armigera in the North- South transect of Benin. An increasing resistance pattern was observed as we moved from the North to the southern Benin. A resistance contrast was also recorded in between populations of H. armigera from cotton, tomato and cowpea. The involvement of P450s metabolizers in the observed deltamethrin resistance was documented. Further investigation is being conducted into: assessing insecticide resistance profiles of H. armigera to other insecticides, screen for developed resistance mechanism pathways and study related fitness costs. This scientific evidence isimportant for the development of more tailored, cost effective and sustainable IPM strategies against this highly polyphagous pest. Supplementary Materials: The following are available online at http://www.mdpi.com/1660-4601/16/11/188 Table S1: LD50 for deltamethrin with PBO on susceptible and resistant strains of H. armigera in Benin. Author Contributions: E.T., R.D. and M.T. designed the study; E.T., F.Z., G.T.-Y., R.D., O.K.D.K., R.A., G.T., R.S., B.D. and A.H.B.-G. conducted experiments; E.T., R.D. wrote the manuscript and I.D., J.V., T.M., C.W., M.T., G.T.-Y. and A.H.B.-G. crosschecked the manuscript prior to submission. Funding: This research received funding from the Wellcome Trust International Intermediate Fellowship 214201/Z/18/Z awarded to Rousseau Djouaka. It also received support from Fp5-A4NH program of the CGIAR coordinated by Bernard Bett, Jo Line and JeffWaage. Acknowledgments: The AgroEcoHealth platform of International Institute of Tropical Agriculture–Benin supported this research. The authors are indebted to Théodore LAWE (Sodecoton/IRAD Cameroon) for providing the ‘SVS’ strain, Robert AHOMANGNON for his assistance in the collection and rearing of field strains of H. armigera in Benin. All thanks to Elie DANNON (IITA-Benin) for his contributions to the discussion section of this manuscript. Conflicts of Interest: The authors declare no conflict of interest. 4.4. Resistance Mechanisms Developed by H. Armigera Populations to Deltamethrin When field populations of H. armigera were exposed to PBO synergists prior to deltamethrin bio-assays, we recorded a significant increase in observed mortalities; implying the consistent involvement of P450-mediated detoxification enzymes in observed resistance mechanisms. These results 12 of 15 12 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 are similar to those reported by Durigan et al. [20] in Brazil; Achaleke et al. [41] and Brun-Barale et al. [19] in Central Africa and West Africa respectively. However, the fact that mortalities below 100% were recorded in Djidja and Abomey-Calavi even in the presence of synergist PBO may indicate the possible presence of other mechanisms of resistance in these H. armigera populations. Previous studies had revealed the involvement of esterase enzymes in highly resistant populations of Helicoverpa spp. from farms under IPM [42,43]. 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Available online: https://www.researchgate.net/publication/7346565_Use_of_agricultural_ insecticides_in_Benin (accessed on 25 February 2019). 35. Martin, T.; Ochou, G.O.; Djihinto, A.; Traore, D.; Togola, M.; Vassal, J.M.; Vaissayre, M.; Fournier, D. Controlling an insecticide-resistant bollworm in West Africa. Agric. Ecosyst. Environ. 2005, 107, 409–411. [CrossRef] 36. Corbel, V.; N’Guessan, R.; Brengues, C.; Chandre, F.; Djogbenou, L.; Martin, T.; Akogbéto, M.; Hougard, J.M.; Rowland, M. Multiple insecticide resistance mechanisms in Anopheles gambiae and Culex quinquefasciatus from Benin, West Africa. Acta Trop. 2007, 101, 207–216. [CrossRef] [PubMed] 37. Djègbè, I.; Boussari, O.; Sidick, A.; Martin, T.; Ranson, H.; Chandre, F.; Akogbéto, M.; Corbel, V. Dynamics of insecticide resistance in malaria vectors in Benin: First evidence of the presence of L1014S kdr mutation in Anopheles gambiae from West Africa. Malar. J. 2011, 10, 261. [CrossRef] 38. Djouaka, R.; Akoton, R.I.; Tchigossou, G.M.; Atoyebi, S.M.; Irving, H.; Kusimo, M.O.; Djegbe, I.; Riveron, J.M.; Tossou, E.; Yessoufou, A.; et al. Mapping the distribution of Anopheles funestus across Benin highlights a sharp contrast of susceptibility to insecticides and infection rate to Plasmodium between southern and northern populations. Wellcome Open Res. 2017, 1, 28. [CrossRef] 39. Djogbénou, L.; Noel, V.; Agnew, P. Costs of insensitive acetylcholinesterase insecticide resistance for the malaria vector Anopheles gambiae homozygous for the G119S mutation. Malar. J. 2010, 9, 12. [CrossRef] 40. Ratan, M.; Rafiq, L.; Javid, M.; Razia, S. Imbalance due to Pesticide Contamination in Different Ecosystems. Int. J. Theor. Appl. Sci. 2018, 10, 239–246. Available online: https://www.researchgate. net/publication/325945183_Imbalance_due_to_Pesticide_Contamination_in_Different_Ecosystems (accessed on 11 April 2019). 41. 42. Gunning, R.V.; Moores, G.D.; Devonshire, A.L. Esterase inhibitors synergise the toxicity of pyrethroids in Australian Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae). Pestic. Biochem. Physiol. 1999, 63, 50–62. [CrossRef] 43. Young, S.J.; Gunning, R.V.; Moores, G.D. The effect of piperonyl butoxide on pyrethroid-resistance-associated esterases in Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae). Pest Manag. Sci. 2005, 61, 397–401. [CrossRef] [PubMed] © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). References Achaleke, J.; Martin, T.; Ghogomu, R.T.; Vaissayre, M.; Brévault, T. Esterase-mediated resistance to pyrethroids in field populations of Helicoverpa armigera (Lepidoptera: Noctuidae) from Central Africa. Pest Manag. Sci. 2009, 65, 1147–1154. [CrossRef] [PubMed] 15 of 15 15 of 15 Int. J. Environ. Res. Public Health 2019, 16, 1882 42. Gunning, R.V.; Moores, G.D.; Devonshire, A.L. Esterase inhibitors synergise the toxicity of pyrethroids in Australian Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae). Pestic. Biochem. Physiol. 1999, 63, 50–62. [CrossRef] 43. Young, S.J.; Gunning, R.V.; Moores, G.D. The effect of piperonyl butoxide on pyrethroid-resistance-associated esterases in Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae). Pest Manag. Sci. 2005, 61, 397–401. [CrossRef] [PubMed] © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
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HPV-Mediated (p16-Positive) Oropharyngeal Cancer Pathologic Primary Tumor TNM Finding v8
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Qeios · Definition, February 2, 2020 Open Peer Review on Qeios Open Peer Review on Qeios HPV-Mediated (p16-Positive) Oropharyngeal Cancer Pathologic Primary Tumor TNM Finding v8 National Cancer Institute National Cancer Institute Qeios ID: 7TSGJH · https://doi.org/10.32388/7TSGJH Source National Cancer Institute. HPV-Mediated (p16-Positive) Oropharyngeal Cancer Pathologic Primary Tumor TNM Finding v8. NCI Thesaurus. Code C132861. A pathologic finding about one or more characteristics of HPV-mediated (p16-positive) oropharyngeal cancer, following the rules of the TNM AJCC v8 classification system as they pertain to staging of the primary tumor. Qeios ID: 7TSGJH · https://doi.org/10.32388/7TSGJH 1/1
W4240969670.txt
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MET Protein Variant
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Qeios · Definition, February 8, 2020 Ope n Pe e r Re v ie w on Qe ios MET Protein Variant National Cancer Institute Source National Cancer Institute. MET Protein Variant. NCI T hesaurus. Code C136286. A variation in the amino acid sequence for the hepatocyte growth factor receptor protein. Qeios ID: LNL7Y4 · https://doi.org/10.32388/LNL7Y4 1/1
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On the Bacteriology of Initial Dental Caries: A Reply to the Foregoing Statement by Dr. J. Leon Williams
Journal of dental research
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public-domain
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permission. at Univ of Connecticut / Health Center / Library on April 12, 2015 For personal use only. No other uses without jdr.sagepub.com Downloaded from ON THE BACTERIOLOGY OF INITIAL DENTAL CARIES O O GO G WILLIAM J. GIES Biochemical Laboratory of Columbia University, at the College of Physicians and Surgeons, New York City WILLIAM J. GIES Biochemical Laboratory of Columbia University, at the College of Physicians and Surgeons, New York City WILLIAM J. GIES Biochemical Laboratory of Columbia University, at the College of Physicians and Surgeons, New York City Dr. Williams is quite correct in his assumption, as stated in the paper preceding this, that we have been working without detailed knowledge of what he has done in dental bacteriology. In our first review of the situation in this field, my collaborator, Dr. Lothrop (1), referred to a paper, by Dr. Williams (2), in which Dr. Williams de- scribed Vincentini's Leptothrix racemosa. It was said, in that review, that L. racemosa is probably a fungus. We knew of Goadby's com- ment in this relation, as follows (3): "This organism (L. racemosa), according to Vincentini and Leon Williams, belongs to a higher order than the bacteria or schizomycetes, and it is suggested that it should be placed among the fungi. Williams thinks that the process of sporulation that he has seen is nearly allied to the uridineae or rusts." In our earlier laboratory observations in this connection, my col- laborator, Dr. Kligler, identified and cultivated two species of Lepto- thrix from dental deposits. One of them, L. buccalis, was referred to as follows (4): "L. buccalis. Fifteen strains of the true Leptothrix were studied in detail. They correspond with the description usually given for the typical organism. They all showed the same mor- phology and resembled microscopically both the L. buccalis of Miller and the L. racemosa of Vincentini and Williams." In our next publication on this subject, in an early issue of this JOURNAL, we shall present a full review of Dr. Williams' work in this relation, with particular reference to its bearing on the present status of dental bacteriology. It has been a part of our plan, from the beginning, to include the type of study and photomicrographic demonstration that Dr. Williams mentions as a deficiency in our reports to date. We have found it 27 28 WILLIAM J. GIES impossible to progress as rapidly or as comprehensively as we hoped, because of lack of financial resources on which to proceed. impossible to progress as rapidly or as comprehensively as we hoped, because of lack of financial resources on which to proceed. It is very gratifying to receive Dr. permission. at Univ of Connecticut / Health Center / Library on April 12, 2015 For personal use only. No other uses without jdr.sagepub.com Downloaded from WILLIAM J. GIES Biochemical Laboratory of Columbia University, at the College of Physicians and Surgeons, New York City Williams' proffer of a gift of $500 to this JOURNAL, to promote the purpose of the JOURNAL itself, to assist us in our bacterio-chemical study, and to help us to prepare, for educational purposes, dental specimens showing the mucin plaque in situ. I have assured Dr. Williams that his generosity is very greatly appreciated and that we shall be happy to endeavor to execute all his suggestions. I have before me, as I write, the two excellent reproductions, in Goadby's book (5), of photomicrographs of specimens made by Dr. Williams showing "a section of enamel with layer of attached organ- isms and formation of pits between enamel rods" (p. 135), and "dental caries affecting dentine under enamel pit" (p. 144). It is evident, from the effectiveness of these photomicrographs, that Dr. Williams' experience in work of this kind will be of the greatest possible assist- ance to us in our endeavor to make similar specimens, for permanent use in dental schools and for study in our research. With Goadby's book still before me I note further, with pleasure, the following comment, on p. 137: "Leon Williams has demonstrated the plaques of microorganisms on the enamel surface of teeth, and the incipient caries occurring under these plaques." Readers of my reports to the First District Dental Society of the State of New York, on the dentifricial efficacy of food-acid media, as published in the Journal of the Allied Dental Societies since the issue of December, 1910, will doubtless be interested in the following com- ment by Goadby, in the same book, p. 139, quoting Dr. Williams: "Dr. Leon Williams tells me that the Sicilians, who are particularly free from caries, are large consumers of lemons." The generous attitude of Dr. Williams, as expressed in the pre- ceding paper, toward the furtherance of dental research and the pro- motion of dental education, is very gratifying evidence of his abiding active interest in the advancement of his profession. It is a pleasure and an honor to accept, and to try to merit, for the JOURNAL OF DENTAL RESEARCH, such a valued and stimulating practical expression of idealism as Dr. Williams presents to the readers of this JOURNAL. 29 permission. at Univ of Connecticut / Health Center / Library on April 12, 2015 For personal use only. No other uses without jdr.sagepub.com Downloaded from LITERATURE CITED (1) LOTHROP 1911 Journal of the Allied Dental Societies, vi, p. 305. (1) LOTHROP 1911 Journal of the Allied Dental Societies, vi, p. 305. ( ) (2) WILLIAMS 1899 Dental Cosmos, xli, p. 317. (3) GOADBY 1903 Mycology of the mouth, p. 187. (4) KLIGLER AND GIES 1915 Journal of the Al (4) KLIGLER AND GIES 1915 Journal of the Allied Dental Societies, x, p. 328. (5) GOADBY 1903 Mycology of the mouth.
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https://www.research.ed.ac.uk/files/325704712/gkac1232.pdf
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Cryo-EM structure of the fully assembled Elongator complex
Nucleic acids research
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General rights C i h f h General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Edinburgh Research Explorer Digital Object Identifier (DOI): 10.1093/nar/gkac1232 Document Version: Publisher's PDF, also known as Version of record Published In: Nucleic Acids Research Cryo-EM structure of the fully assembled elongator complex Citation for published version: Jaciuk, M, Scherf, D, Kaszuba, K, Gaik, M, Rau, A, Kościelniak, A, Krutyhołowa, R, Rawski, M, Indyka, P, Graziadei, A, Chramiec-Głąbik, A, Biela, A, Dobosz, D, Lin, T-Y, Abbassi, N-E-H, Hammermeister, A, Rappsilber, J, Kosinski, J, Schaffrath, R & Glatt, S 2023, 'Cryo-EM structure of the fully assembled elongator complex', Nucleic Acids Research, vol. 51, no. 5, gkac1232, pp. 2011-2032. https://doi.org/10.1093/nar/gkac1232 Citation for published version: Citation for published version: Jaciuk, M, Scherf, D, Kaszuba, K, Gaik, M, Rau, A, Kościelniak, A, Krutyhołowa, R, Rawski, M, Indyka, P, Graziadei, A, Chramiec-Głąbik, A, Biela, A, Dobosz, D, Lin, T-Y, Abbassi, N-E-H, Hammermeister, A, Rappsilber, J, Kosinski, J, Schaffrath, R & Glatt, S 2023, 'Cryo-EM structure of the fully assembled elongator complex', Nucleic Acids Research, vol. 51, no. 5, gkac1232, pp. 2011-2032. https://doi.org/10.1093/nar/gkac1232 Take down policy Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. 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Oct. 2024 Nucleic Acids Research, 2023 1 https://doi.org/10.1093/nar/gkac1232 NAR Breakthrough Article Cryo-EM structure of the fully assembled Elongator complex Marcin Jaciuk1, David Scherf2, Karol Kaszuba3,4, Monika Gaik 1, Alexander Rau5, Anna Ko´scielniak1, Ro´scisław Krutyhołowa1, Michał Rawski1,6, Paulina Indyka1,6, Andrea Graziadei5, Andrzej Chramiec-Gł˛abik1, Anna Biela1, Dominika Dobosz1, Ting-Yu Lin1, Nour-el-Hana Abbassi1,7, Alexander Hammermeister1,2, Juri Rappsilber 5,8, Jan Kosinski 3,4,9, Raffael Schaffrath 2 and Sebastian Glatt 1,* 1Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland, 2Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany, 3European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany, 4Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany, 5Bioanalytics, Institute of Biotechnology, Technische Universit¨at Berlin, Berlin 13355, Germany, 6National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland, 7Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw 02-091, Poland, 8Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK and 9Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany Received August 22, 2022; Revised November 22, 2022; Editorial Decision November 23, 2022; Accepted Dec C⃝The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. *To whom correspondence should be addressed. Tel: +48 12 664 6321; Fax: +48 12 664 6902; Email: sebastian.glatt@uj.edu.pl Present address: Ro´scisław Krutyhołowa, Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland. ABSTRACT fully assembled mouse Elongator complex at 5.9 ˚A resolution. Our results confirm the structural con- servation of Elongator and its intermediates among eukaryotes. Furthermore, we complement our analy- ses with the biochemical characterization of the as- sembled human Elongator. Our results provide the molecular basis for the assembly of Elongator and its tRNA modification activity in eukaryotes. ar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Transfer RNA (tRNA) molecules are essential to de- code messenger RNA codons during protein synthe- sis. All known tRNAs are heavily modified at mul- tiple positions through post-transcriptional addition of chemical groups. Modifications in the tRNA an- ticodons are directly influencing ribosome decod- ing and dynamics during translation elongation and are crucial for maintaining proteome integrity. In eu- karyotes, wobble uridines are modified by Elonga- tor, a large and highly conserved macromolecular complex. Elongator consists of two subcomplexes, namely Elp123 containing the enzymatically active Elp3 subunit and the associated Elp456 hetero- hexamer. The structure of the fully assembled com- plex and the function of the Elp456 subcomplex have remained elusive. Here, we show the cryo-electron microscopy structure of yeast Elongator at an overall resolution of 4.3 ˚A. We validate the obtained struc- ture by complementary mutational analyses in vitro and in vivo. In addition, we determined various struc- tures of the murine Elongator complex, including the eceived August 22, 2022; Revised November 22, 2022; Editorial Decision November 23, 2022; Accepted Decemb INTRODUCTION strate (31). Of note, the structure of yeast Elp3 resembles previously resolved crystal structures of bacterial and ar- chaeal Elp3 proteins (32,33). In detail, the Elp3 subunit specifically binds the tRNA anticodon stem loop (ASL) in the vicinity of its radical S-adenosyl methionine (rSAM) and lysine acetyltransferase (KAT) domains to modify the well-positioned U34 nucleotide (32–34). tRNA binding is aided by additional contacts in the CTD of Elp1, which was previously shown to be heavily phosphorylated (35) and in- volved in tRNA binding (36). Transfer RNAs (tRNA) are one of the most essential biomolecules in all living organisms. Together with mes- senger RNAs (mRNA), they are responsible for the cor- rect transfer of information from the genomic DNA into functional polypeptide chains. tRNAs undergo significant post-transcriptional modifications, which confer stabiliza- tion of the folded tRNA, regulate the interaction with other molecules or tune the codon-anticodon pairing during the mRNA translation process within the ribosome (1). In eu- karyotes, almost all wobble uridines at position 34 (U34), are carboxymethylated on the fifth carbon of their base (cm5) by the activity of the highly conserved Elongator complex aided by its accessory proteins Kti11, Kti12, Kti13, Kti14 and Sit4 (2–6). Subsequently, cm5 is further modi- fied by other enzymes to 5-methoxycarbonylmethyl (mcm5), 5-carbamoylmethyl (ncm5) or 5-methoxy-carbonyl-methyl- 2-thio (mcm5s2) (7,8). These modifications regulate proper tRNA binding in the A-site of translating ribosomes during the elongation phase (9–11) and thus maintain an optimal speed during polypeptide synthesis, supporting proper co- translational folding of the nascent proteins. Decreased lev- els of wobble uridine modifications lead to ribosome paus- ing, incorrect protein folding and consequently trigger in- tracellular protein aggregation and proteotoxic stress (12– 14). Furthermore, Elongator is a clinically highly relevant enzyme, as mutations that disturb the structure or func- tion of the complex result in severe human diseases (15), like familial dysautonomia (16), rolandic epilepsy (17), in- tellectual disability (18), amyotrophic lateral sclerosis (19), other neurodevelopmental diseases (20–22) and childhood medulloblastoma (23). g ( ) Despite all previous efforts, several fundamental ques- tions concerning Elongator’s function remain elusive. For instance, the tRNA modification reaction has not been re- constituted in vitro (37,38), which leaves the exact molecu- lar mechanisms and the observed substrate specificity unan- swered. INTRODUCTION One of the main open questions concerns the func- tional role of the Elp456 subcomplex, which interacts with Elp123 and is essential for the activity of Elongator in yeast (39). To address these outstanding questions, we investi- gated the cryo-EM structures of the yeast Elongator com- plex in its native and bis(sulfosuccinimidyl)suberate (BS3) stabilized state. Next, we validated the functional relevance of the newly identified structural features in vivo using es- tablished phenotypic assays. Furthermore, we were able to confirm the high structural conservation of Elongator and its active site by determining structures of Elp123, Elp123– tRNA and Elongator complexes from yeast and mouse. Finally, through biochemical characterization of human Elp123 and Elp456 we can propose a detailed reaction mechanism and suggest a role for the Elp456 subcomplex during the reaction cycle of the Elongator. GRAPHICAL ABSTRACT e - - e n ll c- o - e GRAPHICAL ABSTRACT ax: +48 12 664 6902; Email: sebastian.glatt@uj.edu.pl f Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland. 23 containing the enzymatically active t and the associated Elp456 hetero- e structure of the fully assembled com- function of the Elp456 subcomplex have sive. Here, we show the cryo-electron structure of yeast Elongator at an overall 4.3 ˚A. We validate the obtained struc- plementary mutational analyses in vitro n addition, we determined various struc- murine Elongator complex, including the GRAPHICAL ABSTRACT ondence should be addressed. Tel: +48 12 664 6321; Fax: +48 12 664 6902; Email: sebastian.glatt@uj.edu.pl ´scisław Krutyhołowa, Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland. *To whom correspondence should be addressed. Tel: +48 12 664 6321; Fax: +48 12 664 6902; Email: sebastian.glatt@uj.edu.pl Present address: Ro´scisław Krutyhołowa, Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland. 2 Nucleic Acids Research, 2023 MATERIALS AND METHODS The Elongator complex harbors two copies of each of its six subunits, namely Elongator proteins 1–6 (Elp1–Elp6) (24). The complex can be divided into two discrete sub- complexes - the larger catalytic Elp123 and the smaller hex- americ ring-shaped Elp456 (25,26). Studies applying nega- tive stain electron microscopy, revealed that Saccharomyces cerevisiae Elp123 (ScElp123) adopts a symmetric ‘moth’- like shape, with two distinguishable lobes that are sepa- rated by a cleft and connected by an arch region. In con- trast, the structure of the fully assembled Elongator com- plex seems asymmetric as Elp456 only binds to one lobe of the dimeric Elp123 subcomplex (27,28). Based on these initial low-resolution reconstructions the following subunit arrangement of the Elp123 subcomplex was proposed – the two N-terminal WD40 domains of Elp1 and Elp2 (29), en- compass the enzymatically active Elp3 subunit from op- posite directions creating a lobe of Elp123. The remaining C-terminal domain (CTD) of Elp1 consisting of tetratri- copeptide repeats (TPRs) and the CTD of the second copy of Elp1 dimerize into an arch-like structure that connects two Elp123 lobes, respectively (30). Subsequent single par- ticle cryo-electron microscopy (cryo-EM) studies resulted in high-resolution structures of yeast Elp123 in its free and tRNA-bound states. Intriguingly, these structures revealed the spatial organization of the active site in the eukaryotic Elp3 protein, including the coordination of an iron-sulfur cluster, the S-adenosyl-methionine (SAM) cleavage product 5′-deoxyadenosine (5′-dA) and the respective tRNA sub- Bulk yeast tRNA isolation To obtain yeast bulk tRNA, S. cerevisiae strains were grown in YPD (Yeast Extract–Peptone–Dextrose) to an OD600 nm of 1, harvested, washed and resuspended in NucleoZOL (Machery Nagel). Cells were lysed by bead beating in 6 cy- cles each 60 s, 20% v/v volume of chloroform was added and samples were vigorously vortexed for another 60 s. Sub- sequently, the suspension was incubated for 15 min at 4◦C and centrifugated for 30 min at 21 000 × g. The aqueous RNA-containing phase was transferred into a new reaction tube and large RNAs were precipitated for 3 h at −20◦C us- ing 2/3 volume of 8 M LiCl. Large RNAs were pelleted for 30 min at 4◦C and 21 000 × g. To increase tRNA purity, the LiCl precipitation step was repeated. The tRNA-containing supernatant was precipitated with 10% v/v 3 M sodium acetate pH 5.2 and 2.5 volumes 100% ethanol overnight at −20◦C. The tRNA containing pellet was washed twice with 75% v/v ethanol, air dried and resuspended in 10 mM sodium acetate pH 5.2. tRNA concentrations were deter- mined using the Epoch (Agilent BioTek) spectrophotome- ter and stored at −80◦C. Protein production and purification DS1-2b yeast cells (MAT  his3-Δ200, leu2-Δ1, trp1-Δ63, ura3-52), co-transformed with the constructs expressing all six Elongator genes, were grown on synthetic drop-out (SD) media plates (2% w/v agar and 2% w/v glucose) lacking tryptophan, leucine and uracil. Cells were grown shaking overnight at 30◦C in the SD media (2% w/v glucose), reinoc- ulated (3:50 ratio) on the next day into fresh SD medium and further incubated overnight at 30◦C with shaking. For protein overproduction, cells were inoculated (1:20) in fresh SD media containing 2% w/v raffinose and incubated for 5–7 h at 30◦C while shaking. ELP genes expression was induced by addition of galactose to a final concentration of 2% w/v and cells were left shaking for 21 h at 30◦C. Cells were harvested by centrifugation, resuspended in lysis buffer (250 mM HEPES (pH 7.5), 100 mM NaCl, 10% v/v glycerol, 0.1% v/v Tween 20, 1 mM sodium orthovanadate, 20 mM sodium fluoride, aprotinin (2 g/ml), leupeptin (5 g/ml), 1 M pepstatin A, and 1 mM PMSF) and small cell suspensions droplets were flash frozen in liquid nitro- gen. Droplets were lysed by cryo-milling (Qiagen TissueL- yser II) and stored as a powder at −80◦C until use. All pu- rification steps were performed at 4◦C or on ice. 12 ml of fresh lysis buffer was added per 40 g of dry yeast pellet and thawed for 1 h under agitation. Lysates were clarified by two consecutive centrifugation steps at 21 000 × g for 30 min. Cell extracts were incubated for 30 min with 3 ml of IgG Sepharose™6 Fast Flow resin (GE Healthcare) and washed three times with lysis buffer. Proteins were eluted in 5 ml lysis buffer by TEV protease cleavage (1 mg) in pres- ence of 1 mM dithiothreitol (DTT) for 1 h. Subsequently, the eluent was applied to a 1 ml StrepTrap HP column (GE Healthcare) and eluted with 20 mM D-desthiobiotin. The complex was concentrated using an Amicon Ultra- 15 centrifugal filter (100 kDa cut-off) and the Elonga- tor was further purified on a Superose 6 Increase 10/300 GL column (GE Healthcare) equilibrated with 20 mM HEPES (pH 7.5), 100 mM NaCl and 3 mM DTT. Selected fractions were pooled and concentrated with an Amicon Ultra-0.5 centrifugal filter (100 kDa cut-off). Aliquots were frozen in liquid nitrogen and stored at −80◦C for further use. Preparation of expression constructs Eluates were concentrated using Amicon Ultra- 15 centrifugal filters (100 kDa cut-off) and subjected to a Superose S6 Increase 10/300 GL column (GE Healthcare) equilibrated with 20 mM HEPES (pH 7.5), 100 mM NaCl and 5 mM DTT. Purity, integrity, protein quality and all complexes stoichiometry were monitored during every step by SDS-PAGE analysis and visualization with Coomassie stain. and pBig1b plasmids to obtain ELP123 and ELP456, re- spectively (41). Mutagenesis in human ELP1, ELP4 and ELP5 were carried out using the QuikChange method. All genetic constructs were confirmed by DNA sequencing and moved to the insect cells expression system using standard Bac-to-Bac protocols. Preparation of expression constructs The ORFs of Saccharomyces cerevisiae ELP1 to ELP6 were amplified by polymerase chain reactions (PCRs) and cloned in pairs into three individual vectors with inducible GAL1 and GAL10 promoters to allow for simultaneous expres- sion of two gene products from a single vector (40). Yeast cells co-transformed with all three constructs, were selected for tryptophan, leucine and uracil prototrophy. Coding se- quences for FLAG and Twin-Strep-tag (IBA Lifesciences) were added in frame to ELP1 and ELP3, respectively. In addition, Elp6 was overproduced with a Staphylococcus au- reus protein A tag and a tobacco etch virus (TEV) pro- tease cleavage site to facilitate the purification from yeast cells. All sequences were introduced at the 3′ end of the individual ORFs. Mus musculus and Homo sapiens biG- Bac (41,42) constructs containing the ORFs of ELP123 and ELP456 were prepared using a similar tagging strat- egy. After PCR amplification all expression cassettes (ex- cept for ELP2) were cloned separately into pFastBac1 plas- mids. ELP3 was cloned in frame with a Twin-Strep-Tag se- quence and ELP6 with FLAG-TEV-Protein A sequence at their 3′ ends. ELP2 genes were cloned into pFastBac-HTA with a 6xHis-tag sequence at its 5′ end. All genes were am- plified from the pFastBac plasmids by PCR using primers with predefined 5′ and 3′ overhangs in each gene, followed by Gibson assembly reactions (43,44) (NEB) using pBig1a Nucleic Acids Research, 2023 3 methylsulfonyl fluoride in presence of DNase I by three freeze-thaw cycles and sonication. Lysates were clarified by two consecutive centrifugation steps at 4◦C and 63 000 × g for 30 and 60 min. Elp123 subcomplexes were purified from cell extracts using a 5 ml StrepTrap HP column (GE Health- care) and eluted with 10 mM d-desthiobiotin. Next, Elp123 subcomplexes were further purified on a 5 ml HiTrap Hep- arin HP column (GE Healthcare) and eluted with a linear KCl gradient (50 mM HEPES pH 7.5, 1000 mM KCl, 1 mM DTT). The final purification step was carried out on a Su- perose 6 Increase 10/300 GL column (GE Healthcare) equi- librated with 20 mM HEPES (pH 7.5), 100 mM NaCl and 5 mM DTT. Mouse and human Elp456 subcomplexes were purified from cell extracts using IgG Sepharose™6 Fast Flow resin equilibrated with 50 mM HEPES (pH 7.5), 300 mM NaCl, 1 mM DTT and 5% v/v glycerol. Elution from the resin was accomplished by TEV protease cleavage (1 mg/5 ml). Human bulk tRNA isolation Mouse and human Elp123 were overproduced in Super Sf9-1, Sf9-3 respectively, while both Elp456 in Hi-5 cells. Cells were cultured in ESF921 medium (Expression Sys- tems) to a density of 800 000 cells/ml for Super Sf9-1/Sf9-3 and 500 000 cells/ml for Hi-5 cells, followed by baculovirus infection with the multiplicity of infection (MOI) of 1 and grown for 3 days at 27◦C while shaking. Cell pellets were harvested and lysed in 50 mM HEPES (pH 7.5), 100 mM NaCl for Elp123 and 300 mM NaCl for Elp456, 2 mM MgCl2, 2 mM DTT, 5% v/v glycerol, aprotinin (2 g/ml), leupeptin (5 g/ml), 1 M pepstatin A, 1 mM phenyl- HEK293T cells cultured on 15-cm Petri dishes were washed with PBS and lysed for 5 min in 250 l RNA lysis buffer (10 mM Tris–HCl (pH 7.5), 100 mM NaCl, 10 mM MgCl2, 1% TritonX-100 v/v, 0.5% v/v sodium deoxycholate, 0.5 mM DTT) at 4◦C. The lysate was mixed with MiliQ water at a 1:1 ratio v/v and the RNA was isolated three times with 1 volume of acid-phenol:chloroform (1:1 ratio v/v), followed by an additional step using 1 volume chloroform. After each step the sample was vortexed and centrifugated for 10 min at 4500 × g at 4◦C and the aqueous phases were collected, 4 Nucleic Acids Research, 2023 WARP 1.0.9 (46) for ScElongator, and cryoSPARC (47) for MmElp123–tRNA and MmElongator. Averaged micro- graphs for all datasets were imported into cryoSPARC and the contrast transfer function (CTF) was corrected. Blob picking was performed on 10–15% of micrographs to select an initial set of particles for template picking (MmElp123– tRNA) and to train the TOPAZ particle picker (48). For ScElp456 and MmElp123 two separate trainings were per- formed for different orientations. The resulting TOPAZ models were used next to pick particles from all micro- graphs of respective data sets. A similar approach was ap- plied for the MmElongator dataset, where two TOPAZ picking jobs were used during the analysis. Extracted par- ticles were binned as indicated in respective processing pipeline panels and particle curation was performed via 2D classification and ab-initio reconstructions. All Elongator- related particles, except for MmElp123–tRNA, were next converted with pyem (49) and imported into Relion for fur- ther sub-classification. For ScElongator and MmElongator, masked 3D classifications around Elp456 were applied to improve the densities of the smaller subcomplex. Model building, refinement and validation Atomic models for both, yeast and mouse structures, were prepared via SWISS-MODEL homology model building (50–58), using PDB entries 6QK7 and 4A8J as templates. The model of the yeast Elp3 subunit from Elp123–tRNA was replaced with the AlphaFold2 model (59) to include the previously missing N-terminus. After rigid body fitting into the cryo-EM density map, the models were manually curated and corrected in Coot (60) and further fitted by molecular dynamic flexible fit using MDFF (61) and Nam- dinator (62). The obtained atomic models were refined in Phenix (63,64), analyzed in Coot and validated with Mol- Probity (65) (Table 1). Figures were prepared using PyMOL (The PyMOL Molecular Graphics System, Version 2.5.1 Schr¨odinger, LLC) and UCSF ChimeraX (66). Elongator reconstitution and pull-down assays Mouse or human Elp123 were incubated with the respec- tive Elp456 subcomplex for 30 min at 25◦C with 1:2 weight ratio and subsequent purification on a Superose 6 In- crease 10/300 GL column (GE Healthcare) equilibrated with 20 mM HEPES (pH 7.5), 100 mM NaCl and 5 mM DTT. For the pull-down experiments 10 g of bait and 20 g of prey were used. Elp123 was immobilized on StrepTactin™Sepharose™(Cytiva) beads via Twin-Strep- tagged Elp3 or in case of Elp456 via anti-DYKDDDDK Human bulk tRNA isolation The precipitate, was centrifuged at 8000 × g for 30 min at 4◦C and the super- natant was discarded. The pellet was resuspended in 100 l equilibration buffer without TritonX-100 (10 mM Bis– Tris (pH 6.3), 15% ethanol v/v, 200 mM KCl). RNA con- centration was measured using a NanoDrop spectropho- tometer and the sample was stored at −80◦C until use. To isolate bulk tRNA 900 g of total RNA (diluted in 2 ml equilibration buffer without TritonX-100) was loaded on an equilibrated NucleoBond AX100 column (10 mM Bis– Tris (pH 6.3), 15% v/v ethanol, 200 mM KCl, 0.15% v/v TritonX-100) and washed twice with 12 ml washing buffer (10 mM Bis–Tris (pH 6.3), 15% v/v ethanol, 500 mM KCl) tRNA was eluted with 12 ml elution buffer (10 mM Bis– Tris (pH 6.3), 15% v/v ethanol, 800 mM KCl) and mixed with 2.5 volumes of 100% ethanol, 1 l of glycogen and in- cubated overnight at −80◦C. After precipitation, the sam- ple was centrifuged for 30 min at 8000 × g (4◦C), and the supernatant was discarded. The tRNA pellet was washed with 40 ml 80% v/v EtOH by vortexing. Afterward, the tRNA was centrifuged for 30 min at 8000 × g (4◦C). Subse- quently, the tRNA pellet was air dried and resuspended in 30 l RNAse free water. tRNA concentration was measured using a NanoDrop spectrophotometer and the sample was stored at −80◦C for later use. Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac Electron microscopy QUANTIFOIL® R 2/1 copper grids (200 mesh) were glow- discharged on a Leica EM ACE 200 glow discharger (8 mA, 60 s). 2.5 l of the sample at 0.4–0.6 mg/ml con- centration was plunge-frozen using a Vitrobot Mark IV (Thermo Fisher) set to 100% humidity and 4◦C with the following blotting parameters −15 s wait time, blot force 5 and 5 s blot time. tRNA was used at 3–5 molar ex- cess with 15 min incubation on ice for ScElp123–tRNA and 37◦C for mouse Elp123 (MmElp123)–tRNA samples. ScElp123–tRNA micrographs were acquired at 300 kV us- ing a Titan Krios 2 (FEI; EMBL, Germany) equipped with a Gatan Quantum energy filter and a K2 Summit direct electron detector. 11,080 micrographs were collected with 0.81 ˚A pixel size and 0.8–2 m under-focus for a total of 40 frames accumulating 42.45 e−/ ˚A2 dose. The remain- ing datasets were collected on Titan Krios G3i (Thermo Fisher; Solaris, Poland) equipped with a Gatan Quan- tum energy filter and a K3 Summit direct electron detec- tor. The used under-focus range was 0.9–3 m for a total of 40 frames accumulating an overall dose of 40 e−/ ˚A2. 6339, 4716, 6415, 7000 and 5232 micrographs were col- lected for ScElongator, ScElp456, MmElp123, MmElp123– tRNA and MmElongator, respectively with a pixel size of 1.1 ˚A for ScElp456 and 0.86 ˚A for the remaining data sets. Human bulk tRNA isolation For ScElp123–tRNA masked tRNA 3D classification followed by CTF refinement and Bayesian polishing were performed to improve the tRNA density. For the MmElp123 active site, a masked 3D classification was performed that resulted in an improved density around the bound SAM molecule. The final maps after post-processing were obtained at the following resolutions −4.35 ˚A for ScElongator, 3.96 ˚A for ScElp123–tRNA, 3.7 ˚A for ScElp456, 4.01 ˚A for MmElp123 and 5.92 ˚A for MmElongator, respectively. The analysis of MmElp123–tRNA was exclusively per- formed in cryoSPARC resulting in an overall resolution of 4.35 ˚A. combined and mixed with 10% volume of 3 M sodium ac- etate pH 5.5, three volumes of 100% ethanol, 1 l of glyco- gen and incubated overnight at −80◦C. The precipitate, was centrifuged at 8000 × g for 30 min at 4◦C and the super- natant was discarded. The pellet was resuspended in 100 l equilibration buffer without TritonX-100 (10 mM Bis– Tris (pH 6.3), 15% ethanol v/v, 200 mM KCl). RNA con- centration was measured using a NanoDrop spectropho- tometer and the sample was stored at −80◦C until use. To isolate bulk tRNA 900 g of total RNA (diluted in 2 ml equilibration buffer without TritonX-100) was loaded on an equilibrated NucleoBond AX100 column (10 mM Bis– Tris (pH 6.3), 15% v/v ethanol, 200 mM KCl, 0.15% v/v TritonX-100) and washed twice with 12 ml washing buffer (10 mM Bis–Tris (pH 6.3), 15% v/v ethanol, 500 mM KCl) tRNA was eluted with 12 ml elution buffer (10 mM Bis– Tris (pH 6.3), 15% v/v ethanol, 800 mM KCl) and mixed with 2.5 volumes of 100% ethanol, 1 l of glycogen and in- cubated overnight at −80◦C. After precipitation, the sam- ple was centrifuged for 30 min at 8000 × g (4◦C), and the supernatant was discarded. The tRNA pellet was washed with 40 ml 80% v/v EtOH by vortexing. Afterward, the tRNA was centrifuged for 30 min at 8000 × g (4◦C). Subse- quently, the tRNA pellet was air dried and resuspended in 30 l RNAse free water. tRNA concentration was measured using a NanoDrop spectrophotometer and the sample was stored at −80◦C for later use. combined and mixed with 10% volume of 3 M sodium ac- etate pH 5.5, three volumes of 100% ethanol, 1 l of glyco- gen and incubated overnight at −80◦C. Image processing Frame alignment and dose weighting were performed with Relion 3.1 (45) implementation of motion correc- tion for ScElp123–tRNA, ScElp456 and MmElp123; with Nucleic Acids Research, 2023 5 Table 1. Cryo-EM data collection, refinement and validation statistics ScElongator EMD-15622 PDB ID 8ASV ScElp456 EMD-15635 PDB ID 8AT6 ScElp123–tRNA EMD-15623 PDB ID 8ASW MmElp123 EMD-15682 PDB ID 8AVG MmElp123–tRNA EMD-15625 MmElongator EMD-15626 Data collection and processing Magnification 105 000× 81 000× 165 000× 105 000× 105 000× 105 000× Voltage (keV) 300 300 300 300 300 300 Electron exposure (e-/ ˚A2) 40 40 42.45 40 40 40 Defocus range −0.9 to −3.0 −0.9 to −3.0 −0.8 to −2.0 −0.9 to −3.0 −0.9 to −1.5 −0.9 to −3.0 Pixel size ( ˚A) 0.86 1.1 0.81 0.86 0.86 0.86 Symmetry imposed C1 C1 C1 C1 C1 C1 Initial particle images (no.) 188 389 364 424 693 585 364 424 161 871 581 666 Final particle images (no.) 12 514 128 593 16 809 42 894 24 829 27 128 Map resolution ( ˚A) 4.35 3.7 3.96 4.01 4.35 5.9 FSC threshold 0.143 0.143 0.143 0.143 0.143 0.143 Map resolution range ( ˚A) 3.9 to >10 3.6 to 6.6 3.7 to 9.7 3.8 to >10 2.8 to >10 4.4 to >10 Refinement Initial model used 6QK7 and 4A8J 4A8J 6QK7 6QK7 Model resolution ( ˚A) 3.5 3.7 3.5 3.5 FSC threshold 0.143 0.143 0.143 0.143 Model resolution range ( ˚A) n/a n/a n/a n/a Map sharpening B factor ( ˚A2) −141.69 −129.16 −67.83 −131.78 Model composition Non-hydrogen atoms 35 795 12 587 24 783 13 749 Protein residues 4478 1580 2897 1732 Nucleotide residues 73 Ligands 1 0 2 2 B factors ( ˚A2) Protein 99.05 107.76 97.38 84.42 Nucleotide 254.23 Ligands 60.85 61.57 55.04 R.m.s. deviations Bond lengths ( ˚A) 0.004 0.004 0.006 0.004 Bond angles (◦) 0.990 0.974 1.014 0.989 Validation MolProbity score 2.13 1.92 2.35 2.17 Clashscore 12.59 9.75 19.37 13.21 Poor rotamers (%) 0.02 0.00 0.71 0.07 Ramachandran Favored (%) 90.93 93.80 89.25 90.48 Allowed (%) 9.00 5.88 10.51 9.34 Disallowed (%) 0.07 0.32 0.24 0.18 CC volume 0.65 0.85 0.76 0.71 (Pierce™) resin and FLAG-tagged Elp6. The respective sub- complex was added and incubated for 30–60 min at 4◦C, followed by three wash steps with 20 mM HEPES (pH 7.5), 100 mM NaCl, 1 mM DTT, 0.05% v/v Tween 20. Microscale thermophoresis (MST) and gel shift for tRNA binding assay The internally Cy5-labeled tRNA ArgUCU (0.2 M) or tRNA AlaUGC (0.3 M) were incubated for 5 min at 37◦C with serial dilutions of Elp123, Elp456 or Elongator vari- ants (starting from 10 M) in MST Buffer (20 mM HEPES (pH 7.5), 100 mM NaCl, 5 mM DTT, 0.0125% v/v Tween 20). Measurements were performed at 60% excitation power in Premium Coated capillaries on the Monolith NT.115 (Nanotemper Technologies) at 37◦C. Obtained data were analyzed and dissociation constant values were calculated Yeast genetic manipulations and phenotypic characterization PCR-based deletions of ELP1, ELP3, ELP4, ELP5 and ELP6 genes were generated in the UMY2893 wild type strain (2) using a KlURA3 marker (67) for later counters- election (68). In order to generate the individual mutations in ELP1, ELP3, ELP4, ELP5 and ELP6, each gene was amplified using a primer pair that binds 200 bp up- and downstream of the ORF from UMY2893 strain and lig- ated into the pJET1.2 blunt vector. Mutations were intro- duced via site-directed mutagenesis and further verified by DNA sequencing. Subsequently, a KlTRP1 marker cassette was integrated in the 3′UTR of all mutants constructs us- ing homologous recombination (69). Mutant alleles were reintroduced into the corresponding knockout strains and transformants were selected for the loss of KlURA3 marker gene by 5-fluoroorotic acid resistance and tryptophan pro- totrophy. Mutants were further confirmed by PCR and ver- ified by DNA sequencing. To analyze Elongator function in the generated mutant alleles, growth behavior on media was analyzed as previously described (70). Introduction of ELP1-(c-myc)3 and ELP5-(FLAG)3 into the genome was facilitated by homologous recombination of the desired tag together with a KlLEU2 (67) or clonNAT marker cassette (71). Descriptions and genotypes of all yeast strains are listed in Supplementary Table S1. Yeast protein extraction, co-immunoprecipitation and west- ern blot analysis To probe for in vivo acetyl-CoA carboxylase (Acc1) in- teraction, co-immunoprecipitation was carried out as de- scribed before (70). 8 mg lysate was incubated with 8 g antibody coupled Dynabeads (Invitrogen, USA) or anti- FLAG M2 magnetic beads (Sigma-Aldrich, USA) over night. Unbound protein was removed via a magnetic rack and precipitated proteins were washed three times with 1 ml B60 buffer (50 mM HEPES–KOH pH 7.3, 60 mM KAc, 5 mM Mg(Ac)2, 0.1% v/v TritonX-100, 10% v/v glyc- erol, 1 mM NaF, 20 mM ß-glycerolphosphate, 1 mM DTT, cOmplete™protease inhibitor cocktail (Roche, Germany)). Bound protein was eluted with elution buffer (50 mM Tris pH 8.0, 0.2% w/v SDS, 0.1% v/v Tween 20) at 50◦C for 15 min and subsequent incubation of 1× Laemmli buffer at 98◦C for 5 min. Proteins were separated on a 10% SDS- PAGE and analysed by Western blotting on a 0.45 M pore sized polyvinylidene difluoride (Merck, Germany) mem- brane. Proteins were detected using anti-c-myc (9E10 hy- bridoma supernatant kindly provided by Prof. Dr M. Ma- niak), anti-GFP antibody (sc-9996 Santa Cruz, USA), anti- FLAG antibody (F7425 Sigma-Aldrich, USA) and anti- Cdc19 serum (kindly provided by Dr. J. Thorner, University of California, Berkley, USA). Image processing Microscale thermophoresis (MST) and gel shift for tRNA binding assay The internally Cy5-labeled tRNA ArgUCU (0.2 M) or tRNA AlaUGC (0 3 M) were incubated for 5 min at 37◦C Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February Table 1. Cryo-EM data collection, refinement and validation statistics 0.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Microscale thermophoresis (MST) and gel shift for tRNA binding assay (Pierce™) resin and FLAG-tagged Elp6. The respective sub- complex was added and incubated for 30–60 min at 4◦C, followed by three wash steps with 20 mM HEPES (pH 7.5), 100 mM NaCl, 1 mM DTT, 0.05% v/v Tween 20. Elution from StrepTactin or anti-DYKDDDK resin was carried out in the same buffer containing either 5 mM d- desthiobiotin or 3× FLAG peptide at a concentration of 300 ng/l. Input controls and pull-downs were analyzed on a SDS-PAGE and visualized with Coomassie or sil- ver staining. ATP and bulk tRNA were used at indicated concentrations. 6 Nucleic Acids Research, 2023 using MO. Affinity software (Nanotemper Technologies) from at least three independent experiments (n > 3). For gel shift experiments internally Cy5-labled tRNA AlaUGC (0.2 M) was incubated with 0.05–1 M wild type Elp123, Elongator or Elp123Elp11132–1224 variant at 4◦C for 15 min. Next samples were separated on NativePAGE™4–16% Bis– Tris Protein Gels at 4◦C for 90 min and 150 V. Gels were imaged on BIO-RAD ChemiDoc™MP Imaging System in Cy5 detection mode. mM NaCl, 2 mM DTT and 1 mg/ml lysozyme. After soni- cation, the lysate was cleared at 40 000 × g for 30 min and the supernatant was cycled on a Protino® 5ml GST/4B col- umn overnight. The column was washed with lysis buffer omitting lysozyme and eluted in the same buffer containing 20 mM glutathione. Eluted fractions were further purified on a Superdex 75 16/600 (GE Healthcare) column, concen- trated, and dialyzed into a storage buffer (50 mM Tris–HCl (pH 7.5) at 4◦C, 150 mM NaCl, 2 mM DTT). GST--toxin purification The GST--toxin construct was expressed in the Es- cherichia coli BL21 (DE3) pRARE strain. Cultures were grown at 37◦C in autoinduction media (72) and were shifted after 5–6 h to 18◦C for overnight induction. Cells were lysed in buffer containing 50 mM Tris–HCl (pH 7.5) at 4◦C, 300 Acetyl-CoA hydrolysis assay To probe for the mcm5s2U34 modification status of Elon- gator mutants an in vitro cleavage assay using GST--toxin was applied as previously described (73). In detail, tRNA levels were adjusted to the same concentration in cleavage buffer containing 20 mM Tris–HCl (pH 8.0) at 4◦C, 150 mM NaCl, 2 mM EDTA and 2 mM DTT. Purified GST--toxin or GST was added to the tRNAs at a final concentration of 4 M and incubated for 30 min at 30◦C. Next, samples were denatured in loading buffer 20 mM Tris–HCl (pH 8.0) at 4◦C, 4 M urea, 20 mM boric acid, 2 mM EDTA, 0.02% w/v xylencyanol ff, 0.01% w/v bromophenol blue at 90◦C for 5 min and resolved on an 10% urea-PAGE (100 mM Tris– HCl (pH 8.0) at 4◦C, 100 mM boric acid, 1 mM EDTA, 10% acrylamide w/v (acrylamide/bis-acrylamide 19:1), 5.12 M urea) at 180 V for 35 min in TBE buffer (100 mM Tris–HCl (pH 8.0) at 4◦C, 100 mM boric acid, 2 mM EDTA). tRNA and cleavage products were stained with SYBR™Gold (In- vitrogen). The assay was performed as previously described (31). In detail, 0.3 M of Elongator variants were mixed with 2 M human bulk tRNA in presence of 100 M acetyl-CoA (ACO) in 1× acetyl-CoA assay buffer and incubated in a thermocycler for 3 h at 37◦C. Next, the samples were fil- tered by a 3 kDa cut-off concentrator (EMD Millipore) and the collected flow-through, of each reaction, was distributed into a 96-well plate. ACO quantity of each sample was determined using the Acetyl-CoA Assay Kit (MAK039, Merck) according to the manufacturer’s instructions. Fluo- rescence intensity was measured on a plate reader (TECAN) at probe-specific excitation (535 nm) and emission (587 nm) wavelengths. Hydrolysis rates were calculated from at least three independent experiments. Sample photo-crosslinking for mass spectrometry The results were then filtered to a false dis- covery rate (FDR) of 3% on the residue-pair level, result- ing in 1047 residue pairs (119 heteromeric). FDR settings at lower error levels were optimised by enabling boosting for heteromeric crosslinks. Single particle cryo-EM structure of yeast Elongator The endogenous Elongator complex is constitutively ex- pressed in yeast cells, but its low abundance has previously complicated the purification of the stoichiometric complex in quantities required for comprehensive structural and bio- chemical analyses (37,84). To overcome this technical limi- tation, we adapted an advanced overexpression system for S. cerevisiae Elongator (ScElongator) enabling us to simul- taneously overexpress the full-length versions of Elp1, Elp2, Elp3, Elp4, Elp5 and Elp6 in suitable yeast strains (Supple- mentary Figure S1A). The incorporation of specific affinity tags for Elp1, Elp3 and Elp6 allowed us to establish a ro- bust purification protocol that reproducibly resulted in pure and homogenous samples of fully assembled ScElongator containing all six subunits (Figure 1A, B and Supplemen- tary Figure S1B). We typically obtained 5–15 g of purified complex per liter of yeast culture, which was sufficient for biochemical and structural analyses by single particle cryo- EM. The purified stoichiometric complex eluted from a size exclusion chromatography column at a calculated molecu- lar weight of ∼850 kDa. Like the endogenous complex (85), the recombinant Elongator contains two copies of each sub- unit. The 260/280 nm absorption ratio indicates that the purified complex had no co-purified endogenous tRNAs nor other nucleic acids (Figure 1A). We observed a higher molecular weight protein at ∼250 kDa, which we identi- fied as Acetyl-CoA carboxylase 1 (Acc1) by mass spec- trometry. Acc1 is a multifunctional homodimeric enzyme of approximately 500 kDa that catalyses the formation of malonyl-coenzyme A from ACO (86). To check whether yeast Acc1 interacts with the Elongator in vivo, we tagged endogenous Elp1 (c-myc), Elp5 (FLAG) in an Acc1 (GFP) Crosslinking mass spectrometry data acquisition For the liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis, an Ultimate 3000 RSLCnano sys- tem (Dionex, Thermo Fisher Scientific) connected to an Or- bitrap Fusion Lumos Tribrid mass spectrometer (Thermo Fisher Scientific) was used. Each SEC fraction was resus- pended in 1.6% v/v ACN and 0.1% v/v formic acid be- fore injection onto a 50-cm EASY-Spray C18 LC column (Thermo Scientific, 50◦C operating temperature). The flow rate during sample loading and separation was 0.3 l/min. The mobile phase consisted of solvent A (0.1% v/v formic acid) and B (80% v/v ACN, 0.1% v/v formic acid). A 2–55% gradient of B was applied over the course of 90–100 min (optimised per SEC fraction) with a final increase to 95% B within 2.5 min. An EASY-Spray source (Thermo Scien- tific) ionised the eluting peptides before introducing them to the mass spectrometer. For each SEC fraction, two ac- quisitions were carried out. Data-dependent MS data were acquired in cycles of 2.5 s using the top-speed setting and the full scan mass spectrum was recorded in the Orbitrap with a resolution of 120 000. Ions with a charge state from 3+ to 7+ were selected for fragmentation by stepped higher- energy collisional dissociation (26%, 28% and 30%) using a decision tree (76). Spectra of fragments were recorded in the Orbitrap with a resolution of 60 000. Peaks were excluded after a single repeat for the duration of 60 s (dynamic exclu- sion). Sample photo-crosslinking for mass spectrometry The search was performed with the ‘Open’ pre-set workflow but with Crystal-C disabled. Crosslinked peptides were identified using xiSEARCH (version 1.7.6.4; (80)) using a database comprising 100 proteins with the highest intensity-based absolute quantification identified in the same experiments by MaxQuant (version 2.0.3.0; (81)). The search was performed using the following parame- ters: Enyzme: Trypsin; Missed Cleavages: 3; Missing Mono- Isotopic Peaks: 2; Cross-Linker ¦ Mass: NonCovalent ¦ 0, SDA Knterm ¦ 82; MS Tolerance: 3 ppm; MS2 Tolerance: 5 ppm; Fixed Modifications: carbamidomethylation (C); Variable Modifications: SDA-hydro (K, S, T, Y), SDA-loop (K, S, T, Y), acetylation (K, C, S, T, N-terminus), acetalde- hyde + 26 (H, K, N-terminus), carboxyamidomethylation (M, C, U), deamidation (N, R, Q), amidination (K, N- terminus). Search results were filtered using xiFDR (version 2.1.5.6; (82,83)). Prior to FDR calculation, prefilters were applied on both target and decoy matches (peptide1 unique matched conservative > 2.0; peptide2 unique matched con- servative > 2.0; peptide1 unique crosslinked matched non lossy > 0.0; peptide2 unique crosslinked matched non lossy > 0.0). The results were then filtered to a false dis- covery rate (FDR) of 3% on the residue-pair level, result- ing in 1047 residue pairs (119 heteromeric). FDR settings at lower error levels were optimised by enabling boosting for heteromeric crosslinks. 4.3.0; (78,79). The search was performed with the ‘Open’ pre-set workflow but with Crystal-C disabled. Crosslinked peptides were identified using xiSEARCH (version 1.7.6.4; (80)) using a database comprising 100 proteins with the highest intensity-based absolute quantification identified in the same experiments by MaxQuant (version 2.0.3.0; (81)). The search was performed using the following parame- ters: Enyzme: Trypsin; Missed Cleavages: 3; Missing Mono- Isotopic Peaks: 2; Cross-Linker ¦ Mass: NonCovalent ¦ 0, SDA Knterm ¦ 82; MS Tolerance: 3 ppm; MS2 Tolerance: 5 ppm; Fixed Modifications: carbamidomethylation (C); Variable Modifications: SDA-hydro (K, S, T, Y), SDA-loop (K, S, T, Y), acetylation (K, C, S, T, N-terminus), acetalde- hyde + 26 (H, K, N-terminus), carboxyamidomethylation (M, C, U), deamidation (N, R, Q), amidination (K, N- terminus). Search results were filtered using xiFDR (version 2.1.5.6; (82,83)). Prior to FDR calculation, prefilters were applied on both target and decoy matches (peptide1 unique matched conservative > 2.0; peptide2 unique matched con- servative > 2.0; peptide1 unique crosslinked matched non lossy > 0.0; peptide2 unique crosslinked matched non lossy > 0.0). Sample photo-crosslinking for mass spectrometry 85 g of ScElongator complex at 2.22 M concentration was crosslinked with sulfo-SDA (sulfosuccinimidyl 4,4′- Nucleic Acids Research, 2023 7 azipentanoate, Thermo Scientific) at 1:500 and 1:1000 sam- ple:crosslinker molar ratios. The reaction was incubated at room temperature for 60 min irradiated with UV light at 365 nm using a Luxigen34 LZ1 LED emitter (Osram Sylvania Inc.) for 10 s, and quenched with a final con- centration of 50 mM ammonium bicarbonate (ABC). The crosslinked complex was separated from single subunits on a Novex Bis–Tris 4–12% SDS-PAGE gel (Life Tech- nologies). Gel pieces containing the crosslinked complex were excised. The sample was reduced with DTT and free sulfhydryl groups were alkylated using iodoacetamide (74). Proteins were digested overnight at 37◦C with 1 g trypsin (Thermo Scientific Pierce) per 20 g of protein sample. The digested peptides were recovered and desalted using C18 StageTips (75). The eluates of the StageTips were pooled and fractionated by size exclusion chromatography (SEC) using a Superdex™30 Increase 3.2/300 column (GE Health- care) and a mobile phase consisting of 30% v/v ACN and 0.1% v/v trifluoric acid at a flow rate of 10 l/min. The first six fractions (50 l each) containing peptides were collected and the solvent was removed using a vacuum concentrator. azipentanoate, Thermo Scientific) at 1:500 and 1:1000 sam- ple:crosslinker molar ratios. The reaction was incubated at room temperature for 60 min irradiated with UV light at 365 nm using a Luxigen34 LZ1 LED emitter (Osram Sylvania Inc.) for 10 s, and quenched with a final con- centration of 50 mM ammonium bicarbonate (ABC). The crosslinked complex was separated from single subunits on a Novex Bis–Tris 4–12% SDS-PAGE gel (Life Tech- nologies). Gel pieces containing the crosslinked complex were excised. The sample was reduced with DTT and free sulfhydryl groups were alkylated using iodoacetamide (74). Proteins were digested overnight at 37◦C with 1 g trypsin (Thermo Scientific Pierce) per 20 g of protein sample. The digested peptides were recovered and desalted using C18 StageTips (75). The eluates of the StageTips were pooled and fractionated by size exclusion chromatography (SEC) using a Superdex™30 Increase 3.2/300 column (GE Health- care) and a mobile phase consisting of 30% v/v ACN and 0.1% v/v trifluoric acid at a flow rate of 10 l/min. The first six fractions (50 l each) containing peptides were collected and the solvent was removed using a vacuum concentrator. 4.3.0; (78,79). Crosslinking mass spectrometry data processing MS2 peak lists were generated from the mass spectromet- ric raw data with the MSConvert module of ProteoWiz- ard (version 3.0.11729). Precursor and fragment m/z val- ues were recalibrated based the average mass error of lin- ear peptide spectrum matches. Additional peptide modifi- cations were identified using FragPipe (version 18.0) with MSFragger (version 3.4; (77)) and philosopher (version 8 Nucleic Acids Research, 2023 Nucleic Acids Research, 2023 gure 1. Cryo-EM structure of yeast Elongator. (A) Purification chromatogram profile of yeast Elongator. Red and blue lines represent UV260 and UV280 sorbance, respectively. The peak corresponding to Elongator is indicated with a black arrow. (B) SDS-PAGE representing the final purification quality the Elongator sample. (C) Reference-free 2D class averages of yeast Elongator data set, scale bar 100 ˚A. (D) Cryo-EM reconstruction of yeast Elongator 4.35 ˚A resolution visualized at indicated map contouring with the atomic model at two orientations (upper and lower right). A schematic representation the complex is shown in the middle with Elp456 highlighted in color on the cryo-EM reconstruction and all subunits colored in accordance with the heme on the atomic model. Front view on the density and atomic model of Elp456 (lower left). Double lobe low-resolution cryo-EM reconstruction of ongator (upper left), coloring corresponds to the atomic model of native ScElongator. Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac e/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Figure 1. Cryo-EM structure of yeast Elongator. (A) Purification chromatogram profile of yeast Elongator. Red and blue lines represent UV260 and UV280 absorbance, respectively. The peak corresponding to Elongator is indicated with a black arrow. (B) SDS-PAGE representing the final purification quality of the Elongator sample. (C) Reference-free 2D class averages of yeast Elongator data set, scale bar 100 ˚A. (D) Cryo-EM reconstruction of yeast Elongator at 4.35 ˚A resolution visualized at indicated map contouring with the atomic model at two orientations (upper and lower right). A schematic representation of the complex is shown in the middle with Elp456 highlighted in color on the cryo-EM reconstruction and all subunits colored in accordance with the scheme on the atomic model. Front view on the density and atomic model of Elp456 (lower left). Double lobe low-resolution cryo-EM reconstruction of Elongator (upper left), coloring corresponds to the atomic model of native ScElongator. Figure 1. Cryo-EM structure of yeast Elongator. (A) Purification chromatogram profile of yeast Elongator. Crosslinking mass spectrometry data processing As mentioned above, we did not observe a sta- bilization of the second Elp123 lobe upon recruitment of Elp456 to the Elp123 dimer. As previously anticipated, the two copies of the largest subunit, namely Elp1 (∼150 kDa), act as the central scaffold for the lobe and the whole Elonga- tor assembly. The two N-terminal WD40 domains of each Elp1 molecule create a platform for the catalytic Elp3 sub- unit, which is clamped from the opposite side by Elp2. In our map, we observed an additional unaccommodated den- sity in the proximity of the rSAM domain of Elp3, into which we fit a previously uncharacterized loop region of the first WD40 domain of Elp1 (aa191–237). This unantic- ipated loop stretches from the third -sheet of the WD40 domain along Elp3 towards the base of Elp2 and returns to the fourth -sheet of the same WD40 domain (Figure 2B). Characteristic densities for the iron-sulfur cluster are clearly recognizable in both native and crosslinked struc- tures of ScElongator. However, we were not able to iden- tify densities for bound SAM or 5′-dA molecules, which were present in proximity to the cluster in the previous cryo-EM structure of the Elp123 subcomplex (Figure 1D) (92). Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gka ( ) Our Elongator cryo-EM structure reveals that the hetero- hexameric Elp456 occupies a position that faces the active site of Elp3 and bridges between the enzymatic subunit and the C-terminal region of Elp1. Both copies of Elp4 and one copy of Elp5 and Elp6 each are interacting with the Elp123 subcomplex. Although Elp2 does not seem to be directly involved in Elp456 binding, it might contribute indirectly by stabilizing the Elp123 lobe (93). Furthermore, the re- solved structure of Elongator is in full agreement with spa- tial restraints derived from a cross-linking mass spectrom- etry analysis of TAP-tag purified endogenous Elongator complex (27). In detail, Elp123 and Elp456 subcomplexes interact with each other at three individual contact points involving Elp1, Elp3, Elp4, Elp5, and Elp6. The first contact point (CP1) is formed between less conserved residues of the Elp3 rSAM domain (Trp341 and Lys342) and a loop re- gion in Elp4 (Tyr369, Ser371, Gln372, Lys375 and Glu401). The second contact point (CP2) is formed between a loop region of Elp4 (aa172-195) and helices 27 and 28 of the dimerization domain of Elp1 (Asp1160, Gln1164, Arg1171, Tyr1254, Arg1261 and Arg1265). Crosslinking mass spectrometry data processing The maps from both approaches show a very similar over- all shape of the complex, independently confirming the po- sition of Elp456 after two different routes of sample prepa- ration (Supplementary Figure S2B). The dimensions of the complex are ∼200 × 162 × 140 ˚A, in line with the estima- tion from a previous low-resolution negative stain recon- struction (27). The local resolution estimation indicates that the center of the Elp123 lobe extends to 3.9 ˚A, whereas parts of Elp456 as well as the TPR and dimerization re- gion of Elp1 are less well resolved. Similar to our previous high-resolution reconstructions of yeast Elp123 (with and without bound tRNA), the density of the second Elp123 lobe is not clearly visible. In addition, 2D class averages al- ready show that the second Elp123 lobe is blurred after im- age averaging, suggesting relatively high flexibility between the two Elp123 lobes, which is also observable in presence of Elp456. Nevertheless, we managed to reconstruct a map for the complete complex with both lobes visible at an esti- mated overall resolution of 17.2 ˚A, when stabilized with BS3 (Figure 1D). As we could only visualize the second lobe at low map thresholds and did not see any density of Elp456 in the second lobe, we decided to exclude the empty lobe from subsequent refinement procedures. In summary, our results reveal the overall arrangement of the yeast Elongator complex at an unprecedented resolution. Furthermore, the cryo-EM structure(s) independently confirm that the hex- americ ring-shaped Elp456 subcomplex is indeed asymmet- rically localized on only one lobe. The high quality of our cryo-EM map shows details of the complex and allows us to unambiguously determine the orientation of the ScElp456 subcomplex. Additionally, the presented maps allow for the precise structural characterization of all individual Elonga- tor subunits, their relative position and their interaction net- work within the fully assembled complex at high resolution (Figure 1D). remain flexible also in the fully assembled complex. In ad- dition, we compared the structure of the Elp123 subcom- plex after binding of Elp456 with the previously determined Elp123 subcomplex in absence and presence of tRNA (31). We did not detect any major rearrangements of the Elp123 subcomplex after binding of Elp456 (Supplementary Figure S3C), although the lobe adopts a slightly less compacted topology. Crosslinking mass spectrometry data processing Red and blue lines represent UV260 and UV280 absorbance, respectively. The peak corresponding to Elongator is indicated with a black arrow. (B) SDS-PAGE representing the final purification quality of the Elongator sample. (C) Reference-free 2D class averages of yeast Elongator data set, scale bar 100 ˚A. (D) Cryo-EM reconstruction of yeast Elongator at 4.35 ˚A resolution visualized at indicated map contouring with the atomic model at two orientations (upper and lower right). A schematic representation of the complex is shown in the middle with Elp456 highlighted in color on the cryo-EM reconstruction and all subunits colored in accordance with the scheme on the atomic model. Front view on the density and atomic model of Elp456 (lower left). Double lobe low-resolution cryo-EM reconstruction of Elongator (upper left), coloring corresponds to the atomic model of native ScElongator. as potential Elongator binding partners in other studies (29,89–91). background (87) and conducted co-immunoprecipitation (co-IP) assays. As we did not observe any interaction of Acc1 with Elongator in these assays (Supplementary Fig- ure S1C), we conclude that Acc1 is an co-purifying con- taminant in our preparations. Of note, we also co-purified sub-stoichiometric amounts of Kti11 and Kti12, whereas other regulatory proteins known to temporarily associate with yeast Elongator were undetectable (88). Furthermore, we did not find any hits for actin, tubulin, RNA poly- merase subunits or histones, which have been proposed Next, we prepared cryo-EM grids with the freshly pu- rified sample and analyzed the structure of the complex using single particle cryo-EM. After vitrification and grid optimization, we collected a dataset of 6339 micrographs on a Titan Krios microscope. We analyzed the complete dataset by applying basic image curation steps as well as it- erative rounds of particle picking, 2D/3D classification rou- tines and refinement procedures. Thereby, we determined Nucleic Acids Research, 2023 9 the structure of ScElongator at an overall resolution of 4.35 ˚A (Figure 1C, D, Supplementary Figure S2A and Table 1). The reconstruction shows an additional, unambiguous den- sity for the ScElp456 ring next to one of the two Elp123 lobes. In an attempt to further improve the resolution of the reconstruction, we stabilized the sample with a low con- centration of BS3. However, the stabilized sample resulted in a reconstruction at a lower overall resolution of 6.6 ˚A. Crosslinking mass spectrometry data processing This larger interface also involves the N-terminus of Elp5 and a not well-defined loop region of Elp1 (aa1176-1251) known to carry functionally relevant phosphorylation sites (35). The third contact point (CP3) is an interface that is created at the three-way junc- tion between the KAT domain of Elp3 and the C-terminal residues of Elp6 (Figure 2B). Noteworthy, the N-terminus of Elp4 (Elp4 1–66), which was shown to contribute to the interaction with Elp1 (27), was not visible in our densi- ties and did not participate in any long-range interactions with Elp1. All interacting residues of Elp456 are involved only once in the interaction with Elp123, and the respec- Crosslinking mass spectrometry data processing The maps from both approaches show a very similar over- all shape of the complex, independently confirming the po- sition of Elp456 after two different routes of sample prepa- ration (Supplementary Figure S2B). The dimensions of the complex are ∼200 × 162 × 140 ˚A, in line with the estima- tion from a previous low-resolution negative stain recon- struction (27). The local resolution estimation indicates that the center of the Elp123 lobe extends to 3.9 ˚A, whereas parts of Elp456 as well as the TPR and dimerization re- gion of Elp1 are less well resolved. Similar to our previous high-resolution reconstructions of yeast Elp123 (with and without bound tRNA), the density of the second Elp123 lobe is not clearly visible. In addition, 2D class averages al- ready show that the second Elp123 lobe is blurred after im- age averaging, suggesting relatively high flexibility between the two Elp123 lobes, which is also observable in presence of Elp456. Nevertheless, we managed to reconstruct a map for the complete complex with both lobes visible at an esti- mated overall resolution of 17.2 ˚A, when stabilized with BS3 (Figure 1D). As we could only visualize the second lobe at low map thresholds and did not see any density of Elp456 in the second lobe, we decided to exclude the empty lobe from subsequent refinement procedures. In summary, our results reveal the overall arrangement of the yeast Elongator complex at an unprecedented resolution. Furthermore, the cryo-EM structure(s) independently confirm that the hex- americ ring-shaped Elp456 subcomplex is indeed asymmet- rically localized on only one lobe. The high quality of our cryo-EM map shows details of the complex and allows us to unambiguously determine the orientation of the ScElp456 subcomplex. Additionally, the presented maps allow for the precise structural characterization of all individual Elonga- tor subunits, their relative position and their interaction net- work within the fully assembled complex at high resolution (Figure 1D). the structure of ScElongator at an overall resolution of 4.35 ˚A (Figure 1C, D, Supplementary Figure S2A and Table 1). The reconstruction shows an additional, unambiguous den- sity for the ScElp456 ring next to one of the two Elp123 lobes. In an attempt to further improve the resolution of the reconstruction, we stabilized the sample with a low con- centration of BS3. However, the stabilized sample resulted in a reconstruction at a lower overall resolution of 6.6 ˚A. The interaction interfaces between Elp123 and Elp456 are crucial for Elongator’s tRNA modification activity We generated numerous yeast strains that carry specific sin- gle amino acid substitutions or deleted regions in Elp1, Elp3, Elp4, Elp5 and Elp6. Next, we tested these strains in previously established phenotypical assays that indi- rectly probe the tRNA modification activity of Elongator in vivo (2,94,95). In addition, we used an in vitro -toxin tRNA cleavage assay to further validate the observed phe- notypes of the structure-guided mutations (73) (Supple- mentary Figure S4A). -toxin (the active tRNase subunit of trimeric killer toxin zymocin) acts as a nuclease that re- quires the mcm5s2U34 modification to cleave tRNAs at the anticodon. Therefore, any mutation that reduces or abol- ishes the tRNA modification activity of Elongator, leads to reduced mcm5s2U34 modification levels in vivo and protects tRNAs from cleavage by -toxin (95,96). Since the readout of the aforementioned -toxin-based assays predominantly samples the modification status of tRNA GluUUC, we also monitored the Elongator dependent mcm5U34 modification of the SUP4 nonsense suppressor tRNA TyrUUA via its ef- ficiency of ochre stop codon readthrough (2). As expected, gene deletions of elp1, elp3, elp4, elp5, and elp6 were found to be resistant to zymocin and the toxic arginine analogue canavanine in a SUP4 tRNA and can1-100 allele containing background (for more details, see (2)), Figure 2C and Sup- plementary Figure S4B, C). Furthermore, we show that the newly identified loop (aa191–237) from the first WD40 of Elp1 and the unstructured N-terminal region of Elp4 (aa1– 66) are crucial for Elongator function in vivo. g p To further validate our structural model we carried out a photo-crosslinking mass spectrometry (XL-MS) analysis of the purified yeast Elongator complex. 638 out of 883 detected cross links are in agreement (30 ˚A distance) with our structural model (Supplementary Figure S5A). In ad- dition, 125 out of 189 crosslinks that disagree with our model are located in loop regions of Elp1, namely aa191– 237 and aa1176–1251. Therefore, it seems these loops can become flexible, which is in agreement with the previous high-resolution reconstruction of yeast Elp123 (92) where no density was detectable for them. We also checked for any specific crosslinks between Elongator and Acc1, but only a single crosslink was detected, indicating that the two com- plexes indeed do not interact or share a large interface. The interaction interfaces between Elp123 and Elp456 are crucial for Elongator’s tRNA modification activity Al- though, the second Elp123 lobe is not well-resolved in our maps the presence of a few crosslinks indicated that the two Elp123 lobes could get in close proximity of each other also in the presence of Elp456. Hence, we used additional 3D variability and masked 3D classification analyses to check whether the second lobe can obtain any specific conforma- tions upon Elp456 binding (Supplementary Figure S5B). We indeed managed to partially enhance the density of the second lobe, but due to reduced number of particles the res- olution decreased (Supplementary Figure S5B). None of the obtained reconstructions revealed a complete second lobe or specific conformation, which is consistent with the low resolution of the two-lobed BS3 stabilized Elongator complex (Figure 1D). These additional results further sup- port our notion that the second lobe stays flexible in the fully assembled Elongator complex. 0.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 ) g Next, we analyzed the structure-guided mutation in the three identified contact points CP1, CP2 and CP3 to understand the importance of these regions individually. The mutations of Elp3 residues ( W341A/K342A) and Elp4 (E401A, Y369A/S371A and Q372A/K375A) in CP1 show no measurable effects on the tRNA modification activity of Elongator. Strikingly, all tested mutations in CP2 nearly abolished Elongator’s tRNA modifica- tion activity. Mutations and deletions of the identified residues in Elp1 (Δ191–237, Y1254A/R1261A/R1265A, D1160A/Q1164A/R1171A, Δ1176–1200, Δ1201–1225, Δ1226–1251), Elp4 (Δ172–195, Δ357–376) and Elp5 (Δ1–20) display tRNA hypo-modification phenotypes that are indistinguishable from their respective gene deletion mutants, in all conducted in vivo and in vitro tRNA modi- fication assays (Figure 2C and Supplementary Figure S4). The third and most central interface (CP3) appears to be as important for Elongator activity as CP2. Mutations in Elp3 (R399A/D402A/L403A) and Elp6 (Δ271–273, T226A/F228A/K230A) are resistant to growth inhibition by zymocin. Of note, mutants in Elp123 demonstrate iden- tical phenotypes in all applied assays, whereas individual mutations in Elp456 (e.g. elp4 Δ172–195, elp5 Δ1–7, elp6 Δ271–273 and elp6 T226A/F228A/K230A) exhibited Elp456 bridges between Elp3 and the C-terminus of Elp1 The cryo-EM structure of yeast Elp456 in complex with Elp123 almost perfectly resembles the previously solved structures of the truncated Elp456 hexamer determined by macromolecular crystallography (85,90). As we ob- served unbound ring-shaped Elp456 particles in one of our datasets, we also determined the cryo-EM structure of free full-length ScElp456 at 3.7 ˚A overall resolution (Figure 2A, Supplementary Figure S3A and Table 1). The newly ob- tained structures of full-length Elp456 are almost identi- cal to the truncated crystal structure of the Elp456 sub- complex (Supplementary Figure S3B). The structure con- firms that Elp456 contains two copies of Elp4, Elp5 and Elp6, forming a symmetric dimer of trimers. However, the N- and C-terminal extensions of Elp4 and Elp5 (including a small predicted domain at the C-terminus of Elp5 (85)) 10 Nucleic Acids Research, 2023 10 Nucleic Acids Research, 2023 Figure 2. Functional validation of yeast Elongator. (A) Cryo-EM map and atomic model of the apo ScElp456 subcomplex. (B) Front view on the atomic model of yeast Elongator (left). Atomic model in surface representation at different orientations with a position of selected mutations represented in sticks (point mutation) and cartoon (deletion or truncation). Colouring corresponds to the affiliation of the particular position to the given subunit. (C) Phenotypic analyses of various yeast strains carrying variations in Elp1, Elp3, Elp4, Elp5 and Elp6 using zymocin resistance assays. Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1 g Figure 2. Functional validation of yeast Elongator. (A) Cryo-EM map and atomic model of the apo ScElp456 subcomplex. (B) Front view on the atomic model of yeast Elongator (left) Atomic model in surface representation at different orientations with a position of selected mutations represented in y y g y Figure 2. Functional validation of yeast Elongator. (A) Cryo-EM map and atomic model of the apo ScElp456 subcomplex. (B) Front view on the atomic model of yeast Elongator (left). Atomic model in surface representation at different orientations with a position of selected mutations represented in sticks (point mutation) and cartoon (deletion or truncation). Colouring corresponds to the affiliation of the particular position to the given subunit. (C) Phenotypic analyses of various yeast strains carrying variations in Elp1, Elp3, Elp4, Elp5 and Elp6 using zymocin resistance assays. Elp456 bridges between Elp3 and the C-terminus of Elp1 Nucleic Acids Research, 2023 11 tive second copy of the residues within the ring appear to be irrelevant for the respective interactions. Therefore, we were able to mutate selected residues and regions to ana- lyze their specific role for the in vivo function of Elongator (Figure 2B, C). a slightly divergent phenotype. These variations mostly affect mutants that display intermediate phenotypes and might occur due to different sensitivity of performed assay formats. These results also support the recent observation that Elp456 function might only be relevant for a subset of cellular tRNAs (22). All zymocin and canavanine-sensitive mutants and the latter mentioned variable phenotype mutants are susceptible to in vivo and in vitro -toxin cleavage. In conclusion, our data show that interfaces of CP2 and CP3 are crucial for Elongator’s tRNA modi- fication activity, whereas the CP1 region, between Elp3 and Elp4 appears to be functionally dispensable. These results directly validate our structural model that depicts the complicated interaction network between individual subunits of the assembled Elongator complex. The interaction interfaces between Elp123 and Elp456 are crucial for Elongator’s tRNA modification activity The structure of the Elp123 subcomplex is highly conserved among eukaryotes Surprisingly, we could identify an intact SAM molecule bound to the iron-sulfur cluster of MmElp123, which was co-purified from the host cells. The coordination of this ligand is similar to the 5′-dA molecule found in ScElp123. At the current stage, it remains unclear if the difference results from different catalytic rates, ap- plied classification schemes or from the fact that we iso- late ScElp123 from yeast cells, whereas MmElp123 was pro- duced in insect cells, though in case of archaeal Elp3 SAM remained uncleaved in the absence of tRNA (34). Nonethe- less, the structural similarities between the subcomplexes (pre and post SAM cleavage), suggest that the cleavage reac- tion itself does not induce major rearrangements in the ac- tive site of Elp3 or in the coordination of the adenosine moi- ety. Thus, our detailed analyses of the active sites in ScElp3 and MmElp3 further highlight the homology of yeast and mouse Elongator complexes. Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac To determine the structure of MmElp123, we vitrified freshly purified samples in absence and presence of in vitro transcribed mouse tRNA ArgUCU. We optimized the sample preparation procedure, collected large datasets and solved structures that are with and without tRNA at 4.35 ˚A and 4.0 ˚A resolutions, respectively (Supplementary Figure S7A,B and Table 1). Meanwhile, we also collected a dataset for ScElp123 in complex with yeast tRNA AlaUGC and ob- tained a reconstruction at an improved resolution of 3.96 ˚A (Supplementary Figure S8 and Table 1). This new tRNA- bound structure of ScElp123 allowed us to build a more re- liable atomic model of the tRNA-bound complex (Figure 3A), which facilitated the structural comparison of individ- ual regions in ScElp123 and MmElp123. Both, yeast and mouse Elp123–tRNA structures, contain characteristic L- shaped tRNA densities, spanning from the center of Elp3 to the C-terminus of Elp1 (Figure 3A and Supplementary Figure S9). tRNA molecules are positioned in both com- plexes in a similar conformation – the ASL is inserted in the active site of Elp3 and the T-arm is in contact with the CTD of Elp1, while the acceptor stem points away from the com- plex. The second Elp123 lobe remains flexible and poorly defined, in both structures. Thus, tRNA binding does not affect the relative orientation between the two lobes, and the second lobe was excluded from the subsequent refinement process. The structure of the Elp123 subcomplex is highly conserved among eukaryotes Like in yeast, the murine Elongator consists of six sub- units. However, the sequence similarity and identity of the mouse proteins vary between the subunits compared to their yeast counterparts. Although Elp1, Elp2, Elp3 and Elp4 proteins show high sequence identity, Elp5 and Elp6 display surprisingly low sequence similarity among eukary- otes (84). Therefore, we asked whether the Elongator com- plex is structurally and functionally conserved in higher eu- karyotes, particularly in mammals. We employed the biG- Bac expression system to overproduce mouse subcomplexes by co-expressing MmElp123 and MmElp456 genes sepa- rately in insect cells. The incorporation of affinity tags on 12 Nucleic Acids Research, 2023 12 Elp3 (TST) and Elp6 (FLAG) facilitated the purification of the individual subcomplexes using standard affinity and size exclusion chromatography. The gel filtration profiles of MmElp123 (∼610 kDa) and MmElp456 (∼220 kDa) show that they all elute at the expected elution volume (Supple- mentary Figure S6) demonstrating that the mouse complex also form dimers like the yeast counterparts. tural details of the active sites of ScElp123 and MmElp123 (Figure 3B). Both complexes harbor an iron-sulfur-cluster [4Fe4S] involved in the generation of a 5′-dA radical, which is necessary for the U34 modification reaction, and the cluster is coordinated by three highly conserved cysteine residues, which contact the respective iron atoms of the clus- ter. Although we did not supplement the sample with SAM before vitrification, we identified a bound 5′-dA molecule in the yeast active site next to the cluster. Gln257 contacts one of the hydroxyl groups in 5′-dA and positions the radi- cal carrying methyl group in close proximity to Tyr136 and Tyr327, which both are positioned in a similar distance to the base of U34 and to the methyl group of 5′-dA. Further- more, we observed that the density of Tyr136 connects to the one of U34, suggesting direct interaction. This tyrosine possibly pulls the uridine closer to the iron-sulfur cluster and the 5′-dA molecule. As for the fourth iron atom of the cluster, it is not coordinated by any cysteine residue but it is bordered by an additional, adjacent density, which most likely can be attributed to bound methionine. Methionine is the second cleavage product of SAM which was also re- ported in crystal structures of the bacterial rSAM proteins RlmN (97) and MiaB (98). The structure of the Elp123 subcomplex is highly conserved among eukaryotes Of note, we used masked 3D classification to iden- tify a subfraction of particles that shows a tRNA-like den- sity also in the second Elp123 lobe. Nonetheless, due to nec- essary subclassification procedures the resulting maps lack the quality to ultimately confirm that mouse Elp123 can si- multaneously bind tRNAs in each of its lobes, like yeast Elp123 (92). As for the mouse apo Elp123 structure, the obtained density is significantly smaller and only the core lobe of the subcomplex is structured, resulting in decreased overall dimensions (∼140 × 100 × 65 ˚A; Figure 3A). In detail, the spatial arrangement of Elp2, Elp3 and the N- terminal region of Elp1 are very similar to the tRNA-bound MmElp123 and the ScElp123 structures (92). Strikingly, the CTD of MmElp1, which is visible in the yeast Elp123, re- mains flexible in MmElp123 in the absence of tRNA (Fig- ure 3A). This observation indicates that yeast Elp123 is inherently more stable in the absence of tRNAs and that the binding of tRNAs induces structural rearrangements in the Elp1 CTD of mammals. Nonetheless, both yeast and murine Elp123 appear very similar in its tRNA bound form. Our comparative analyses of the tRNA-bound ScElp123 and MmElp123 show that both subcomplexes bind their tRNA substrates in an almost identical fashion and that the involvement of several regions in tRNA binding might have contributed to the high sequence conservation in Elp1 and Elp3 amongst eukaryotes. As aforementioned, the enzymatically active Elp3 sub- The structure of the fully assembled Elongator is highly con- served among eukaryotes Finally, we also investigated whether in mouse Elp456 inter- acts with Elp123 in a similar way as in yeasts. For this, we reconstituted the Elongator in vitro from individually pu- rified MmElp123 and MmElp456 subcomplexes and ana- lyzed the obtained complex by single particle cryo-EM (Fig- ure 4, Supplementary Figures S10 and S11A). In detail, we observed efficient complex formation after combing both purified subcomplexes without the addition of other co- factors. The reconstituted complex shows a stoichiometric composition of all six subunits, indicating that the bi-lobal Elp123 in mouse Elongator also preferentially binds only one hetero-hexameric Elp456 subcomplex. Subsequently, we used the reconstituted and re-purified complex after gel- filtration to prepare cryo-EM grids. After sample optimiza- tion and data collection, we determined the cryo-EM struc- ture of the mouse Elongator at an overall resolution of 5.9 ˚A (Table 1). The structure of MmElongator is very similar to yeast Elongator, with a clearly distinguishable lobe, an arch As aforementioned, the enzymatically active Elp3 sub- unit shows a high overall sequence conservation. This simi- larity becomes even more evident, by comparing the struc- Nucleic Acids Research, 2023 13 r structural conservation in eukaryotes. (A) Cryo-EM reconstructions of MmElp123–tRNA (upper left), MmElp123 (lower left) and upper right) complexes with atomic models in the same orientation. tRNA colored in deep teal. (B) Comparison of the active site of nd MmElp123. Selected, structurally conserved residues in stick representation, with densities shown for iron-sulfur clusters (ScElp123– , 5′-dA (ScElp123–tRNA) and SAM (MmElp123). Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 Febru Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Figure 3. Elongator structural conservation in eukaryotes. (A) Cryo-EM reconstructions of MmElp123–tRNA (upper left), MmElp123 (lower left) and ScElp123–tRNA (upper right) complexes with atomic models in the same orientation. tRNA colored in deep teal. (B) Comparison of the active site of ScElp123–tRNA and MmElp123. Selected, structurally conserved residues in stick representation, with densities shown for iron-sulfur clusters (ScElp123– tRNA/MmElp123), 5′-dA (ScElp123–tRNA) and SAM (MmElp123). g y y g Figure 3. Elongator structural conservation in eukaryotes. (A) Cryo-EM reconstructions of MmElp123–tRNA (upper left), MmElp123 (lower left) and ScElp123–tRNA (upper right) complexes with atomic models in the same orientation. tRNA colored in deep teal. (B) Comparison of the active site of ScElp123–tRNA and MmElp123. The structure of the fully assembled Elongator is highly con- served among eukaryotes tion showed that the tRNA molecule would fit without any significant clashes into the space formed between the two subcomplexes and that the binding of the ASL in the ac- tive site of Elp3 would be unaffected. Moreover, the rela- tively long and not well-structured loop region (aa169–233) in Elp4, which binds the CTD of Elp1, might provide addi- tional flexibility to accommodate a tRNA molecule. In ad- dition, our ScElongator model also clearly shows that the tRNA binding loop (aa1176–1251) of Elp1 is displaced by Elp456 and would not be able to interact with the T-arm of tRNAs (Figure 5A). This observation is in line with the fact that ScElongator has a lower tRNA binding affinity com- pared to the ScElp123 subcomplex (31). Of note, the second lobe of Elp123, which is not occupied by Elp456, would in tion showed that the tRNA molecule would fit without any significant clashes into the space formed between the two subcomplexes and that the binding of the ASL in the ac- tive site of Elp3 would be unaffected. Moreover, the rela- tively long and not well-structured loop region (aa169–233) in Elp4, which binds the CTD of Elp1, might provide addi- tional flexibility to accommodate a tRNA molecule. In ad- dition, our ScElongator model also clearly shows that the tRNA binding loop (aa1176–1251) of Elp1 is displaced by Elp456 and would not be able to interact with the T-arm of tRNAs (Figure 5A). This observation is in line with the fact that ScElongator has a lower tRNA binding affinity com- pared to the ScElp123 subcomplex (31). Of note, the second lobe of Elp123, which is not occupied by Elp456, would in The structure of the fully assembled Elongator is highly con- served among eukaryotes Selected, structurally conserved residues in stick representation, with densities shown for iron-sulfur clusters (ScElp123– tRNA/MmElp123), 5′-dA (ScElp123–tRNA) and SAM (MmElp123). We would like to highlight that although the fully as- sembled Elongator binds tRNAs (31), despite our intense experimental efforts, we were still not able to attain the yeast or mouse tRNA-bound Elongator structure. To ex- plore whether Elongator could in principle accommodate tRNA molecules in an Elp456-occupied Elp123 lobe, we su- perimposed ScElp123–tRNA on ScElongator via its Elp3 subunit (RMSD 1.22 ˚A2) (Figure 5A). The superimposi- region between the lobes and an asymmetrically positioned Elp456 ring on one of the two Elp123 lobes. The quality of the obtained map allowed the unambiguous placement of the Elp456 subcomplex, revealing the same three contact points formed between the subcomplexes in yeast. However, the limited resolution of our reconstruction prevented us from analyzing the molecular details of the active site in the fully assembled mouse Elongator complex. region between the lobes and an asymmetrically positioned Elp456 ring on one of the two Elp123 lobes. The quality of the obtained map allowed the unambiguous placement of the Elp456 subcomplex, revealing the same three contact points formed between the subcomplexes in yeast. However, the limited resolution of our reconstruction prevented us from analyzing the molecular details of the active site in the fully assembled mouse Elongator complex. 14 Nucleic Acids Research, 2023 ure 4. Mouse Elongator complex. Cryo-EM reconstructions of MmElongator complex with an atomic model in the same orientation. Elp456 is colored accordance to the scheme from Figure 1D. For comparison, yeast density and model are in the same orientation above. p p g y y Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac Figure 4. Mouse Elongator complex. Cryo-EM reconstructions of MmElongator complex with an atomic model in the same orientation. Elp456 is colored in accordance to the scheme from Figure 1D. For comparison, yeast density and model are in the same orientation above. Figure 4. Mouse Elongator complex. Cryo-EM reconstructions of MmElongator complex with an atomic model in th in accordance to the scheme from Figure 1D. For comparison, yeast density and model are in the same orientation a principle be able to bind tRNA, strongly complicating the interpretation of the results from the binding assays. The CTD of Elp1 is responsible for tRNA binding and sub- complex interaction We further investigated the importance of these structural rearrangements by complementary biochemical analyses. We used human Elongator subcomplexes produced in in- sect cells and reconstituted them as we did with the mouse Elongator sample (Supplementary Figures S6B and S11A). First, we measured the binding affinity of mouse and hu- man Elp123 and Elongator towards in vitro transcribed (IVT) tRNAs. Like yeast Elp123 (31), mouse and human Elp123 bound mouse tRNA AlaUGC with higher affinity Nucleic Acids Research, 2023 15 Figure 5. Biochemical and functional characterization of Elongator complex from higher eukaryotes. (A) Superposition of ScElp123–tRNA and ScElongator in two orientations, showing a possibility of the tRNA (deep teal) binding by the latter complex (above). Below: yeast CP2 comparison etween ScElp123–tRNA and ScElongator complexes showing Elp1 tRNA binding loop displacement. (B) Microscale thermophoresis measurements, espective fits, and calculated dissociation constant (Kd) values for the mouse (top) and human (bottom) Elp123 (red) and Elongator (black). In both cases, he Hill coefficient is close to 1, indicating the presence of independent binding sites. n = 3. (C) SDS-PAGE gel comparing in vitro reconstitution of human Elongator complex with the use of Elp1, Elp4 and Elp5 functional variants of CP2 structural features presented in the previous panel. Twin-Strep-tag ndicated on Elp3 subunit. (D) EMSA assay using wild type human Elp123 (left), human Elp123Elp11132–1224 (right), and fluorescently labeled tRNA AlaUGC. The positions of free tRNA and protein–tRNA complexes (*) are indicated next to the native polyacrylamide gel electrophoresis. Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 Febr Downloaded from https://academic.oup.com/nar/advance article/doi/10 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac Figure 5. Biochemical and functional characterization of Elongator complex from higher eukaryotes. (A) Superposition of ScElp123–tRNA and ScElongator in two orientations, showing a possibility of the tRNA (deep teal) binding by the latter complex (above). Below: yeast CP2 comparison between ScElp123–tRNA and ScElongator complexes showing Elp1 tRNA binding loop displacement. (B) Microscale thermophoresis measurements, respective fits, and calculated dissociation constant (Kd) values for the mouse (top) and human (bottom) Elp123 (red) and Elongator (black). In both cases, the Hill coefficient is close to 1, indicating the presence of independent binding sites. n = 3. (C) SDS-PAGE gel comparing in vitro reconstitution of human Elongator complex with the use of Elp1, Elp4 and Elp5 functional variants of CP2 structural features presented in the previous panel. The CTD of Elp1 is responsible for tRNA binding and sub- complex interaction Twin-Strep-tag indicated on Elp3 subunit. (D) EMSA assay using wild type human Elp123 (left), human Elp123Elp11132–1224 (right), and fluorescently labeled tRNA AlaUGC. The positions of free tRNA and protein–tRNA complexes (*) are indicated next to the native polyacrylamide gel electrophoresis. Figure 5. Biochemical and functional characterization of Elongator complex from higher eukaryotes. (A) Superposition of ScElp123–tRNA and ScElongator in two orientations, showing a possibility of the tRNA (deep teal) binding by the latter complex (above). Below: yeast CP2 comparison between ScElp123–tRNA and ScElongator complexes showing Elp1 tRNA binding loop displacement. (B) Microscale thermophoresis measurements, respective fits, and calculated dissociation constant (Kd) values for the mouse (top) and human (bottom) Elp123 (red) and Elongator (black). In both cases, the Hill coefficient is close to 1, indicating the presence of independent binding sites. n = 3. (C) SDS-PAGE gel comparing in vitro reconstitution of human Elongator complex with the use of Elp1, Elp4 and Elp5 functional variants of CP2 structural features presented in the previous panel. Twin-Strep-tag indicated on Elp3 subunit. (D) EMSA assay using wild type human Elp123 (left), human Elp123Elp11132–1224 (right), and fluorescently labeled tRNA AlaUGC. The positions of free tRNA and protein–tRNA complexes (*) are indicated next to the native polyacrylamide gel electrophoresis. than the fully assembled Elongator complex, but when we used mouse or human tRNA ArgUCU we observed no dif- ferences in affinity (Figure 5B). These data again support the notion that Elp456 might discriminate between sub- pools of tRNAs (22). Second, we examined whether the recombinantly produced mouse and human Elongator as- semblies hydrolyze (ACO) faster upon tRNA binding (33). Initially, we employed HEK293 cells-derived human bulk tRNA for the assay, and it did not stimulate the ACO ac- tivity of yeast Elongator (Supplementary Figure S11B). To exclude any incompatibility of ScElongator with human- specific tRNA modification patterns, we then tested yeast samples with extracted yeast bulk tRNA. Our results show that all used Elongator complexes can hydrolyze ACO in the presence of tRNAs to different degree. Elongator displays slightly lower activity than their respective Elp123 coun- 16 Nucleic Acids Research, 2023 16 We also performed the experiments for both mouse and hu- man proteins in the presence of purified bulk tRNA to test if any minor tRNA species or tRNAs carrying modification intermediates may affect the reconstitution. The CTD of Elp1 is responsible for tRNA binding and sub- complex interaction Again, the full complex assembly is independent of tRNA, ATP or com- binations thereof (Figure 6B and Supplementary Figure S12B, C). As the presence of ATP influences tRNA binding ability of Elp456, but not the assembly of the full complex, we further determined the impact of ATP on tRNA bind- ing of the fully assembled reconstituted complex. The gel shift assay showed that the fully assembled human Elonga- tor complex has slightly lower affinity towards tRNA in the presence of ATP (Figure 6C). The ATP effect on decrease of tRNA binding is also found in the Elp123. Based on this finding we would like to propose a molecular mechanism, in which Elp456 acts as a molecular extruder that binds tRNA with greater affinity and pulls it away from Elp123. A stronger Elp456–tRNA complex may fall apart upon suc- cessful ATP hydrolysis, releasing the tRNA and prepare Elp456 for another round of the reaction cycle, which in principle could promote the overall fidelity of tRNA modi- fication. (Figure 7). terparts, but a high batch-to-batch variation and the use of different bulk tRNAs limit the outcome of these analy- ses (Supplementary Figure S11C). Third, we produced sev- eral human Elongator variants that lack the regions impor- tant for tRNA or other subcomplex binding (i.e. CP2). In detail, we produced variants lacking (i) the tRNA binding loop of Elp1 (Elp11132–1224), (ii) the Elp1 binding loop of Elp4 (Elp4133–175) and (iii) the very N-terminus of Elp5 (Elp51–9). The pull-down assays showed that all mutations moderately affect Elongator reconstitution, with stronger effects for Elp11132–1224 and Elp4133–175 and less promi- nent reduction of binding by the Elp5 truncation (Figure 5C and Supplementary Figure S11D). These data indicated that the regions creating CP2 indeed affect the complex for- mation and that the loop region in Elp1, which was previ- ously shown to contact the bound tRNA molecule is also in- volved in Elp456 recruitment. They also confirm a close link between tRNA binding and Elp456 recruitment. However, electrophoretic mobility shift assay (EMSA) showed that the 1132–1224 deletion in Elp1 displayed no significant effect on affinity of Elp123 variant toward mouse tRNA AlaUGC compared to wild type subcomplex (Figure 5D). DISCUSSION tRNA anticodon modifications by Elongator have a broad implication for biomedicine and translational research, as its dysfunction is associated with a variety of severe human diseases. Yet, details of its mechanistic mode of action have remained elusive, leaving some of the most important ques- tions related to this large macromolecular complex unan- swered. In this work, we developed novel protocols that allow overexpression and purification of the whole Elongator complex from yeast cells for the first time. Furthermore, we managed to overproduce, purify and reconstitute mouse and human Elongator complexes using advanced insect cell expression systems. We have determined several high- resolution cryo-EM structures for yeast and mouse Elonga- tor complexes in the presence and absence of tRNAs. Fore- most, the comparison of our cryo-EM structures demon- strates high similarities between yeast and mouse Elonga- tor and their intermediates. Our results reveal how both subcomplexes interact with each other and that in both cases, the Elp456 ring binds to only one Elp123 lobe, leav- ing the second one unoccupied. As the reconstitutions of the mammalian Elongator complexes were carried out in excess of the smaller subcomplex the possibility existed that both Elp123 lobes would bind one Elp456 ring, re- sulting in a 1:2 stoichiometry of the subcomplexes. Yet, in our MmElongator structure the ring again binds only to one Elp123 lobe with a 1:1 stoichiometry, suggesting that the alternative scenario with two Elp456 rings bind- ing both lobes of Elp123 at the same time appears rather unlikely. The poorly defined density of the second Elp123 lobe in both the ScElongator and MmElongator struc- tures indicates its high flexibility, even in the presence of Elp456. Surprisingly, the CTD of Elp1 remains disordered in MmElp123. Nonetheless, binding of either tRNA or Elp456 do not cause major structural rearrangement but instead lead to a more compact and rigid complex. There- The CTD of Elp1 is responsible for tRNA binding and sub- complex interaction This is likely due to that tRNA binding seems to be dom- inated by Elp3 and the second contact site located in the Elp1 CTD might simply sense the presence of a tRNA or serves a role during specific transition states. This could explain our observation that the CTD loop deletion in- deed displays functional importance in vivo even though there is no significant contribution to tRNA binding in the in vitro assay. It should also be noted that we were only able to test individual mutations and the observed inter- faces are rather large. Hence, the remaining sites in a re- spective mutant (Elp11132–1224) might be sufficient to main- tain tRNA binding. Finally, tRNA binding might not be af- fected by the tested mutants as the second Elp456-free lobe of Elp123 could mediate tRNA binding in the presence of Elp456. Nonetheless, the biochemical analyses of human Elongator support our structural findings, and several as- pects need to be addressed by additional analyses in the future. High ATP concentration stimulates tRNA binding of Elp456 It was previously shown that yeast Elp456 binds tRNA in an ATP hydrolysis regulated manner (26). To verify whether mouse and human Elp456 behave in a similar fashion, we measured the binding affinity towards mouse tRNA AlaUGC using MST assays with varying ATP concentra- tions (Figure 6A). Similar to yeast Elp456, low ATP con- centration indeed decreases the affinity of both mammalian Elp456 complexes towards tRNA in comparison to samples without ATP. When physiologically relevant ATP concen- trations (e.g. 2.5 mM) (99–101) were used, we detected a dramatic increase in binding affinities (Figure 6A). As our data show that Elp456 cannot only release tRNA upon hy- drolysis of ATP but also bind strongly to tRNA at higher ATP concentration, we next investigated whether the inter- action between human Elp123 and Elp456 could be ATP- dependent. The pull-down interaction assay showed no dif- ferences in the full complex assembly in the presence of var- ious concentrations of ATP (Supplementary Figure S12A). Nucleic Acids Research, 2023 17 re 6. Biochemical and functional characterization of Elp456. (A) Microscale thermophoresis measurements, respective fits, and calculated dissociation tant (Kd) values for mouse and human Elp456 at varying ATP concentrations. n = 3, n = 4 for mouse Elp456 and 0 mM ATP. (B) SDS-PAGE gel vitro reconstitution of human Elongator under varying ATP concentration and bulk tRNA presence. Twin-Strep-tag indicated on Elp3 subunit. (C) SA assay using fluorescently labeled tRNA AlaUGC (0.2 M), human Elp123 (top) and Elongator (bottom) (0.05–1 M) in the absence and presence TP. The positions of free tRNA and protein–tRNA complexes (*) are indicated next to the native polyacrylamide gel electrophoresis. Downloaded from https://academic.oup.com/nar/advance article/doi/10.1093/nar/gkac1232/6970223 by Unive Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac Figure 6. Biochemical and functional characterization of Elp456. (A) Microscale thermophoresis measurements, respective fits, and calculated dissociation constant (Kd) values for mouse and human Elp456 at varying ATP concentrations. n = 3, n = 4 for mouse Elp456 and 0 mM ATP. (B) SDS-PAGE gel of in vitro reconstitution of human Elongator under varying ATP concentration and bulk tRNA presence. Twin-Strep-tag indicated on Elp3 subunit. (C) EMSA assay using fluorescently labeled tRNA AlaUGC (0.2 M), human Elp123 (top) and Elongator (bottom) (0.05–1 M) in the absence and presence of ATP. The positions of free tRNA and protein–tRNA complexes (*) are indicated next to the native polyacrylamide gel electrophoresis. High ATP concentration stimulates tRNA binding of Elp456 fore, the rather flexible mammalian Elongator complexes at the start of the reaction might undergo unanticipated structural rearrangements upon substrate binding, absent in yeast Elongator. It is noteworthy that we resolved a loop region (aa184–238) in yeast Elp1, which is essential for the modification activity in vivo and seems to sup- port the integrity of the Elp123 subcomplex. As this loop is not visible in any of the previous cryo-EM structures and produces several violating crosslinks, it might become structured only under certain conditions indicating a dy- namic component of complex assembly also for the yeast complex. leagues proposed a catalytic reaction mechanism based on the biochemical characterizations of archaeal Elp3. The Elp3 utilizes its rSAM domain to accommodate and cleave SAM to produce a 5′-dA radical. The 5′-dA radical is then used to generate an acetyl radical where the acetyl group comes from the hydrolyzed ACO product or from a cova- lent acetyl-Elp3 intermediate (34). An unresolved issue is how the radical is transferred. The radical transfer may be similar to some ribonucleotide reductases, which are known to transfer generated radicals through a tyrosine relay sys- tem over a distance of ∼30 ˚A (102). Indeed, two struc- turally highly conserved tyrosine residues, namely Tyr136 and Tyr327, are present in yeast Elp3 active site, which are juxtaposed to the radical carrying methyl group of 5′-dA. For the full catalytic reaction to finish, it still requires the hydrolyzed acetyl group from the KAT domain to be trans- ferred to the proposed Lys325 residue, which is residing in the rSAM domain. We speculate that Tyr327 might mediate the acetyl radical formation by bridging between the 5′-dA leagues proposed a catalytic reaction mechanism based on the biochemical characterizations of archaeal Elp3. The Elp3 utilizes its rSAM domain to accommodate and cleave SAM to produce a 5′-dA radical. The 5′-dA radical is then used to generate an acetyl radical where the acetyl group comes from the hydrolyzed ACO product or from a cova- lent acetyl-Elp3 intermediate (34). An unresolved issue is how the radical is transferred. The radical transfer may be similar to some ribonucleotide reductases, which are known to transfer generated radicals through a tyrosine relay sys- tem over a distance of ∼30 ˚A (102). High ATP concentration stimulates tRNA binding of Elp456 After the cre- ation of acetyl radical on Lys325, the C5 atom of U34 is ide- ally positioned to be modified, resulting in cm5U34. More- over, our structures represent snapshots at certain stages of the catalytic reaction. First, the MmElp123 harbors a SAM molecule that is bound to the iron-sulfur cluster, in- dicating that SAM binding occurs before tRNA binding. Second, the ScElp123 in complex with tRNA harbors the SAM cleavage products, namely 5′-dA and methionine, in its catalytic site. Third, we could not identify any SAM molecule in the full Elongator, suggesting SAM is con- sumed. Hence, we depict the catalytic reaction as follows: (i) the Elp123 structure with intact SAM represents the initial state prior to tRNA binding and SAM cleavage; (ii) subse- quently Elp123 mediates SAM cleavage upon tRNA bind- ing (i.e. the Elp123–tRNA structure) which represents the stage of a radical generation just before its transfer from 5′- dA; (iii) the SAM free-Elongator depicts the post state of the catalytic reaction. radical and the acetyl group (Figure 7). Of note, Tyr327 is crucial for Elongator’s activity in yeast (31). After the cre- ation of acetyl radical on Lys325, the C5 atom of U34 is ide- ally positioned to be modified, resulting in cm5U34. More- over, our structures represent snapshots at certain stages of the catalytic reaction. First, the MmElp123 harbors a SAM molecule that is bound to the iron-sulfur cluster, in- dicating that SAM binding occurs before tRNA binding. Second, the ScElp123 in complex with tRNA harbors the SAM cleavage products, namely 5′-dA and methionine, in its catalytic site. Third, we could not identify any SAM molecule in the full Elongator, suggesting SAM is con- sumed. Hence, we depict the catalytic reaction as follows: (i) the Elp123 structure with intact SAM represents the initial state prior to tRNA binding and SAM cleavage; (ii) subse- quently Elp123 mediates SAM cleavage upon tRNA bind- ing (i.e. the Elp123–tRNA structure) which represents the stage of a radical generation just before its transfer from 5′- dA; (iii) the SAM free-Elongator depicts the post state of the catalytic reaction.i sufficient structural details to provide pseudo-atomic mod- els. Based on these structure analyses, we further biochem- ically characterized the role of Elp456 during the Elonga- tor reaction cycle. High ATP concentration stimulates tRNA binding of Elp456 Indeed, two struc- turally highly conserved tyrosine residues, namely Tyr136 and Tyr327, are present in yeast Elp3 active site, which are juxtaposed to the radical carrying methyl group of 5′-dA. For the full catalytic reaction to finish, it still requires the hydrolyzed acetyl group from the KAT domain to be trans- ferred to the proposed Lys325 residue, which is residing in the rSAM domain. We speculate that Tyr327 might mediate the acetyl radical formation by bridging between the 5′-dA Apart from the overall structural similarities between fungal and murine Elongator, the spatial organization of their active sites is highly conserved as well. As the molecu- lar mechanism of the tRNA modification reaction is still not fully characterized, we analyzed the conserved fea- tures of the various active sites in all our structures to understand the underlying principles. Selvadurai and col- 18 Nucleic Acids Research, 2023 Figure 7. Elongator’s reaction scheme. A schematic overview of the individual reaction intermediates of the eukaryotic Elongator complex. In higher mammalians highly flexible Elp123 binds tRNA substrate, SAM and Ac-CoA to modify U34. Bound tRNA substrate tethers the lobe with the CTD of Elp1. Next, SAM is cleaved to methionine and 5′-dA radical. The radical is passed on acetylated lysine with the help of tyrosine residue. Acetyl radical can then react with C5 of U34. After U34 modification, Elp456 assists in the release of certain tRNA species via Elp1 tRNA binding loop displacement. To allow tRNA binding to the Elp123 lobe occupied by Elp456 the smaller subcomplex needs to dissociate. How this occurs needs further investigation. Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac Figure 7. Elongator’s reaction scheme. A schematic overview of the individual reaction intermediates of the eukaryotic Elongator complex. In higher mammalians highly flexible Elp123 binds tRNA substrate, SAM and Ac-CoA to modify U34. Bound tRNA substrate tethers the lobe with the CTD of Elp1. Next, SAM is cleaved to methionine and 5′-dA radical. The radical is passed on acetylated lysine with the help of tyrosine residue. Acetyl radical can then react with C5 of U34. After U34 modification, Elp456 assists in the release of certain tRNA species via Elp1 tRNA binding loop displacement. To allow tRNA binding to the Elp123 lobe occupied by Elp456 the smaller subcomplex needs to dissociate. How this occurs needs further investigation. radical and the acetyl group (Figure 7). Of note, Tyr327 is crucial for Elongator’s activity in yeast (31). DATA AVAILABILITY veniently explained why we have not obtained a structure of the fully assembled complex with tRNA and that the full complex shows a decreased affinity for certain tRNAs. Af- ter comparing the structures of Elp123-tRNA and Elonga- tor, we nevertheless had to realize that also the full complex would be able to accommodate a single tRNA molecule in the space formed between the Elp123 lobe and the Elp456 ring. Although, the tRNA binding loop in the CTD of Elp1 would not be able to interact with the elbow region of the bound tRNA, as it is displaced by the bound Elp456 ring. To gain further insights, we introduced specific mutations in human Elp1, which either remove the whole loop re- gion or target specific regions of the loop (1176–1200, 1201–1225 and 1226–1251). All three deletions in vivo in yeast Elp1 result in the inactivation of the Elongator pathway, but its removal in human Elp123 is not suffi- cient to diminish tRNA binding to Elp123, clearly prov- ing that tRNA binding mainly occurs through the ASL bound in the active site of Elp3. The mechanistic rational behind tRNA selectivity and detailed intramolecular relay of tRNA remain elusive, but as Elp123 does not require Elp456 to bind tRNAs, we believe that Elp456 is impor- tant for the late stages of the modification reaction. Strik- ingly, we found that at physiologically relevant ATP con- centration the affinity of mammalian Elp456 towards tR- NAs exceeds the one measured for Elp123, respectively. As neither ATP nor tRNA influenced the interaction of Elp123 and Elp456, we speculate that ATP-binding might trigger the transition of an already modified tRNA to the Elp456 complex, which then releases the tRNA after ATP hydrolysis (Figure 7). As we were not able to detect any SAM molecule in the Elongator structures from mouse and yeast, we conclude that the Elp456-bound intermedi- ate, represents the latest stage of the modification reaction and that after release from the Elp456 ring, the next reac- tion is initiated by binding of SAM, ACO and a modifiable tRNA.i The models and cryo-EM densities map have been de- posited in the EMData Bank (EMDB) and the Protein Data Bank (PDB) – yeast Elongator (PDB ID 8ASV and EMD- 15622), mouse Elongator (EMD-15626), yeast Elp456 (PDB ID 8AT6 and EMD-15635), mouse Elp123 (PDB ID 8AVG and EMD-15682), yeast Elp123–tRNA (PDB ID 8ASW and EMD-15623), mouse Elp123–tRNA (EMD- 15625). High ATP concentration stimulates tRNA binding of Elp456 It is interesting to see that the Elp456 ring occupies a similar region as the tRNA suggesting that Elp456 could spatially compete with a bound tRNA substrate. However, by super-positioning the structures of Elp123–tRNA and Elongator, we had to realize that tRNA still can spatially fit between Elp123 and Elp456. Despite the extensive efforts, we still could not manage to obtain any Elongator–tRNA structure. We further present that the CTD of Elp1 is essential for the catalytic activity and it has dual interacting targets, tRNA and Elp456. It seems that the interaction is discriminated to one or the other. However, the tRNA interaction with CTD is not crucial for tRNA recruitment. tRNA binding to Elp123 is an independent event that does not require the presence of Elp456. However, the full Elongator complex displays different affinities to individ- ual tRNA targets, suggesting a role for Elp456. The most obvious model, where binding of Elp456 directly competes with a bound tRNA molecule in Elp123, would have con- y This is the first study to present the interaction of the Elp123 and Elp456 subcomplexes at high-resolution with Nucleic Acids Research, 2023 19 veniently explained why we have not obtained a structure of the fully assembled complex with tRNA and that the full complex shows a decreased affinity for certain tRNAs. Af- ter comparing the structures of Elp123-tRNA and Elonga- tor, we nevertheless had to realize that also the full complex would be able to accommodate a single tRNA molecule in the space formed between the Elp123 lobe and the Elp456 ring. Although, the tRNA binding loop in the CTD of Elp1 would not be able to interact with the elbow region of the bound tRNA, as it is displaced by the bound Elp456 ring. To gain further insights, we introduced specific mutations in human Elp1, which either remove the whole loop re- gion or target specific regions of the loop (1176–1200, 1201–1225 and 1226–1251). All three deletions in vivo in yeast Elp1 result in the inactivation of the Elongator pathway, but its removal in human Elp123 is not suffi- cient to diminish tRNA binding to Elp123, clearly prov- ing that tRNA binding mainly occurs through the ASL bound in the active site of Elp3. High ATP concentration stimulates tRNA binding of Elp456 The mechanistic rational behind tRNA selectivity and detailed intramolecular relay of tRNA remain elusive, but as Elp123 does not require Elp456 to bind tRNAs, we believe that Elp456 is impor- tant for the late stages of the modification reaction. Strik- ingly, we found that at physiologically relevant ATP con- centration the affinity of mammalian Elp456 towards tR- NAs exceeds the one measured for Elp123, respectively. As neither ATP nor tRNA influenced the interaction of Elp123 and Elp456, we speculate that ATP-binding might trigger the transition of an already modified tRNA to the Elp456 complex, which then releases the tRNA after ATP hydrolysis (Figure 7). As we were not able to detect any SAM molecule in the Elongator structures from mouse and yeast, we conclude that the Elp456-bound intermedi- ate, represents the latest stage of the modification reaction and that after release from the Elp456 ring, the next reac- tion is initiated by binding of SAM, ACO and a modifiable tRNA.i Supplementary Data are available at NAR Online. Supplementary Data are available at NAR Online. DATA AVAILABILITY All XL-MS data are available at https://repository. jpostdb.org/entry/JPST001914 (ID JPST001914). All other data generated in this study are available from correspond- ing authors on reasonable request. ACKNOWLEDGEMENTS We thank all members of the Glatt and Schaffrath labo- ratories for discussion and suggestions. The GST--toxin construct was a kind gift from Anders S. Bystr¨om. This publication was developed under the provision of the Pol- ish Ministry of Education and Science project: ‘Support for research and development with the use of research in- frastructure of the National Synchrotron Radiation Centre SOLARIS’ under contract nr 1/SOL/2021/2. We acknowl- edge SOLARIS Centre for the access to the Titan Krios, where the measurements were performed. Part of this work used iNEXT Discovery platform to gain access to the Cryo- Electron Microscopy Imaging Centre at EMBL Heidelberg. Finally, this research was partially supported by PLGrid In- frastructure (Academic Computer Centre Cyfronet AGH). The open-access publication of this article was funded by the Priority Research Area BioS under the program ‘Initia- tive of Excellence – Research University’ at the Jagiellonian University in Krakow. oi/10.1093/nar/gkac1232/6970223 by University of Edinburgh user on 08 February 2023 Based on previous findings, we conclude that Elongator can bind all types of tRNAs, but only the recognition of specific bases in certain tRNAs triggers ACO hydrolysis in the KAT domain and SAM cleavage in the rSAM domain. In mammals, the binding of tRNAs induces large structural rearrangements in the arch domain, which might confer ad- ditional selectivity and create a second contact at the elbow region of the bound tRNA molecule. All modifiable tRNAs would receive cm5 at U34 by the activity of the Elp123, but some tRNAs additionally require the assistance of Elp456 to be unloaded from the complex after the modification re- action. To release certain modified tRNAs from Elp123, the smaller subcomplex would bind again and displace the loop in the Elp1 CTD allowing the tRNA to be released. We speculate that the affinity of certain tRNAs is simply too high for a release from Elp123 and that the displacement of the loop, facilitates the ATP-dependent transfer of tR- NAs to the Elp456 ring. How the transfer from Elp123 to Elp456 exactly happens will require additional studies. In summary, our data provide novel insights into the structural and functional conservation of Elongator in eukaryotes and our work paves the way for further analyses of the intrinsic dynamics of Elongator and the specific differences between its tRNA substrate molecules. FUNDING OPUS16 grant [2018/31/B/NZ1/03559 to M.J., R.K., N.H.A., S.G.] from the National Science Centre; Eu- ropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation pro- gramme [101001394 to S.G.]; MCB structural biology core facility (supported by the TEAM TECH CORE FACILITY/2017–4/6) grant from Foundation for Polish Science to M.R., P.I., S.G.]; PhD scholarship support by the Otto Braun-Fonds (B. Braun, Melsungen AG, Ger- many to D.S.); Deutsche Forschungsgemeinschaft, Ger- many [SCHA750/20, SCHA750/25 to R.S.]. Funding for open access chrge: Priority Research Area BioS under the program ‘Initiative of Excellence––Research University’ at the Jagiellonian University in Krakow. C fli t f i t t t t t N d l d 1. Machnicka,M.A., Olchowik,A., Grosjean,H. and Bujnicki,J.M. (2014) Distribution and frequencies of post-transcriptional modifications in tRNAs. RNA Biol., 11, 1619–1629. SUPPLEMENTARY DATA Supplementary Data are available at NAR Online. 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https://openalex.org/W2902145381
https://dspace.lib.cranfield.ac.uk/bitstream/1826/13705/4/Assessment_of_silt_from_sand_and_gravel_processing-2018.pdf
English
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Assessment of silt from sand and gravel processing as a suitable sub-soil material in land restoration: A glasshouse study
Chemosphere
2,019
cc-by
8,929
ERROR: type should be string, got "https://doi.org/10.1016/j.chemosphere.2018.11.155\n0045-6535/© 2018 Elsevier Ltd. All rights reserved. a r t i c l e\ni n f o Annually, sand and gravel processing generates approximately 20 million tonnes of non-commercial by-\nproduct as fine silt particles (<63 mm) which constitutes approximately 20% of quarry production in the\nUK. This study is significant as it investigated the use of quarry silt as a sub-soil medium to partially\nsubstitute soil-forming materials whilst facilitating successful post-restoration crop establishment. In a\nglasshouse pot experiment, top-soil and sub-soil layering was simulated, generating an artificial sub-soil\nmedium by mixing two quarry non-commercial by-products, i.e. silt and overburden. These were\nblended in three ratios (100:0, 70:30, 50:50). Pots were packed to two bulk densities (1.3 and 1.5 g cm-3)\nand sown with three cover crops used in the early restoration process namely winter rye (Secale cereale),\nwhite mustard (Sinapis alba) and a grassland seed mixture (Lolium perenne, Phleum pratense, Poa\npratensis, Festuca rubra). Three weeks into growth, the first signs of nitrogen (N) deficiency were\nobserved in mustard plants, with phosphorus (P) and potassium (K) deficiencies observed at 35 days. Rye\nexhibited minor N deficiency symptoms four weeks into growth, whilst the grassland mixture showed\nno deficiency symptoms. The 70:30 silt:overburden sub-soil blend resulted in significantly higher Root\nMass Densities of grassland seed mixture and rye in the sub-soil layer as compared with the other blends. The innovation in this work is the detailed physical, chemical and biological characterisation of silt:o-\nverburden blends and effects on root development of plants commonly used in early restoration to bio-\nengineer soil structural improvements. 2018 El\ni\nL d All i h\nd Article history:\nReceived 30 August 2018\nReceived in revised form\n11 November 2018\nAccepted 23 November 2018\nAvailable online 1 December 2018 Article history:\nReceived 30 August 2018\nReceived in revised form\n11 November 2018\nAccepted 23 November 2018\nAvailable online 1 December 2018\nKeywords:\nQuarry silt\nCover crops\nRestoration\nRoot mass density\nNutrients Article history:\nReceived 30 August 2018\nReceived in revised form\n11 November 2018\nAccepted 23 November 2018\nAvailable online 1 December 2018 Keywords:\nQuarry silt\nCover crops\nRestoration\nRoot mass density\nNutrients © 2018 Elsevier Ltd. All rights reserved. h i g h l i g h t s \u0001 Silt is not fully utilised in quarries as a resource. \u0001 Silt is not fully utilised in quarries as a resource. \u0001 Root development of mustard tap roots was restricted compared to grass. \u0001 Quarry silt blended with growing medium is a suitable subsoil medium for grass and rye. \u0001 Root development of mustard tap roots was restricted compared to grass. \u0001 Quarry silt blended with growing medium is a suitable subsoil medium for grass and rye. Assessment of silt from sand and gravel processing as a suitable\nsub-soil material in land restoration: A glasshouse study Lucie Ma\u0001skov\u0003a a, Robert W. Simmons a, Sarah De Baets a, Enrique Moran Montero b,\nAude Delmer b, Ruben Sakrabani a, * a School of Water, Energy and Environment, Cranfield University, Building 52a, Cranfield Bedfordshire, MK43 0AL, UK\nb Tarmac Ltd., Panshanger Park, Hertford, Hertfordshire, SG14 2NA, UK * Corresponding author.\nE-mail address: r.sakrabani@cranfield.ac.uk (R. Sakrabani). Contents lists available at ScienceDirect Contents lists available at ScienceDirect * Corresponding author.\nE-mail address: r.sakrabani@cranfield Chemosphere 219 (2019) 58e65 Chemosphere 219 (2019) 58e65 E-mail address: r.sakrabani@cranfield.ac.uk (R. Sakrabani). * Corresponding author.\nE-mail address: r.sakrab © 2018 Elsevier Ltd. All rights reserved. 2.3. Winter rye The aim of this project was to determine the suitability of non-\ncommercial by-product such as quarry silt from mining lagoons in\ncombination with overburden as a replacement for sub-soil to\nfacilitate cover crop establishment on restoration sites and whole\nprofile bio-remediation of soil structure. Outcomes will inform\nrecommendations for the successful use of non-commercial by-\nproducts such as quarry silt and overburden in future restoration\nprojects by mineral operators. Seeding rates for Winter Rye depend on local climate conditions\nand seeding method being either drill or broadcast. Values as low as\n62e67 kg ha\u00041\n(Government\nof\nAlberta,\n2016)\nand\nup\nto\n56e224 kg ha\u00041 (Casey, 2012) can be used. Based on this, a seeding\nrate of 90 kg ha\u00041 was used, as an approximate average value for\nthis experiment. Winter Rye can germinate in temperatures as low as 1 \u0005C\nallowing seeding as late as September, the end of October, or even\nDecember (AGRAVIS, 2017; Rosenfeld and Rayns, 2011). It is the\nmost frost tolerant of all cereals (Oelke et al., 1990). It prefers well-\ndrained light loams and sandy soils, but can also be established on\nheavy clays (Bj€orkman and Shail, 2014; Oelke et al., 1990). It has a\ndense, fibrous branching root system that grows especially vigor-\nously in the upper 0.3 m of soil. 2.2. Experimental design In typical quarry restorations conducted by Tarmac Ltd, a 0.6 m\nlayer of sub-soil would be capped with a 0.3 m layer of top-soil\nstripped from the surface prior to sand and gravel extraction. This\nsubstrate layering ratio was also simulated in the pot experiment. As a sub-soil medium, 3 quarry silt:overburden blend ratios were\nselected, 100:0, 70:30 and 50:50, aiming for a high quarry silt\ncontent. Quarry restoration can result in spatial variation in sub-soil and\ntop-soil bulk densities (BD). Bulk density values normally vary from\n1.1 to 1.8 g cm\u00043, whilst in extreme conditions surface soil layers\nmay have BD as low as 0.5 g cm\u00043 and heavily compacted soils may\nexceed 2.0 g cm\u00043 (Cresswell and Hamilton, 2002). A value of\n1.3 g cm\u00043 was chosen for top-soil BD and the sub-soil materials\nwere packed at a BD of either 1.3 or 1.5 g cm\u00043 in order to represent\na low and a high degree of sub-soil compaction. Cover crops possess traits that can effectively remediate com-\npacted soils (Kirkegaard et al., 2008). Research has also demon-\nstrated that the generation of biopores through a ‘bio-drilling’\neffect of cover crops in compacted soils can result in increased yield\nof follow-on crops (Chen and Weil, 2010; Cresswell and Kirkegaard,\n1995; Kirkegaard et al., 2008). Plant roots engineer soil structure\ndirectly by penetrating and displacing soil, depositing adhesive\ncompounds which encourage aggregation, and indirectly via a\nrange of other root deposits which provide energy and nutrient\nsources for soil biota (White and Kirkegaard, 2010). 1.1. Quarry restorations At the end of the operating life of sand and gravel quarries, the\nresulting voids have to be levelled and graded to achieve landscape\nand landform objectives stated in restoration plans to allow agreed\nupon restoration objectives (CEMEX, 2014; DCLG, 2014). Quarry silt\nlagoons would normally be restored into wetland habitats, or\ncapped with a \u00031 m thick layer of overburden and planted with\nwillow rods (Tarmac Ltd., 2008). However, quarries often face a\nshortage of top-soil and sub-soil forming materials. Moreover, it is a\npriority to use materials available on-site to minimise the high\ntransport costs associated with importing materials (Tarmac Ltd.,\n2008). A possible solution would be the use of non-commercial\nby-product such as quarry silt and overburden as a partial\nreplacement for sub-soil in restorations. The suitability of quarry\nfor use in artificial soils was evaluated by (Mitchell et al., 2004) who\ninvestigated several types of quarry fine blends as a growing me-\ndium for grass species. However biomass was restricted primarily\ndue to nutrient deficiencies. Three restoration cover crops were evaluated in this study. These included white mustard (Sinapis alba) a tap rooted species;\nwinter rye (Secale cereale) as a cereal representative; and a grass-\nland seed mixture (Lolium perenne, Phleum pratense, Poa pratensis,\nFestuca rubra) as a reference crop already used in Tarmac Ltd res-\ntorations. No fertilizers were applied to simulate natural restoration\nprocesses. Each treatment was replicated in triplicate. 1. Introduction crushing and screening of the material to separate sand and gravel\naggregates from fines (<0.063 mm), which consist of silt, clay and\nother non-quartz particles (British Geological Survey, 2013). These\nfines are collected in water, giving rise to a suspension, which is\nthen pumped into lagoons and allowed to settle out (British\nGeological Survey, 2013). The resultant suspension remains in\nsemi-liquid, anaerobic state for many years, or even decades (Jarvis\nand Walton, 2010). This product is then usually referred to as\n‘quarry silt’. Quarry silt, which is generated during sand and gravel pro-\ncessing, is an un-avoidable and significant proportion of quarry\noutputs (Mitchell, 2007). The amount of quarry silt varies between\n5 and 30% of the total volume extracted, averaging around 10e15%\n(Harrison et al., 2001). Mineral processing involves washing, Quarry silt is currently defined as a non-commercial by-product\nas there is currently no market, nevertheless it should be noted that L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 59 quarry silt is an inert and non-hazardous material (Mitchell, 2007). Overburden, which is a layer of material lying above the product to\nbe extracted, is also regarded as a non-commercial by-product. The\nneed to minimise the amount of quarry non-commercial by-\nproduct is driven by environmental and social considerations and\nregulatory compliances (Mitchell, 2007). Quarry silt production can\nexceed storage capacity on site and require excavation in order to\nincrease lagoon capacity, which causes both economical and\nlogistical problems to the quarry operators (Mitchell, 2007). Reduction of quarry non-commercial by-product production usu-\nally starts at source, with an optimisation audit of the processing\ntechnology where emphasis is usually placed on good practice and\nmodernization of the crushing plant (Mitchell, 2007). The main use\nof sand and gravel non-commercial by-products is as a backfill or\nsub-soil material in site landscaping and restoration (Harrison et al.,\n2001). Another possible use of quarry non-commercial by-products\naccording to Mitchell (2007) is as vegetated tips around the quarry\nsite to screen the workings. Reusing mineral non-commercial by-\nproducts such a quarry silt contributes to efficient use of resources,\nreduces environmental impacts, and improves sustainability for\nlocal communities (Mitchell et al., 2004). using excavators. Top-soil was sourced from a compacted vegetated\nbund lining Blashford Quarry using trowels. An 8-point 120 kg top-\nsoil (0e0.3 m depth) sample was collected. 2.1. Study area Materials for this study were obtained from two different\nquarries operated by Tarmac Ltd, where there was an excess pro-\nduction of quarry silt and overburden. Blashford Quarry was the\nsource of the quarry silt sub-soil material and top-soil, and\nMountsorrel Quarry provided overburden. Mountsorrel Quarry is a\ngranite quarry located between the villages of Mountsorrel and\nQuorn in Leicestershire. A total of 80 kg of overburden from this site\nwas collected from 10 randomly selected points. Blashford Quarry\nis located in Hampshire, south of Salisbury with an annual quarry\nsilt production of >20,000 m3. A 10 point 210 kg composite quarry\nsilt sample (0e0.3 m depth) was collected from two silt lagoons 2.6. Glasshouse experiment set-up For both pot experiment and laboratory analyses, growing me-\ndiums (top-soil, quarry silt and overburden) were air dried and\nsieved to <2 mm. It should be noted, that in order to minimise\nheterogeneity between experimental replicates, the coarse aggre-\ngate fraction >2 mm, was removed during sample preparation. Post\nair-drying, quarry silt and overburden were ground to <2 mm using\na mechanical sieved soil grinder. EC was determined on 1:5 soil:water extract, based on the\nBritish Standard BS 7755: Section 3.4:1995. SOM content was\nanalysed using the loss on ignition method following British\nStandard BS EN 13039:2000. Soil pH was determined on a 1:5\nsuspension of soil in water, based on the British Standard BS ISO\n10390:2005. PSD was measured using the sieving and sedimentation\nmethod based on the British Standard BS 7755 Section 5.4:1998. Soil\nmineral-N was measured using KCl extract based on MAFF\nReference Book RB427 (1986). Sub-soil medium was mixed to the desired ratios of 100:0, 70:30\nand 50:50 of quarry silt:overburden. To represent the restoration\nlayering ratio, the sub-soil layer was packed to a depth of 12 cm\nfrom the bottom of the pot, leaving the next 5 cm for the top-soil\nlayer. Sub-soil was packed at two bulk densities (BD), representing\nlow and\nhigh\ncompaction. The\nhighest\nBD\nachievable\nwas\n1.5 g cm\u00043, with the lower value set at 1.3 g cm\u00043. All pots were then\ncapped with a 5 cm layer of top-soil (previously acquired from\nBlashford Quarry) at a BD of 1.3 g cm\u00043 to reach a total pot volume\nof 2313 cm3. 2.8. Statistical analyses Results were analysed using the STATISTICA 12.0 software. Soil\nproperties were analysed using factorial analysis of variance\n(ANOVA) to determine the effects of multiple categorical variables,\nnamely bulk density (BD), quarry silt:overburden ratio (sub-soil\nblend T1, T2 and T3) and cover crop (CC) treatment. One-way and\ntwo-way ANOVA were used to analyse single categorical indepen-\ndent values for either BD or sub-soil blend, where significance for\nthe CC was not proved. Significant values were analysed following\npost-hoc Fisher LSD analysis to show differences between mean\nvalues. Normality was checked and significance was set at p \u0006 0.05. Spearman correlation was carried out on key parameters as shown\nin Table 4. Pots were placed in the Cranfield University Glasshouse in a\ncompletely randomised layout and wetted to field capacity from\nthe base via capillary rise. Cover crop seeds (winter rye, white\nmustard and grassland seed mixture) were broadcasted on the 16th\nof June 2017 (adopted from Tarmac Ltd seeding methods). However\ndue to unexpectedly hot weather (~30 \u0005C, seeds had to be incor-\nporated to a depth of <0.5 mm. Uniform pot watering was under-\ntaken approximately every two days, depending on weather\nconditions to assure crop survival. The experiment was terminated\napproximately 6 weeks after set-up. Pot layout was changed twice\nin order to randomize possible variation in growing conditions\nwithin the glasshouse. During the pot trial, mustard plants were\naffected by several insect species including aphids (Lipaphis ery-\nsimi), mustard leaf miner (Chromatomyia horticola) and large white\nbutterfly (Pieris brassicae). The rye and grass mixture treatments\nhad no pest infestation issues. in Table 4. 2.5. Grassland seed mixture A standard seed mixture for quarry restoration adopted by\nTarmac Ltd when restoring back to an agricultural end-use is a\ngrassland seed mixture. It is commonly used in the first 2e3 years\nwithin a mandatory 5-year aftercare period. Seeding is usually\ncarried out during MarcheApril or SeptembereOctober at a rate of\n34 kg ha\u00041 (Walnes Seeds, 2017). Mixtures containing the same or\nsimilar grass species (Table 1) are usually designed as a damage\nresistant paddock mixture for grazing and hay production (Walnes\nSeeds, 2017). RMD ¼ MD\nV\n\u0001\nkg m\u00043\u0003\n(1) RMD ¼ MD\nV\n\u0001\nkg m\u00043\u0003 (1) Prior to packing in pots a 6-point composite sub-sample of top-\nsoil was collected and analysed at the Cranfield University's Envi-\nronmental Analytics Facility, following Standard Operating Pro-\ncedures based on British Standard Methods. At termination, fresh\nsub-soil blends and top-soil samples were collected and analysed\nfor nitrate and ammonium as plant available nitrogen (N) in a\ncommercial external laboratory. Blended treatments T1-T3 and top-\nsoil was air dried, sieved to <2 mm and analysed for electrical\nconductivity (EC), soil organic matter (SOM), pH and particle size\ndistribution (PSD). has a tap rooting architecture and is frost sensitive. has a tap rooting architecture and is frost sensitive. has a tap rooting architecture and is frost sensitive. penetration through the top-soil and sub-soil layers. One quarter of\neach pot was the used to assess root development. Roots were\nextracted following the root washing method of De Baets et al. (2007). To determine the root mass density (RMD), roots had to\nbe oven-dried at 65 \u0005C for 24 h. Dry root mass (MD (kg)) was then\ndivided by the volume of the soil sample (V (m3)) (De Baets et al.,\n2007) to obtain RMD. 2.5. Grassland seed mixture 2.7. Laboratory analyses In accordance with BS 3882:2015 (BSI, 2015), the texture of the\ntop-soil derived from Blashford Quarry used in the pot experiment\nis classified as a silt loam. With a clay content of 17.9%, soil pH of\n5.7e6.7 and OM of 2.97% the top-soil is defined as a low fertility\ntop-soil (BSI, 2015) (Table 2; Table 4). At termination, the soil was carefully extruded intact from the\npots a cut in half using a palette knife to visually asses root Table 1\nTarmac's standard grassland seed mixture. Common name\nVariety\nScientific name\n%\nPerennial ryegrass\nTemprano\n(Lolium perenne L.)\n32\nPerennial ryegrass\nElital\n(Lolium perenne L.)\n29\nTimothy\nAlma\n(Phleum pratense L.)\n7\nSmooth stalk meadow grass\nPanduro\n(Poa pratensis L.)\n29\nCreeping red fescue\nReport strong\n(Festuca rubra L.)\n3 2.4. Mustard Mustard can be sown from March to September (Rosenfeld and\nRayns, 2011). It prefers fertile, loamy, well drained soils and does\nnot tolerate waterlogging and dry sandy soils (Oplinger et al., 1991). Seeding rates for mustard vary from 10 kg ha\u00041 (Bodner et al., 2010)\nup to 20 kg ha\u00041 (Rosenfeld and Rayns, 2011). A commercially\nadopted seeding rate of 20 kg ha\u00041 was used in this study. Mustard\nseedlings emerge rapidly but continue to grow slowly thereafter. It L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 60 3.2.1. Available N Cover crops significantly influenced the amount of nitrate in\nboth TS and SS, and available N in TS. Different SS blends only had Fig. 1. Visual assessment of mustard root development (T3 (50:50), BD 1.5). Marked correlations are significant at p < 0.05. Table 4 Spearman correlation coefficients between key variables. RMD (kg m\u00043) is for root\nmass density, OM (%) is organic matter, EC (mS cm\u00041) is electrical conductivity, pH is\nsoil acidity, TS stands for topsoil and SS for subsoil. The most significant dependence was found for the TS:SS ratio\n(Table 6). Highest ratios, which indicate uneven root distribution,\nwere observed on mustard treatments. The lowest values for TS:SS\nratio were obtained on rye. RMD (kg\nm\u00043)\nOM (%)\nEC (mS cm\u00041)\nSoil pH\nTS:SS\nTS\nSS\nTS\nSS\nTS\nSS\nTS\nSS\nRMD TS\nRMD SS\n0.82\nOM TS\n\u00040.02\n0.02\nOM SS\n0.00\n\u00040.07\n0.76\nEC TS\n\u00040.17\n\u00040.18\n\u00040.22\n\u00040.33\nEC SS\n0.16\n0.29\n\u00040.56\n\u00040.78\n\u00040.04\npH TS\n0.29\n0.31\n0.37\n0.19\n\u00040.40\n\u00040.55\npH SS\n\u00040.20\n\u00040.13\n\u00040.19\n\u00040.52\n0.17\n0.25\n\u00040.06\nTS:SS\n\u00040.54\n\u00040.89\n\u00040.17\n0.01\n\u00040.01\n\u00040.25\n\u00040.34\n0.13\nBD\n\u00040.04\n\u00040.10\n0.03\n\u00040.02\n0.27\n0.32\n0.36\n\u00040.03\n0.10\nMarked correlations are significant at p < 0.05. Table 2\nMean (n of significant relationships was the SS blend. Root mass densities\nwere most affected by type of cover crop (CC) (Table 5). The RMD of\nSS was also significantly affected by BD. Further, the TS:SS RMD\nratio was significantly affected by CC type. Table 2\nMean (n ¼ 4) particle size distribution (PSD) of blended sub-soil treatments. Sand - 0.6 mm\n- 0.063 mm (%)\nSilt - 0.063 mm\n- 0.002 mm (%)\nClay <0.002\nmm (%)\nTop-soil\n6.66 (±0.90)\n75.4 (±0.66)\n17.9 (±0.49)\nT1\n5.39 (±0.62)\n33.7 (±0.73)\n61.0 (±0.92)\nT2\n6.26 (±0.95)\n46.5 (±0.93)\n47.3 (±0.98)\nT3\n5.08 (±1.01)\n55.1 (±1.26)\n39.8 (±0.75)\nT1 ¼ Sub-soil blend with 100% silt; T2 ¼ 70% silt and 30% overburden; T3 ¼ 50% silt\nand 50% overburden. Values in parentheses indicated ±1 SE. Table 2\nMean (n ¼ 4) particle size distribution (PSD) of blended sub-soil treatments. Correlation coefficients shown in the Table 4 indicate, that there\nis a high correlation between RMD TS/RMD SS and the TS:SS ratio. Also OM TS/SS correlates with EC SS, OM TS correlates with OM SS\nand pH SS correlates with OM SS. Sub-soil blend (quarry silt:overburden ratio) had a significant\neffect on all of the metrics measured. RMD of SS was significantly\nhigher\nin\nSS\nblend\nT2\n(0.1 kg m\u00043)\nas\ncompared\nwith\nT1\n(0.06 kg m\u00043) and T3 (0.06 kg m\u00043), which had comparable values\n(Table 4). 3.2. Soil-root interaction To quantify the root distribution between substrate layers,\nvalues for RMD were used to create a top-soil:sub-soil (TS:SS) ratio. To quantify the root distribution between substrate layers,\nvalues for RMD were used to create a top-soil:sub-soil (TS:SS) ratio. Low TS:SS values represent a balanced root distribution between\nthe TS and SS, high TS:SS ratio values correspond to few or no roots\nfound within the SS layer, hence root mass being mostly restricted\nto the TS layer. Low TS:SS values represent a balanced root distribution between\nthe TS and SS, high TS:SS ratio values correspond to few or no roots\nfound within the SS layer, hence root mass being mostly restricted\nto the TS layer. y\nSignificant relationships between soil and root properties are\nshown in Table 3. The categorical variable with the largest number Fig. 1. Visual assessment of mustard root development (T3 (50:50), BD 1.5). Table 3 Categorical significant responses for all three variables and their combinations. RMD\n(kg m¡3) is for root mass desity, OM (%) is organic matter, EC (mS cm\u00041) is electrical\nconductivity, pH is soil acidity, TS stands for topsoil and SS for subsoil. Cover crop significantly (p \u0006 0.001) influenced RMD in both the\nTS and SS layers (Table 3). A balanced root distribution (TS:SS) was\nnoted\nfor\nrye\ntreatments,\nfollowed\nby\nthe\ngrassland\nmix. Conversely, a significantly lower TS:SS was observed for the\nmustard cover crop treatments (Table 5). This corresponds with the\nvisual assessment of pots where in most cases, mustard roots did\nnot penetrate into the SS layer (Fig. 4). Bulk density significantly\ninfluenced the RMD of the SS (Table 5). RMD (kg\nm\u00043)\nOM (%)\nEC (mS\ncm\u00041)\nSoil pH\nTS:SS\nTS\nSS\nTS\nSS\nTS\nSS\nTS\nSS\nSub-soil blend\n**\n***\n***\n**\n***\nBD\n***\n*\nCC\n***\n***\n**\n***\n***\nBD*CC\n*\n**\n*\nSub-soil blend*BD*CC\n***\nMean values significant at *p \u0006 0.05, **p \u0006 0.01, ***p \u0006 0.001. The combination of CC and BD variables significantly influenced\nRMD of both TS and SS, which is reflected in the TS:SS (Table 6). Mustard had in general significantly lower RMDs as compared with\nrye and grassland cover crop treatments (Table 6). High BD\n(1.5 g cm\u00043) of the SS was associated with increased RMD of TS in\npots with mustard and rye as compared to the low BD treatments\n(1.3 g cm\u00043). High BD (1.5 g cm\u00043) of the SS in grassland mixture\ntreatments was conversely followed by decrease in RMD of TS. Table 1 In accordance with BS 2601:2013 (BSI, 2013), the texture of the\nT1 (100:0) sub-soil blend corresponds to a clay, while both the T2\n(70:30) and T3 (50:50) sub-soil blends are defined a s a silty clay. T1\nand T3 blends are, with pH values of 5.4e8.5 slightly below re-\nquirements (5.5e8.5) for multipurpose sub-soil (Table 4). The T2\nsub-soil blend with a pH of 7.9e8.0 falls within the calcareous sub-\nsoil category. L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 61 Within the same column values followed by the same letter(s) are not significantly different following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses\nindicated ±1 SE. Table 5 grassland mixture showed only minor signs of nutrient deficiency. At the time of termination of the pot trial, mustard plants were fully\nexhausted (Fig. 2). Fig. 3. Mustard plant showing N deficiency signs e stunned growth and chlorosis on\nolder leaves (27 days after sowing) (left) and possible P deficiency signs e purple\npetioles (35 days after sowing) (right) (Berry, 2006; Kumar and Sharma, 2013). 3.3. Plant response In general, roots avoided the sub-soil layer by growing in the\nspace between the soil and the pot. Mustard roots were almost\nalways unable to penetrate into the sub-soil (Fig. 1). 4.1. Cover crop treatment response an effect on the ammonium content (Table 7). In general, mustard\ntreatments were associated with significantly higher amounts of\navailable N in top-soil as compared to rye and grass mixture\ntreatments. Sub-soil blend T1 had the highest amounts of ammo-\nnium\nas\ncompared\nwith\nT2\nand\nT3\nirrespective\nof\nCC\ntreatment(Table 7). Cover crops are used as a temporary measure to facilitate the\nstabilisation and recover of soils and hydrology post restoration\n(BWSR, 2012). In a restoration context, a soil profile is re-created\nusing materials, which might have been kept under anaerobic\nconditions for years, such as quarry silts. Essential first steps for\neffective rehabilitation of restored soil profiles are improving the\nsoil structure and enhancing hydrological and gaseous connectivity\nbetween soil horizons. Planting a mixture of species can be ad-\nvantageous to ensure soil cover and increase organic matter\nthroughout the profile due to different root systems architectures\n(BWSR, 2012; Cresswell and Kirkegaard, 1995). Cover crops influ-\nence soil properties through the decomposition of crop residues\n(Radicetti et al., 2016). If used correctly, they can enhance soil\nproperties by capturing, fixing and recycling nutrients, increase\nSOM, improve soil structure, enhance soil microbiology, mitigate N-\nleaching and protect soil from erosion (Bodner et al., 2010). Table 5 Table 5\nMean (n ¼ 18) significant root mass densities (RMD, kg m\u00043) and soil physico-chemical characteristics between blended treatments. OM (%) is organic matter, EC (mS cm\u00041) is\nelectrical conductivity, pH is soil acidity, TS stands for topsoil and SS for subsoil. Table 5\nMean (n ¼ 18) significant root mass densities (RMD, kg m\u00043) and soil physico-chemical characteristics between blended treatments. OM (%) is organic matter, EC (mS cm\u00041) is\nelectrical conductivity, pH is soil acidity, TS stands for topsoil and SS for subsoil. RMD e SS (kg m\u00043)\nOM - SS (%)\npH - SS\nEC e TS (mS cm\u00041)\nEC e SS (mS cm\u00041)\nT1\n0.06a (±0.014.5)\n4.37b (±0.31)\n5.7b (±0.16)\n8.86a (±0.84)\n19.1a (±0.96)\nT2\n0.1b (±21.1)\n3.80ab (±0.31)\n8.0a (±0.01)\n10.3ab (±1.27)\n27.8a (±1.65)\nT3\n0.06a (±18.4)\n3.15a (±0.35)\n7.9a (±0.16)\n13.8b (±1.70)\n21.3b (±2.16)\nWithin the same column values followed by the same letter(s) are not significantly different following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses\nindicated ±1 SE. Mean (n ¼ 18) significant root mass densities (RMD, kg m\u00043) and soil physico-chemical characteristics between blended treatments\nelectrical conductivity, pH is soil acidity, TS stands for topsoil and SS for subsoil. MD, kg m\u00043) and soil physico-chemical characteristics between blended treatments. OM (%) is organic matter, EC (mS cm\u00041) is\nnds for topsoil and SS for subsoil. RMD e SS (kg m\u00043)\nOM - SS (%)\npH - SS\nEC e TS (mS cm\u00041)\nEC e SS (mS cm\u00041)\nT1\n0.06a (±0.014.5)\n4.37b (±0.31)\n5.7b (±0.16)\n8.86a (±0.84)\n19.1a (±0.96)\nT2\n0.1b (±21.1)\n3.80ab (±0.31)\n8.0a (±0.01)\n10.3ab (±1.27)\n27.8a (±1.65)\nT3\n0.06a (±18.4)\n3.15a (±0.35)\n7.9a (±0.16)\n13.8b (±1.70)\n21.3b (±2.16) L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 62 Fig. 2. Effects of nutrient deficiency on mustard plants 36 days (left) and 47 days\n(right) after sowing. Fig. 4. Mustard leaf showing possible K-deficiency symptoms (35 days after sowing)\n(Kumar and Sharma, 2013). Fig. 2. Effects of nutrient deficiency on mustard plants 36 days (left) and 47 days\n(right) after sowing. Fig. 3. Mustard plant showing N deficiency signs e stunned growth and chlorosis on\nolder leaves (27 days after sowing) (left) and possible P deficiency signs e purple\npetioles (35 days after sowing) (right) (Berry, 2006; Kumar and Sharma, 2013). Fig. 4. Mustard leaf showing possible K-deficiency symptoms (35 days after sowing)\n(Kumar and Sharma, 2013). Table 7 Another advantage of a rye-legume mixture is that rye holds\nN while improving soil structure and legumes fix N, making some\nof it available for rye (Kammermeyer, 2016). Rye can also be useful\nin restoration projects taking place in the autumn, as late seeding is\nrequired, owing to its ability to germinate at low temperatures and\nproduce sufficient soil cover for the winter (AGRAVIS, 2017; CEMEX,\n2014). root length and root anatomy of 7-day old cereals. Materechera\net al. (1991) grew seedlings of twenty-two plant species for 10\ndays and observed that soil compaction reduced root elongation by\n90% while increasing root diameters. Strongly compacted soils are\nusually only penetrated by roots through cracks and/or pre-existing\nbiopores (Gła̧b, 2008). This may in large part explain the RMD re-\nsults observed for rye treatments in this study. Nevertheless, it is\nimportant to note that in this pot study, rye roots avoided pene-\ntrating the SS mainly by growing through the macro-pore space at\nthe soil-pot interface. Evidence suggest that yields of some grasses\nmight be unaffected by compaction (Gła̧b, 2013, 2008). Vallance\nand Sonogan (1995) stated that fibrous roots of rye grow espe-\ncially well in the first 30 cm of soil, however, Chen and Weil (2010)\nclaim that rye roots are strongly affected by soil compaction. Scholefield and Hall (1985) claim that the ability of grasses to\npenetrate highly compacted soils by becoming constricted can be\nconsidered as a compensation of radial pressure. Growing rye may\nhowever be considered in mixtures with other grass species, or\nlegumes. According to Clark (2007), a rye-legume mixture is able to\nadjust to different N levels, meaning that in soils rich on N, rye\ntends to grow better while in soils poor on N, the legume grows\nbetter. Another advantage of a rye-legume mixture is that rye holds\nN while improving soil structure and legumes fix N, making some\nof it available for rye (Kammermeyer, 2016). Rye can also be useful\nin restoration projects taking place in the autumn, as late seeding is\nrequired, owing to its ability to germinate at low temperatures and\nproduce sufficient soil cover for the winter (AGRAVIS, 2017; CEMEX,\n2014). Adaptation for local environmental conditions and suitability\nfor the specific agro-ecological target are however essential\n(Bodner et al., 2010). Materechera et al. Table 7 (1991) have observed, that\nroots of larger diameters such as taproots of dicotyledonous plants\npenetrated soil more than those with smaller diameters. Perkons\net al. (2014) also found, that tap-root plant species create larger\nbiopores thus allow subsequent crop roots to penetrate to deeper\nsoil layers. Yu et al. (2016) claim, that especially for annual plants,\nroot thickness is very important for improving soil structure. Nonetheless, Cresswell and Kirkegaard (1995) suggest that tap\nrooted annual crops are unlikely to improve porosity of deeper,\ncompacted soil horizons. At the higher BD (1.5 g cm\u00043) of SS blends, RMD of rye in the TS\nincreased, with a corresponding decrease in RMD in the SS. This\ncould be explained by the inability of rye to penetrate into the\ncompacted SS, hence the root mass remained limited to the TS\nlayer. Root growth rate is minimally affected by BDs below\n1.4 g cm\u00043, however, values above together with the absence of pre-\nexisting biopores considerably decreases root elongation rate\n(Gaiser et al., 2013). Contrary to this, the TS:SS ratio of rye was\nsignificantly lower (low TS:SS ratio represents even root distribu-\ntion throughout the pot) as compared with mustard, which can be\nexplained by a proportion of the rye roots growing in the space\nbetween the pot and the soil, distorting the RMD ratio. 3.4. Nutrient deficiency Signs of N-deficiency were assessed by visual analysis against\nimages in Berry (2006), visible on mustard plants three weeks after\nsowing (Fig. 3). Four weeks into the experiment all mustard plants\nexhibited significant visible signs of N as well as potential phos-\nphorus (P) and potassium (K) deficiencies (Berry, 2006; Kumar and\nSharma, 2013), (Fig. 4). At four weeks, rye also started displaying N\nnutrient deficiency symptoms through yellowing leaf tips, the Cover crops encourage soil aggregation indirectly via root de-\nposits which provide energy and nutrient sources for soil biota\n(White and Kirkegaard, 2010). These biota improve the architecture\nof the soil by mechanisms including adhesion, kinetic restructuring\nand filamentous binding (Miransari, 2014). Herrera et al. (2017) also L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 63 Table 6\nEffect of cover crop treatment and subsoil blend bulk density (BD) on topsoil (TS) and subsoil (SS) root mass densities (RMDs) and topsoil:subsoil ratio (TS:SS ratio). COVER CROP\nBD (g cm\u00043)\nRMD e TS (kg m\u00043)\nRMD e SS (kg m\u00043)\nTS:SS\nGrassland\nBD 1.3\n0.76bc (±121)\n0.08c (±10.7)\n10.5a (±1.76)\nGrassland\nBD 1.5\n0.56b (±70.3)\n0.04b (±5.55)\n18.5ab (±5.43)\nMustard\nBD 1.3\n0.17a (±22.7)\n0.01a (±1.05)\n45.9c (±9.00)\nMustard\nBD 1.5\n0.21a (±30.8)\n0.01ab (±5.51)\n29.8b (±5.55)\nRye\nBD 1.3\n0.86c (±82.9)\n0.19e (±24.6)\n5.24a (±1.57)\nRye\nBD 1.5\n1.13d (±169)\n0.14d (±14.3)\n8.94a (±1.90)\nWithin the same column values followed by the same letter(s) are not significantly different following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses\nindicated ±1 SE. Table 6\nEffect of cover crop treatment and subsoil blend bulk density (BD) on topsoil (TS) and subsoil (SS) root mass densities (RMDs) and topsoil:subsoil ratio (TS:SS ratio). COVER CROP\nBD (g cm\u00043)\nRMD e TS (kg m\u00043)\nRMD e SS (kg m\u00043)\nTS:SS\nGrassland\nBD 1.3\n0.76bc (±121)\n0.08c (±10.7)\n10.5a (±1.76)\nGrassland\nBD 1.5\n0.56b (±70.3)\n0.04b (±5.55)\n18.5ab (±5.43)\nMustard\nBD 1.3\n0.17a (±22.7)\n0.01a (±1.05)\n45.9c (±9.00)\nMustard\nBD 1.5\n0.21a (±30.8)\n0.01ab (±5.51)\n29.8b (±5.55)\nRye\nBD 1.3\n0.86c (±82.9)\n0.19e (±24.6)\n5.24a (±1.57)\nRye\nBD 1.5\n1.13d (±169)\n0.14d (±14.3)\n8.94a (±1.90)\nWithin the same column values followed by the same letter(s) are not significantly different following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses\nindicated ±1 SE. Table 7\nSoil N values, significantly dependent (p \u0006 0.05) on CC and sub-soil blends. Table 7 a The amount of soil N as kg ha\u00041 has been estimated assuming the standard Tarmac TS depth of 0.3 m for soil N profiling; Within the same column values followed by the\nsame letter(s) are not significantly different (p \u0006 0.05) following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses indicated ±1 SE. a The amount of soil N as kg ha\u00041 has been estimated assuming the standard Tarmac TS depth of 0.3 m for soil N profiling; W\nsame letter(s) are not significantly different (p \u0006 0.05) following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in observed that the choice of CC influences the C and N input into the\nsoil via root decomposition dynamics and variable root biomass\nproduction. Brennan and Acosta-Martinez (2017), observed that\nfrequent cover cropping can have more significant beneficial im-\npacts on soil microbiology than using compost. root length and root anatomy of 7-day old cereals. Materechera\net al. (1991) grew seedlings of twenty-two plant species for 10\ndays and observed that soil compaction reduced root elongation by\n90% while increasing root diameters. Strongly compacted soils are\nusually only penetrated by roots through cracks and/or pre-existing\nbiopores (Gła̧b, 2008). This may in large part explain the RMD re-\nsults observed for rye treatments in this study. Nevertheless, it is\nimportant to note that in this pot study, rye roots avoided pene-\ntrating the SS mainly by growing through the macro-pore space at\nthe soil-pot interface. Evidence suggest that yields of some grasses\nmight be unaffected by compaction (Gła̧b, 2013, 2008). Vallance\nand Sonogan (1995) stated that fibrous roots of rye grow espe-\ncially well in the first 30 cm of soil, however, Chen and Weil (2010)\nclaim that rye roots are strongly affected by soil compaction. Scholefield and Hall (1985) claim that the ability of grasses to\npenetrate highly compacted soils by becoming constricted can be\nconsidered as a compensation of radial pressure. Growing rye may\nhowever be considered in mixtures with other grass species, or\nlegumes. According to Clark (2007), a rye-legume mixture is able to\nadjust to different N levels, meaning that in soils rich on N, rye\ntends to grow better while in soils poor on N, the legume grows\nbetter. 3.4. Nutrient deficiency CC\nNitrate N (þ) (mg kg\u00041)\nAvailable N (þ) 30 cm profilea (kg N ha\u00041)\nSub-soil blend\nAmmonium (þ) (mg kg\u00041)\nTS\nSS\nTS\nSS\nGrassland\n0.58a (±0.50)\n0.19a (±0.00)\n5.22a (±1.82)\nT1\n0.90b (±0.05)\nRye\n1.56a (±0.35)\n0.07a (±0.10)\n8.12a (±1.44)\nT2\n0.50a (±0.15)\nMustard\n5.85b (±0.11)\n0.62b (±0.08)\n24.5b (±0.44)\nT3\n0.51a (±0.07)\na The amount of soil N as kg ha\u00041 has been estimated assuming the standard Tarmac TS depth of 0.3 m for soil N profiling; Within the same column values followed by the\nsame letter(s) are not significantly different (p \u0006 0.05) following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses indicated ±1 SE. Table 6 Table 7\nSoil N values, significantly dependent (p \u0006 0.05) on CC and sub-soil blends. CC\nNitrate N (þ) (mg kg\u00041)\nAvailable N (þ) 30 cm profilea (kg N ha\u00041)\nSub-soil blend\nAmmonium (þ) (mg kg\u00041)\nTS\nSS\nTS\nSS\nGrassland\n0.58a (±0.50)\n0.19a (±0.00)\n5.22a (±1.82)\nT1\n0.90b (±0.05)\nRye\n1.56a (±0.35)\n0.07a (±0.10)\n8.12a (±1.44)\nT2\n0.50a (±0.15)\nMustard\n5.85b (±0.11)\n0.62b (±0.08)\n24.5b (±0.44)\nT3\n0.51a (±0.07)\na The amount of soil N as kg ha\u00041 has been estimated assuming the standard Tarmac TS depth of 0.3 m for soil N profiling; Within the same column values followed by the\nsame letter(s) are not significantly different (p \u0006 0.05) following Factorial ANOVA and post-hoc Fisher LSD analysis. Values in parentheses indicated ±1 SE. 5. Conclusions EC values for the T1-T3 treatments varied between 9 and\n28 mS cm\u00041, which is classified as non-saline and is typical for\nnormal surface soils (Hazelton and Murphy, 2007). To accelerate\nthe process of silt-water separation within silt lagoons, some\nquarries choose to use anionic flocculants such as iron (Fe) and\naluminium (Al) salts to accelerate water and silt separation. This\ncould influence EC values of quarry silt as well as be one of possible\ncauses of highly restricted mustard root development. Testing silt\nfor flocculants or other potentially phytotoxic elements is therefore\nrecommended. Across all cover crop types, the best preforming sub-soil blend\nwas the T2 (70:30) treatment in terms of significantly higher RMD\nin the sub-soil. Mustard with tap roots performed poorly in com-\nparison to the rye and grassland mix treatments which are asso-\nciate\nwith\ndense\nfine\nroots. Therefore,\nmustard\ncannot\nbe\nrecommended as a suitable cover crop for restoration projects\nwhere quarry silt is used in a blended sub-soil medium. Both the\ngrassland mixture and winter rye had significantly better perfor-\nmance, as compared to mustard with a different root type. It can be\nsuggested that improving top-soil/sub-soil connectivity could be\nachieved if rye and grasses were grown together in a mix, or in\nconjunction with legume species to facilitate successful biological\nand hydrological connectivity in restored soils. The results indicate\nthat quarry silt can be used for this purpose, nevertheless, due to its\nhigh clay content, blending quarry silt with overburden, or PAS 100\norganic compost is highly advisable. Soil pH may be used as an indicator for suitability for specific\ngrass or crop species (Hazelton and Murphy, 2007). Baize (1993)\nsuggests that optimum pH should be between 6.5 and 7.5. As\nsub-soil blends T2 and T3 resulted in a pH typical for alkaline soils\n(7.9 and 8.0, respectively), this should be approached with caution. Soil pH above 7 reduces bioavailability of trace metals such as Cu,\nZn and Ni, (Han, 2007). Nevertheless, according to Hazelton and\nMurphy (2007), pH values of the T1-T3 SS blends and TS used in\nthis study should not affect availability of N, P, K, S, Ca, or Mg as they\nwere always >5.0 and < 8.5, with the exception of availability of Fe\nbeing reduced in pH < 7.5, which applies for both T2 and T3. Acknowledgements The authors would like to express their gratitude and thanks to\nTarmac Ltd., for providing the funding and study materials. 4.3. Nutrient deficiency associated with experimental treatments N, P and K, also known as primary nutrients, are essential\nmacronutrients promoting growth, energy storage and higher\nplants cell wall strength (Kumar and Sharma, 2013). In restored\nsoils blended with quarry non-commercial by-product, a lack of\nnutrients should be expected (Mitchell et al., 2004). N-deficiency\nwas visible on mustard plants as early as 3 weeks into growth. The\nlack of N was noticeable through retarded growth and leaf symp-\ntoms. These symptoms were first observed in older leaves owing to\ntranslocation of N through the plant to younger tissues, leaving\nlower leaves yellow chlorotic and in later stages necrotic (Kumar\nand Sharma, 2013). This nutrient deficiency was aggravated by\nbuds being visible at week four. Typically in mustards, buds are\nusually visible after 5 weeks and flowers appear 7e10 days later\n(Oplinger et al., 1991). Early flowering of mustard results in short\nlived preservation of accumulated N, as stated by Herrera and\nLiedgens\n(2009). According\nto\nRosenfeld\nand\nRayns\n(2011),\nmustard will start to flower once its canopy reaches 0.5e0.7 m of\nheight and continues to grow even after that, exceeding 1 m. In this\nstudy, the average height of mustard plants in bloom was only\n0.38 m as a result of stunted growth induced by lack of essential\nnutrients. According to (Kumar and Sharma, 2013), lack of N is\nlikely to occur in waterlogged conditions, and soils with pH < 6.0 or\npH > 8.0. Most plants absorb N as ammonium (NH4þ) or nitrate\n(NO3\u0004), which is also soluble in water and therefore easily leachable\n(Hosier and Bradley, 1999). Laboratory results showed that pots\ntreated with mustard had significantly higher NO3\u0004 concentrations\nin both TS and SS as compared with other CC treatments. This\nsuggests that mustard is not effective in scavenging nutrients due\nto its root structure lacking fine roots. Phosphorus P deficiencies on\nmustard plants were also visible across all blended treatments as\npurple petioles, dwarfed plants (P promotes root development) and\nmarginal and interveinal chlorosis (Berry, 2006; Kumar and\nSharma, 2013). 4.2. Growing media characteristics Soil compaction does not only increase BD, resulting in greater\nmass per volume, it also changes soil properties, such as water\nretention, hydraulic conductivity, nutrient transport and uptake, N\nmineralization, soil gases movement etc. (Guaman et al., 2016;\nLipiec et al., 2003; Miransari et al., 2009; Wolkowski and Lowery,\n2008). Most importantly, soil compaction may alter root penetra-\ntion between restored soil layers, or even limit root growth to the\nTS only, thereby considerably reducing water and nutrient avail-\nability to plants, resulting in plant growth reduction (Lipiec et al.,\n2003; Miransari et al., 2009; Pabin et al., 2003; Wolkowski and\nLowery, 2008). According to results of the PSD, quarry silt contains a large\nproportion of clay sized particles. Clays tend to be chemically and\nphysically active, which means that their ability to hold water and\nnutrients is increased (Hazelton and Murphy, 2007). High clay\ncontent however increases susceptibility to compaction (Frost,\n1988). Critical BDs, which are likely to severely affect plant growth and\nroot penetration, are different for different soil textures. For clay\nloam and clay soils, the critical values are >1.6 and > 1.4 g cm\u00043\n(Hazelton and Murphy, 2007). This may in large part explain the\nobservation that for blends T1, T2 and T3, the higher SS BD Lipiec et al. (2012) observed that soil compaction (Soil pene-\ntration resistance exceeding 2 MPa at field capacity) directly affects L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 64 significantly reduced RMD of rye. significantly reduced RMD of rye. used as sub-soil media. Results from the research project ‘Minerals\nfrom Waste’ suggest that quarry non-commercial by-products can\nbe successfully used; especially if mixed with a green waste\ncompost in order to prevent any possible nutrient depletion and\nimprove the initial soil structure (Mitchell et al., 2004). Quarry silt from Blashford Quarry contained not only fine par-\nticles, but also a coarse fraction of cobbles and boulders (>63 mm),\nwhich is not uncommon for a quarry silt (Harrison et al., 2001). Under field conditions, this may positively influence root penetra-\ntion by creating macro pores and voids within the substrate. References AGRAVIS, 2017. Winter Rye (Secale Cereale) [WWW Document]. URL. https://www. agravis.de/en/pflanzen/saatgut/getreide/winterroggen/index.html\n(accessed\n7.14.18). i\n1993 S il S i\nA\nl\nG id\nC\nil\nS Baize, D., 1993. Soil Science Analyses - a Guide to Current Use. Wiley, Surrey. Berry, W., 2006. Symptoms of deficiency in essential minerals. In: Taiz, L., Zeiger, E ,\n,\ny\ny,\ny\nBerry, W., 2006. Symptoms of deficiency in essential minerals. In: Taiz, L., Zeiger, E.,\nMøller, I.M., Murphy, A. (Eds.), Plant Physiology and Development. Sinauer\nAssociates, Massachusetts. y\ny\np\ny\ng\nMøller, I.M., Murphy, A. (Eds.), Plant Physiology and Development. Sinauer\nAssociates, Massachusetts. Bj€orkman, T., Shail, J.W., 2014. Cornell Cover Crop Guide for Rye, Ver. 1.080324. Cornell University. Bodner, G., Himmelbauer, M., Loiskandl, W., Kaul, H.-P., 2010. Improved evaluation\nof cover crop species by growth and root factors. Agron. Sustain. Dev. 30,\n455e464. https://doi.org/10.1051/agro/2009029. Brennan, E.B., Acosta-Martinez, V., 2017. Cover cropping frequency is the main\ndriver of soil microbial changes during six years of organic vegetable produc-\ntion. Soil Biol. Biochem. 109, 188e204. https://doi.org/10.1016/j.soilbio.2017.01. 014. British\nGeological\nSurvey,\n2013. Construction\nAggregates. Mineral\nPlanning\nFactsheet. BSI, 2013. BS 8601:2013 Specification for Subsoil and Requirements for Use. BSI\nStandards Limited 2013. BSI, 2015. BS 3882:2015 Specification for Topsoil. BSI Standards Limited 2015. BWSR, 2012. Planting Temporary Cover Crops - Technical Guidance Document. Casey, A.P., 2012. Plant Guide for Cereal Rye (Secale Cereale). USDA-Natural Re-\nsources Conservation Service, Elsberry. CEMEX, 2014. East Leake Quarry Landscaping. Restoration CEMEX, 2014. East Leake Quarry Landscaping. Restoration and Aftercare. Chen, G., Weil, R.R., 2010. Penetration of cover crop roots through compacted soils. Plant Soil 331, 31e43. https://doi.org/10.1007/s11104-009-0223-7. Clark, A., 2007. Managing cover crops profitably. In: Handbook Series. Sustainable\nAgriculture Research and Education (SARE), third ed. https://doi.org/10.1017/\nCBO9781107415324.004 Cresswell, H.P., Hamilton, G.J., 2002. Bulk density and pore space relations. In:\nMcKenzie, N.J., Cresswell, H.P., Coughlan, K.J. (Eds.), Soil Physical Measurement\nand\nInterpretation\nfor\nLand\nEvaluation. CSIRO\nPublishing,\nCollingwood,\npp. 35e58. Cresswell, H.P., Kirkegaard, J.A., 1995. Subsoil amelioration by plant rootsdthe\nprocess and the evidence. Aust. J. Soil Res. https://doi.org/10.1071/SR9950221. id\nh\nl\ni\nf\ni\nl\ni\ni\nl\nki\nd DCLG, 2014. Guidance on the Planning for Mineral Extraction in Plan Making and\nthe\nApplication\nProcess\n[WWW\nDocument]. URL. https://www.gov.uk/\nguidance/minerals (accessed 7.21.17). De Baets, S., Poesen, J., Knapen, A., Galindo, P., 2007. Impact of root architecture on\nthe erosion-reducing potential of roots during concentrated flow. Earth Surf. References Harrison, D.J., Bloodworth, A.J., Eyre, J.M., Scott, P.W., MacFarlane, M., 2001. Uti-\nlisation of Mineral Waste: a Scoping Study. Pabin, J., Lipiec, J., Włodek, S., Biskupski, A., 2003. Effect of different tillage systems\nand straw management on some physical properties of soil and on the yield of\nwinter rye in monoculture. Int. Agrophys. 17. Hazelton, P., Murphy, B., 2007. Interpreting Soil Test Results: what Do All the\nNumbers Mean? CSIRO PUBLISHING, Collingwood. Perkons, U., Kautz, T., Uteau, D., Peth, S., Geier, V., Thomas, K., Lutke Holz, K.,\nAthmann, M., Pude, R., Kopke, U., 2014. Root-length densities of various annual\ncrops following crops with contrasting root systems. Soil Tillage Res. 137,\n50e57. https://doi.org/10.1016/j.still.2013.11.005. g\nHerrera, J.M., Liedgens, M., 2009. Leaching and utilization of nitrogen during a\nspring wheat catch crop succession. J. Environ. Qual. 38, 1410. https://doi.org/\n10.2134/jeq2008.0267. Herrera, J.M., Büchi, L., Rubio, G., Torres-Guerrero, C., Wendling, M., Stamp, P.,\nPellet, D., 2017. Root decomposition at high and low N supply throughout a crop\nrotation. Eur. J. Agron. 84, 105e112. https://doi.org/10.1016/j.eja.2016.12.012. Radicetti, E., Mancinelli, R., Moscetti, R., Campiglia, E., 2016. Management of winter\ncover crop residues under different tillage conditions affects nitrogen utiliza-\ntion efficiency and yield of eggplant (Solanum melanogena L.) in Mediterranean\nenvironment. Soil Tillage Res. 155, 329e338. https://doi.org/10.1016/j.still.2015. 09.004. Hosier, S., Bradley, L., 1999. Guide to Symptoms of Plant Nutrient Deficiencies\n[WWW Document]. URL. https://extension.arizona.edu/sites/extension.arizona. edu/files/pubs/az1106.pdf (accessed 7.1.17). Rosenfeld, A., Rayns, F., 2011. Sort Out Your Soil - a Practical Guide to Green Ma-\nnures. COTSWOLD Grass Seeds. Jarvis,\nD.,\nWalton,\nG.,\n2010. Restoration\nof\nAggregate\nQuarry\nLagoons\nfor\nBiodiversity. Scholefield, D., Hall, D.M., 1985. Constricted growth of grass roots through rigid\npores. Plant Soil 85, 153e162. https://doi.org/10.1007/BF02139621. Kammermeyer, K., 2016. Rye-secale Cereale [WWW Document]. URL. https://www. pennington.com/resources/agriculture/wildlife/articles/rye-secale-cereale\n(accessed 7.7.17). Vallance, N., Sonogan, R., 1995. Growing Cereal Rye [WWW Document]. URL. http://\nagriculture.vic.gov.au/agriculture/grains-and-other-crops/crop-production/\ngrowing-cereal-rye (accessed 7.14.17). Kirkegaard, J., Christen, O., Krupinsky, J., Layzell, D., 2008. Break crop benefits in\ntemperate wheat production. Field Crop. Res. 107, 185e195. https://doi.org/10. 1016/j.fcr.2008.02.010. Walnes Seeds, 2017. Grass Seed [WWW Document]. URL. http://www.walnesseeds. com/grass-seed/ (accessed 7.14.17). /j\nKumar, P., Sharma, M.K., 2013. Nutrient Deficiencies of Field Crops: Guide to\nDiagnosis and Management. CABI. White, R.G., Kirkegaard, J.A., 2010. The distribution and abundance of wheat roots in\na dense, structured subsoil - implications for water uptake. Plant Cell Environ. 33, 133e148. https://doi.org/10.1111/j.1365-3040.2009.02059.x. g\ng\nLipiec, J., Arvidsson, J., Murer, E., 2003. References Process Landforms https://doi org/10 1002/esp 1470 The additional of supplementary nutrient sources should be\nconsidered if quarry silt as non-commercial by-products are to be Process. Landforms. https://doi.org/10.1002/esp.1470. Frost, J.P., 1988. Effects on crop yields of machinery traffic and soil loosening Part 1. L. Ma\u0001skov\u0003a et al. / Chemosphere 219 (2019) 58e65 65 seedling roots of different plant species. Plant Soil 135, 31e41. https://doi.org/\n10.1007/BF00014776. seedling roots of different plant species. Plant Soil 135, 31e41. https://doi.org/\n10.1007/BF00014776. Effects on grass yield of traffic frequency and date of loosening. J. Agric. Eng. Res. 39, 301e312. https://doi.org/10.1016/0021-8634(88)90151-5. Miransari, M., 2014. Plant growth promoting rhizobacteria. J. Plant Nutr. 37,\n2227e2235. https://doi.org/10.1080/01904167.2014.920384. Gaiser, T., Perkons, U., Küpper, P.M., Kautz, T., Uteau-Puschmann, D., Ewert, F.,\nEnders, A., Krauss, G., 2013. Modeling biopore effects on root growth and\nbiomass production on soils with pronounced sub-soil clay accumulation. Ecol. Model. 256, 6e15. https://doi.org/10.1016/j.ecolmodel.2013.02.016. Miransari, M., Bahrami, H.A., Rejali, F., Malakouti, M.J., 2009. Effects of arbuscular\nmycorrhiza, soil sterilization, and soil compaction on wheat (Triticum aestivum\nL.) nutrients uptake. Soil Tillage Res. 104, 48e55. https://doi.org/10.1016/j.still. 2008.11.006. Gła̧b, T., 2008. Effects of tractor wheeling on root morphology and yield of lucerne\n(Medicago sativa L.). Grass Forage Sci. 63, 398e406. https://doi.org/10.1111/j. 1365-2494.2008.00647.x. Mitchell, C., 2007. Quarry Fines and Waste [WWW Document]. URL. http://nora. nerc.ac.uk/6290/1/Quarry_Fines_and_Waste.pdf (accessed 7.21.17). Gła̧b, T., 2013. Impact of soil compaction on root development and yield of\nmeadow-grass. Int. Agrophys. 27, 7e13. https://doi.org/10.2478/v10247-012-\n0062-2. Mitchell, C.J., Harrison, D.J., Robinson, H.L., Ghazireh, N., 2004. Minerals from Waste:\nrecent BGS and Tarmac experience in finding uses for mine and quarry waste. Miner. Eng. 17, 279e284. https://doi.org/10.1016/j.mineng.2003.07.020. Government of Alberta, 2016. Fall Rye Production. Alberta Agriculture and Rural\nDevelopment, Edmonton. Oelke, E.A., Oplinger, E.S., Bahri, H., Durgan, B.R., Putnam, D.H., Doll, J.D.,\nKelling, K.A., 1990. Rye - Alternative Field Crops Manual [WWW Document]. URL. www.hort.purdue.edu/newcrop/afcm/rye.html (accessed 7.7.17). Guaman, V., Båth, B., Hagman, J., Gunnarsson, A., Persson, P., 2016. Short time effects\nof biological and inter-row subsoiling on yield of potatoes grown on a loamy\nsand, and on soil penetration resistance, root growth and nitrogen uptake. Eur. J. Agron. 80, 55e65. https://doi.org/10.1016/j.eja.2016.06.014. Oplinger, E.S., Oelke, E.A., Putnam, D.H., Kelling, K.A., Kaminsid, A.R., Teynor, T.M.,\nDoll, J.D., Durgan, B.R., 1991. Mustard - Alternative Field Crops Manual [WWW\nDocument]. URL. www.hort.purdue.edu/newcrop/afcm/mustard.html (accessed\n7.8.17). Han, F.X., 2007. Biogeochemistry of Trace Elements in Arid Environments. Springer\nScience & Business Media, Netherlands. Cranfield University\nCERES Research Repository\nhttps://dspace.lib.cranfield.ac.uk/\nSchool of Water, Energy and Environment (SWEE)\nStaff publications (SWEE)\nAssessment of silt from sand and gravel\nprocessing as a suitable sub-soil\nmaterial in land restoration: A\nglasshouse study\nMašková, Lucie\n2018-12-01\nAttribution 4.0 International\nMašková L, Simmons RW, De Baets S, et al. (2019) Assessment of silt from sand and gravel\nprocessing as a suitable sub-soil material in land restoration: A glasshouse study.\nChemosphere, Volume 219, March 2019, pp. 58-65\nhttps://doi.org/10.1016/j.chemosphere.2018.11.155\nDownloaded from CERES Research Repository, Cranfield University Cranfield University\nCERES Research Repository Cranfield University\nCERES Research Repository https://dspace.lib.cranfield.ac.uk/ School of Water, Energy and Environment (SWEE) Staff publications (SWEE) Mašková L, Simmons RW, De Baets S, et al. (2019) Assessment of silt from sand and gravel\nprocessing as a suitable sub-soil material in land restoration: A glasshouse study.\nChemosphere, Volume 219, March 2019, pp. 58-65\nhttps://doi.org/10.1016/j.chemosphere.2018.11.155\nDownloaded from CERES Research Repository, Cranfield University References Review of modelling crop growth, movement\nof water and chemicals in relation to topsoil and subsoil compaction. Soil\nTillage Res. 73, 15e29. https://doi.org/10.1016/S0167-1987(03)00096-5. Wolkowski, R., Lowery, B., 2008. Soil Compaction : Causes, Concerns, and Cures. Madison. g\n,\np //\ng/\n/\n(\n)\nLipiec, J., Horn, R., Pietrusiewicz, J., Siczek, A., 2012. Effects of soil compaction on\nroot elongation and anatomy of different cereal plant species. Soil Tillage Res. 121, 74e81. https://doi.org/10.1016/j.still.2012.01.013. MAFF Reference Book RB427, 1986. Method 53 Analysis of Agricultural Materials. Materechera, S.A., Dexter, A.R., Alston, A.M., 1991. Penetration of very strong soils by g\np //\ng/\n/\n(\n)\nLipiec, J., Horn, R., Pietrusiewicz, J., Siczek, A., 2012. Effects of soil compaction on\nroot elongation and anatomy of different cereal plant species. Soil Tillage Res. 121, 74e81. https://doi.org/10.1016/j.still.2012.01.013. Yu, Y., Loiskandl, W., Kaul, H.P., Himmelbauer, M., Wei, W., Chen, L., Bodner, G., 2016. Estimation of runoff mitigation by morphologically different cover crop root\nsystems. J. Hydrol. 538, 667e676. https://doi.org/10.1016/j.jhydrol.2016.04.060. MAFF Reference Book RB427, 1986. Method 53 Analysis of Agricultural Materials. Materechera, S.A., Dexter, A.R., Alston, A.M., 1991. Penetration of very strong soils by Assessment of silt from sand and gravel\nprocessing as a suitable sub-soil\nmaterial in land restoration: A\nglasshouse study Mašková, Lucie\n2018-12-01\nAttribution 4.0 International Mašková, Lucie\n2018-12-01\nAttribution 4.0 International Attribution 4.0 International Mašková L, Simmons RW, De Baets S, et al. (2019) Assessment of silt from sand and gravel\nprocessing as a suitable sub-soil material in land restoration: A glasshouse study. Chemosphere, Volume 219, March 2019, pp. 58-65\nhttps://doi.org/10.1016/j.chemosphere.2018.11.155\nDownloaded from CERES Research Repository, Cranfield University Mašková L, Simmons RW, De Baets S, et al. (2019) Assessment of silt from sand and gravel\nprocessing as a suitable sub-soil material in land restoration: A glasshouse study. Chemosphere, Volume 219, March 2019, pp. 58-65\nhttps://doi.org/10.1016/j.chemosphere.2018.11.155\nDownloaded from CERES Research Repository, Cranfield University"
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THE EPIGAMIC BEHAVIOUR OF THE TERMITE MICROTERMES SUDAN ENSIS SJST. OBSERVED AT KAGELU, YEI, EQUATORIAL PROV., ANGLO‐EGYPTIAN SUDAN. ECONOMIC IMPORTANCE OF TERMITES TO THE NATIVE AZANDE.
Proceedings of the Royal Entomological Society of London. Series A, General Entomology
1,938
public-domain
936
THE EPIGAMIC BEHAVIOUR OF THE TERMITE M1CROTERMES SUDANENSIS SJST. OBSERVED AT KAGELU, YEI, EQUATORIAL PROV., ANGLO-EGYPTIAN SUDAN. ECONOMIC IMPORTANCE OF TERMITES TO THE NATIVE AZANDE. By Dr J G M D S By Dr. J. G. My e r s, D.Sc . [Th e following interesting notes were sent by my friend Dr. Myers, together with tubes of specimens bearing the locality and the number 6401. All were kindly named by Mr. F. G. M. Westropp in the Brit. Mus. (Nat. Hist.), where they were compared with a co-type of Microtermes sudanensis.—E. B. Po u l t o n .] Kagelu, Yei, Equatorial Province, Sudan. 25 June, 1937. I send under separate cover some termites illustrating the habit of biting the female during courtship. I never saw anything like it in Invertebrates before. It is mentioned in a recent note in our Proceedings. It is real “ cave man ” stuff. The following is transcribed from my journal:— “ K l 30 M h 1937 Wi d i g y j “ Kagelu : 30 March, 1937.—Winged termites at light between 7 and 8 p.m. At least half chasing each other or holding on, with mandibles, to the tip or side—mostly tip—of the females’ abdomens, like bulldogs : several males often on one female, each interlocked group being preserved in a separ­ ate tube. Some of the males are still maintaining their hold in the alcohol after being killed with cyanide. Even when completely suspended and entangled in spiders’ webs males were still fighting for a place at a female’s side or still hanging on. Sometimes the males were winged and the females de-alated, or vice versa. In one instance two males were pursuing one female, trying hard to get a grip, but she always fought violently, even turning complete somersaults. When I disturbed them by removing the female, they turned on each other and attacked furiously, each trying to take hold on or near the mandibles of the other, thus proving that each was not mistaking the other for a female. Their mandibles clashed like stags’ horns, and one could almost fancy that the sound was audible. I have made no microscopic examination, but assumed the sexes from the behaviour. All can be checked, as fighting and mating sets are all kept separate. There is also included a tubeful col­ lected at random for identification.” [The sets of termites received from Dr. Myers were in five tubes andhave been sexed by Dr. B. M. Hobby. Each tube contained 1 £, the numbers of males being, 1, 2, 2, 3, 3, respectively. THE EPIGAMIC BEHAVIOUR OF THE TERMITE M1CROTERMES SUDANENSIS SJST. OBSERVED AT KAGELU, YEI, EQUATORIAL PROV., ANGLO-EGYPTIAN SUDAN. ECONOMIC IMPORTANCE OF TERMITES TO THE NATIVE AZANDE. By Dr J G M D S The random collection contained 7 £<$, 5 one male being mutilated so that its sex was difficult to determine. No tube contained only males. In these very interesting records Dr. Myers confirms and extends the observations recorded by Prof. G. D. Hale Carpenter in 1936, Proc. R. ent. Soc. Lond. (A) 11: 93-94 : viz. those of Burtt on an unnamed termite in Tangan­ yika Territory; Kofoid; and Fuller on four S. African species. All the observa­ tions, including those of Dr. Myers, appear to concern the methods of courtship alone, and not to include copulation which may perhaps take place underground. —E. B. P.] Incidentally termites of many kinds are immensely important in the economy of the Azande, among whom I have just been working. One of the PROC. R. ENT. SOC. LOND. (a ) 13. PTS. 1-3. (MAR. 1938.) r rcin.org.pl Dr. J. G. Myers on the behaviour of a termite. 8 greatest problems the administration faces with the Azande is diet-deficiency, especially in animal proteins. For sleeping-sickness control they have all been concentrated on the roads; so that hunting covers a much smaller area, and tsetse debars them keeping livestock while the Government prevents them from eating each other. In these circumstances termites form their chief animal food and they know far more about the swarming habits, which seem to be very specific, than any entomologist. They collect them in incredible quantities. I have tasted them roasted with a little salt’ and they are excellent —much better than shrimps—entirely free from the cockroachy odour and taste I somehow expected. In addition to eating the termites themselves they press out an excellent, odourless yellow oil, which at least in some considerable sections is the chief cooking fat throughout the year, used far more extensively than sesame. I am getting some of it analysed officially. Who knows what potent vitamins it may contain ! In addition to the use of termites as food, the natives consult them as oracles. They take two small sticks of two different kinds of wood and thrust them, with, the appropriate spells, into an opened gallery of a large termitarium, but only one built by certain species. According as one or other stick is gnawed (or both) in the morning the answer to the question put is negative or affirma­ tive, or qualified. This is described in minute detail by Evans-Pritchard in his absorbing and magnificent work, Witchcraft, Oracles and Magic Among the Azande (Oxford, 1937). ( ) I have collected about 15 species, with Azande names and lore, and sent them for identification direct to Dr. Snyder, of Washington. I have some other very interesting pinned insects, including a huge Drilid I am now in the middle of studying, which tackles large snails, 3 inches long and more, with no subtilty but a direct attack.
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Efficient Selection of New Immunobiotic Strains With Antiviral Effects in Local and Distal Mucosal Sites by Using Porcine Intestinal Epitheliocytes
Frontiers in immunology
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ORIGINAL RESEARCH published: 08 April 2020 doi: 10.3389/fimmu.2020.00543 Efficient Selection of New Immunobiotic Strains With Antiviral Effects in Local and Distal Mucosal Sites by Using Porcine Intestinal Epitheliocytes Leonardo Albarracin1,2†, Valeria Garcia-Castillo1,3†, Yuki Masumizu2, Yuhki Indo2, Md Aminul Islam2, Yoshihito Suda4, Apolinaria Garcia-Cancino3, Hisashi Aso5,6, Hideki Takahashi7,8, Haruki Kitazawa2,6* and Julio Villena1,2* Leonardo Albarracin1,2†, Valeria Garcia-Castillo1,3†, Yuki Masumizu2, Yuhki Indo2, Md Aminul Islam2, Yoshihito Suda4, Apolinaria Garcia-Cancino3, Hisashi Aso5,6, Hideki Takahashi7,8, Haruki Kitazawa2,6* and Julio Villena1,2* *Correspondence: Haruki Kitazawa Previously, we evaluated the effect of the immunobiotic strain Lactobacillus rhamnosus CRL1505 on the transcriptomic response of porcine intestinal epithelial (PIE) cells triggered by the challenge with the Toll-like receptor 3 (TLR-3) agonist poly(I:C) and successfully identified a group of genes that can be used as prospective biomarkers for the screening of new antiviral immunobiotics. In this work, several strains of lactobacilli were evaluated according to their ability to modulate the expression of IFNα, IFNβ, RIG1, TLR3, OAS1, RNASEL, MX2, A20, CXCL5, CCL4, IL-15, SELL, SELE, EPCAM, PTGS2, PTEGES, and PTGER4 in PIE cells after the stimulation with poly(I:C). Comparative analysis of transcripts variations revealed that one of the studied bacteria, Lactobacillus plantarum MPL16, clustered together with the CRL1505 strain, indicating a similar immunomodulatory potential. Two sets of in vivo experiments in Balb/c mice were performed to evaluate L. plantarum MPL16 immunomodulatory activities. Orally administered MPL16 prior intraperitoneal injection of poly(I:C) significantly reduced the levels of the proinflammatory mediators tumor necrosis factor α (TNF-α), interleukin 6 (IL-6), and IL-15 in the intestinal mucosa. In addition, orally administered L. plantarum MPL16 prior nasal stimulation with poly(I:C) or respiratory syncytial virus infection significantly decreased the levels of the biochemical markers of lung tissue damage. In addition, reduced levels of the proinflammatory mediators TNF-α, IL-6, and IL-8 were found in MPL16-treated mice. Improved levels of IFN-β and IFN-γ in the respiratory mucosa were observed in mice treated with L. plantarum MPL16 when compared to control mice. The immunological changes induced by L. plantarum MPL16 were not *Correspondence: Haruki Kitazawa haruki.kitazawa.c7@tohoku.ac.jp Julio Villena jcvillena@cerela.org.ar †These authors have contributed equally to this work Specialty section: This article was submitted to Nutritional Immunology, a section of the journal Frontiers in Immunology Received: 30 November 2019 Accepted: 10 March 2020 Published: 08 April 2020 1 Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucuman, Argentina, 2 Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan, 3 Laboratory of Bacterial Pathogenicity, Faculty of Biological Sciences, University of Concepción, Concepción, Chile, 4 Department of Food, Agriculture and Environment, Miyagi University, Sendai, Japan, 5 Cell Biology Laboratory, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan, 6 Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan, 7 Laboratory of Plant Pathology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan, 8 Plant Immunology Unit, International Education and Research Centre for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan Edited by: Lijuan Yuan, Virginia Tech, United States Virginia Tech, United States Reviewed by: Francisco José Pérez-Cano, University of Barcelona, Spain Lei Shi, Georgia State University, United States Reviewed by: Francisco José Pérez-Cano, University of Barcelona, Spain Lei Shi, Georgia State University, United States Georgia State University, United States INTRODUCTION randomized controlled trial conducted in children younger than 5 years, it was demonstrated that the immunobiotic CRL1505 strain is capable to enhance mucosal immunity and reduced the incidence and severity of intestinal and respiratory infections (2). Of note, our studies in mice models have clearly shown that the immunomodulatory capacities of L. rhamnosus CRL1505 are a strain-specific property because other immunobiotic strains such as Lactobacillus plantarum CRL1506 can stimulate only the intestinal immunity after their oral administration (7–10). More than a third of child deaths worldwide are attributed to malnutrition and its profound impact on the immune system and the host resistance to infections. In this sense, pneumonia and diarrhea remain the leading causes of death of children. Together, these two infectious diseases account for 29% of all deaths of children younger than 5 years and result in the loss of 2 million young lives annually (1). In 2009, the World Health Organization (WHO) separately published two strategies for the control of pneumonia and diarrhea. Since these strategies were implemented globally, it has been recognized that pneumonia and diarrhea could be treated more effectively in a coordinated manner. Thus, WHO-UNICEF published in 2013 an Integrated Global Action Plan for the Prevention and Control of Pneumonia and Diarrhea (GAPPD), which proposes a cohesive approach to ending deaths from preventable pneumonia and diarrhea in children (1). The GAPPD proposes interventions to create healthy environments, promotes practices to protect children from infectious diseases, and ensures that all children have access to appropriate preventive and treatment measures. The document emphasizes the importance of healthy nutrition to reduce the incidence and severity of pneumonia and diarrhea simultaneously. y ( ) It is well known that intestinal epithelial cells (IECs) had a central role in determining the type of immune response triggered by antigens in the intestinal mucosa through their interactions with immune cells (11, 12). In this regard, studies have reported that immunomodulatory LAB modulate intestinal immune responses by regulating the functions of IECs (13). Therefore, we hypothesized that transcriptomic analysis evaluating the effect of L. rhamnosus CRL1505 and L. plantarum CRL1506 on IECs could bring valuable information about their capacity of modulating the intestinal innate antiviral immune response, as well as provide some clues about their differential ability to influence immunity in the respiratory tract. INTRODUCTION By using porcine intestinal epithelial (PIE) cells that express the pattern recognition receptor (PRR) Toll-like receptor 3 (TLR-3) and respond to poly(I:C) stimulation (14, 15); we studied the similarities and differences of L. rhamnosus CRL1505 and L. plantarum CRL1506 in terms of their ability to modulate the immunotranscriptomic response of epithelial cells (16). The transcriptional profiling performed in PIE cells allowed us to characterize the immune and immune- related genes involved in their response to TLR3 activation, which included type I interferons (IFNs), antiviral factors, cytokines, chemokines, adhesion molecules, enzymes involved in prostaglandin biosynthesis, PRRs, and negative regulators of the TLR signaling pathway. In addition, we were able to confirm that the CRL1505 and CRL1506 strains differently regulated the immunotranscriptomic response of poly(I:C)-challenged PIE cells (16). Quantitative and qualitative differences in the expression of immune and immune-related genes in PIE cells were found when L. rhamnosus CRL1505 and L. plantarum CRL1506 treatments were compared. Moreover, the comparative analysis of the effect of the two strains allowed us to identify a group of genes that could be used as potential biomarkers for the efficient selection of new antiviral immunobiotics in PIE cells, which could beneficially influence both the intestinal and the respiratory antiviral immunity. Various clinical trials and studies in animal models have demonstrated the ability of probiotic lactic acid bacteria (LAB) with immunomodulatory activities, also known as immunobiotics, to improve the resistance to intestinal viral infections (2, 3). Although most of the research related to the beneficial effect of immunobiotics on the host’s immune system has focused on the stimulation of intestinal immunity to protect against viral infections (4), it has also been shown that the oral administration of some immunobiotics strains can beneficially modulate not only the local intestinal immunity but also immune responses in distant mucosal sites such as the respiratory tract (5, 6). Then, it is believed that appropriate immunobiotic LAB strains can be effectively used as preventive therapies to improve antiviral defenses and reduce the complications from the deregulated inflammatory responses in both the intestine and the respiratory tract. Therefore, the efficient selection of immunobiotic strains that orally administered are capable of favorably modulating intestinal and respiratory antiviral immunity could contribute to reducing the risk of viral infections, having a simultaneous impact on resistance to pneumonia and diarrhea. Citation: Albarracin L, Garcia-Castillo V, Masumizu Y, Indo Y, Islam MA, Suda Y, Garcia-Cancino A, Aso H, Takahashi H, Kitazawa H and Villena J (2020) Efficient Selection of New Immunobiotic Strains With Antiviral Effects in Local and Distal Mucosal Sites by Using Porcine Intestinal Epitheliocytes. April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 1 Albarracin et al. Selection of Antiviral Immunobiotics in PIE Cells different from those previously reported for the CRL1505 strain in in vitro and in vivo studies. The results of this work confirm that new immunobiotic strains with the ability of stimulating both local and distal antiviral immune responses can be efficiently selected by evaluating the expression of biomarkers in PIE cells. Keywords: porcine intestinal epithelial cells, TLR3, Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum MPL16, antiviral response, respiratory immunity Keywords: porcine intestinal epithelial cells, TLR3, Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum MPL16, antiviral response, respiratory immunity Frontiers in Immunology | www.frontiersin.org PIE Cells The PIE cell line was originally derived from intestinal epithelia isolated from an unsuckled neonatal swine (17). Porcine intestinal epithelial cells are intestinal non-transformed cultured cells that assume a monolayer with a cobblestone and epithelial-like morphology and with close contact between cells during culture (14, 17, 18). Porcine intestinal epithelial cells were maintained in Dulbecco modified eagle medium (DMEM) (Invitrogen Corporation, Carlsbad, CA, United States) supplemented with 10% fetal calf serum, 100 mg/mL streptomycin and 100 U/mL penicillin at 37◦C in an atmosphere of 5% CO2 (16, 18–20). Microorganisms Lactobacillus rhamnosus CRL1505, L. plantarum CRL1506, L. rhamnosus CRL576, and L. plantarum CRL681 belong to CERELA Culture Collection; L. rhamnosus IBL07 belongs to the Infection Biology Laboratory of IMMCA-CONICET-UNT and was kindly given by Dr. Vizoso-Pinto. Lactobacillus plantarum MPL16 belongs to the Food and Feed Immunology Group Culture Collection, These strains were grown in Man–Rogosa– Sharpe broth at 37◦C. For the in vitro immunomodulatory assays, overnight cultures were harvested by centrifugation, washed three times with sterile phosphate-buffered saline (PBS), counted in a Petroff–Hausser counting chamber, and resuspended in DMEM until use. Two sets of experiments were performed in treated and control mice. In the first set of experiments, mice were challenged by the intraperitoneal route with 100 µL of PBS containing 30 µg poly(I:C) according to our previous publication (8). Biochemical markers of injury as well as intestinal cytokines’ concentrations were evaluated 2 days after poly(I:C) administration as described below. In the second set of experiments, mice were lightly anesthetized, and 100 µL of PBS, containing 250 µg poly(I:C) (equivalent to 10 mg/kg body weight), was administered via the nares according to our previous publication (7). Mice received three doses of poly(I:C) with 24-h rest period between each administration. INTRODUCTION Lactobacillus rhamnosus CRL1505, orally administered to mice, is able to differentially modulate both intestinal (7, 8) and respiratory (9, 10) antiviral immunity. Moreover, in a In this work, we tested this hypothesis by evaluating the influence of several immunomodulatory and non- immunomodulatory lactobacilli strains in the expression of April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 2 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. IFNα, IFNβ, RIG1, TLR3, OAS1, RNASEL, MX2, A20, CXCL5, CCL4, IL-15, SELL, SELE, EPCAM, PTGS2, PTEGES, and PTGER4 in poly(I:C)-challenged PIE cells and by studying in vivo the effect of orally administered lactobacilli on the intestinal and respiratory antiviral innate immune responses. cDNAs according to the manufacturer’s recommendations. Real- time qPCR was carried out using a 7300 real-time PCR system (Applied Biosystems, Warrington, United Kingdom) and the Platinum SYBR green qPCR SuperMix uracil-DNA glycosylase with 6-carboxyl-X-rhodamine (ROX) (Invitrogen). The primers used for the study of IFNα, IFNβ, RIG1, TLR3, OAS1, RNASEL, MX2, A20, CXCL5, CCL4, IL-15, SELL, SELE, EPCAM, PTGS2, PLA2G4A, PTEGES, and PTGER4 expressions in this study were described before (16, 20, 21). The PCR cycling conditions were 2 min at 50◦C, followed by 2 min at 95◦C, and then 40 cycles of 15 s at 95◦C, 30 s at 60◦C, and 30 s at 72◦C. The reaction mixtures contained 5 µL of sample cDNA and 15 µL of master mix, which included the sense and antisense primers. According to the minimum information for publication of quantitative real-time PCR experiments guidelines, β-actin was used as a housekeeping gene because of its high stability across porcine various tissues (14, 15, 21). Expression of β-actin was used to normalize cDNA levels for differences in total cDNA levels in the samples. Animals, Feeding Procedures, and Poly(I:C) Challenge Male 6-week-old BALB/c mice were obtained from the closed colony kept at CERELA-CONICET. Animals were housed in plastic cages in a controlled atmosphere (22◦C ± 2◦C temperature, 55% ±2% humidity) with a 12-h light/dark cycle. Lactobacilli were orally administered to different groups of mice for five consecutive days at a dose of 108 cells/mouse per day in the drinking water (22, 23). The treated groups and the untreated control mice were fed a conventional balanced diet ad libitum. Respiratory Syncytial Virus Infection Respiratory Syncytial Virus Infection Infection with human respiratory syncytial virus (RSV) strain A2 was performed as described previously (9). Briefly, RSV was grown in Vero cells for 3 h at 37◦C, 5% CO2 at multiplicity of infection of 1 in 5 mL of DMEM. After cell lysis, virus supernatant was sucrose density gradient purified and stored in 30% sucrose at −80◦C. For infection, mice were lightly anesthetized with isoflurane and intranasally challenged with 3.1 × 106 plaque forming units (PFU) of RSV (9). Immunomodulatory Effect of Lactobacilli in PIE Cells The study of the immunomodulatory capacity of lactobacilli was performed in PIE cells as described previously (15, 16, 18, 20). Porcine intestinal epithelial cells were seeded at 3 × 104 cells per well in 12-well type I collagen-coated plates (Sumitomo Bakelite Co., Tokyo, Japan) and cultured for 3 days. After changing medium, lactobacilli (5 × 108 cells/mL) were added, and 48 h later, each well was washed vigorously with medium at least three times to eliminate all stimulants. Then cells were stimulated with poly(I:C) (60 µg/mL) for 12 h for reverse transcription– polymerase chain reaction (RT-PCR) studies. Quantitative Expression Analysis by Two-Step Real-Time Quantitative PCR Two-step real-time quantitative PCR (qPCR) was performed to characterize the expression of selected genes in PIE cells as described previously (16). TRIzol reagent (Invitrogen) was used for total RNA isolation from each PIE cell sample, and Quantitect RT kit (Qiagen, Tokyo, Japan) was used for the synthesis of all For the evaluation of viral infection, the RSV immunoplaque assay was performed (9). In brief, lung tissue was removed from mice, homogenized using a pellet pestle, and centrifuged at 2,600 × g for 10 min at 4◦C to clarify supernatant. Serial dilutions of lung tissue–clarified supernatants were added into fresh Vero April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 3 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. cells monolayers and incubated at 37◦C, 5% CO2 for 3 h. All samples were run in triplicate. After incubation and removal of supernatant, 1 mL of fresh DMEM medium containing 10% fetal bovine serum, 0.1% penicillin-streptomycin, and 0.001% ciprofloxacin was added to monolayers. When extensive syncytia developed, monolayers were fixed with 1 mL of ice-cold acetone:methanol (60:40). Then, wells were treated with primary RSV anti-F (clones 131-2A; Chemicon, Temecula, CA, United States) and anti-G{mouse monoclonal [8C5 (9B6)] to RSV glycoprotein; Abcam} antibodies for 2 h, followed by secondary horseradish peroxidase anti–mouse immunoglobulin antibody (anti–mouse immunoglobulin G, horseradish peroxidase–linked antibody #7076; Cell Signaling Technology, Danvers, MA, United States) for 1 h. Plates washed twice with PBS containing 0.5% Tween 20 (Sigma, St. Louis, MO, United States) after each antibody incubation step. Individual plaques were developed using a DAB substrate kit (ab64238; Abcam, Cambridge, United Kingdom) following the manufacturer’s specifications. Results were expressed as log10 PFU/g of lung. 10 min at 900 × g; the pellet was discarded, and the fluid was frozen at −70◦C for subsequent analyses. Albumin content was determined colorimetrically based on albumin binding to bromocresol green using an albumin diagnostic kit (Wiener Lab). Lactate dehydrogenase activity, expressed as units per liter of BAL fluid, was determined by using the Wiener reagents and procedures (Wiener Lab) (7). Lung wet-to-dry weight ratio was measured as previously described (7, 9). Wet-to-dry weight ratio was calculated as an index of intrapulmonary fluid accumulation, without correction for blood content. Statistical Analysis Statistical analyses were performed using GLM and REG procedures available in the SAS computer program (SAS, 1994). Comparisons between mean values were carried out using one-way analysis of variance and Fisher least significant difference test. For these analyses, P < 0.05 and P < 0.01 were considered significant. All experiments were carried out in compliance with the Guide for Care and Use of Laboratory Animals and approved by the Ethical Committee of Animal Care at CERELA, Argentina (protocol no. BIOT-CRL/14 and BIOT-CRL/11) (7, 8). Cytokine Concentrations Serum and BAL samples were obtained as described before (9). Briefly, blood samples were obtained by cardiac puncture under anesthesia. For BAL samples, the trachea was exposed surgically and intubated with a catheter. A small incision was made in the trachea, and two sequential lavages were performed in each mouse by injecting sterile PBS with 1% heparin. The recovered fluid was centrifuged for 10 min at 300 revolutions/min, and the supernatant was recovered. Intestinal fluid samples were obtained according to our previous publication (8). Briefly, the small intestine was flushed with 5 mL of PBS, and the fluid was centrifuged (10,000 × g, 4◦C 10 min) to separate particulate material. The serum, BAL and intestinal supernatant samples were kept frozen at −80◦C until use. Frontiers in Immunology | www.frontiersin.org Markers of Injury Lactate dehydrogenase (LDH) and aspartate aminotransferase (AST) activities were determined in the serum to evaluate general toxicity of poly(I:C) in mice challenged by the intraperitoneal injection. Blood samples were obtained through cardiac puncture under anesthesia. LDH and AST activities, expressed as units per liter of serum, were determined by measuring the formation of the reduced form of nicotinamide adenine dinucleotide using the Wiener reagents and procedures (Wiener Lab, Buenos Aires, Argentina) (8). Ethics Statement Animals were housed in plastic cages and environmental conditions were kept constant, in agreement with the standards for animal housing. Animal welfare was in charge of researchers and special stafftrained in animal care and handling at CERELA. The minimal number of animals required for an appropriate statistical analysis was calculated with the help of the Biostatistics Laboratory of CERELA. Tumor necrosis factor α (TNF-α), interleukin 6 (IL-6), IL- 10, IL-15, IFN-β, and IFN-γ concentrations in serum, intestinal fluid, and BAL samples were measured with commercially available enzyme-linked immunosorbent assay technique kits following the manufacturer’s recommendations (R&D Systems, Minneapolis, MN, United States). Animals were housed individually during the experiments. All efforts were made to minimize the number of animals and their suffering. Animal health and behavior were monitored twice a day. Animals were euthanized immediately after the time point was reached by using xylazine and ketamine. No signs of discomfort or pain and no deaths were observed before mice reached the endpoints. Modulation of TLR3-Induced Immunotranscriptome Changes in PIE Cells by Lactobacilli Previously, we analyzed the effect of L. rhamnosus CRL1505 and L. plantarum CRL1506 on the innate immune response of PIE cells after the challenge with poly(I:C) by using a transcriptomic approach (16). From that study, we were able to select a set of potential biomarkers that would allow us to efficiently select new immunobiotic strains with antiviral capabilities including IFNα, IFNβ, RIG1, TLR3, OAS1, RNASEL, MX2, A20, CXCL5, CCL4, IL-15, SELL, SELE, EPCAM, PTGS2, PLA2G4A, PTEGES, and PTGER4. Then, in order to validate this assumption, PIE cells were stimulated with different lactobacilli including Albumin content, a measure to quantitate increased permeability of the bronchoalveolar–capillarity barrier, and LDH activity, an indicator of general cytotoxicity, were determined in bronchoalveolar lavage (BAL) fluid. Bronchoalveolar lavage samples were obtained as described previously (7, 15). Briefly, the trachea was exposed and intubated with a catheter, and two sequential lavages were performed by injecting sterile PBS in each mouse lung. The recovered fluid was centrifuged for April 2020 | Volume 11 | Article 543 4 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. immunomodulatory (L. rhamnosus CRL1505, L. plantarum CRL1506, L. rhamnosus IBL07, and L. plantarum MPL16) (8, 16, 24, 25) and non-immunomodulatory (L. rhamnosus CRL576 and L. plantarum CRL681) strains and then challenged with poly(I:C). The expression of the biomarkers was then evaluated. When the expressions of type I IFNs, antiviral factors, and the negative regulator A20 were analyzed, a strain-dependent effect was observed (Figure 1, Supplementary Figure S1). The CRL1505, CRL1506, and MPL16 strains were highly efficient for increasing IFNα, MX2, OAS1, and TLR3 expression. In addition, L. rhamnosus CRL1505, and L. plantarum MPL16 were the lactobacilli with the highest capacity to increase the expression of IFNβ and RNASEL (Figure 1). Lactobacillus rhamnosus IBL07 was capable of enhancing the mRNA levels of IFNα, IFNβ, OAS1, TLR3, and RNASEL, but it was not as efficient as the CRL1505 and MPL16 strains. RIG-1 was enhanced by all the immunomodulatory strains CRL1505, CRL1506, IBL027, and MPL16, whereas the non-immunomodulatory strains CRL681 and CRL576 were not able to induce changes in the expression of type I IFNs or antiviral factors (Figure 1, Supplementary Figure S1). Lactobacillus rhamnosus CRL1505, L. plantarum CRL1506, and L. plantarum MPL16 significantly reduced the expression of A20 in poly(I:C)-challenged PIE cells, whereas no effect was observed for the other studied strains (Figure 1). Modulation of TLR3-Induced Immunotranscriptome Changes in PIE Cells by Lactobacilli The CRL1505 and MPL16 strains were highly efficient in enhancing the expression of CCL4, CXCL5, EPCAM, and SELE (Figure 2). The CRL1506 and IBL027 augmented the expression of CCL4, but the levels of this mRNA were significantly lower than in the CRL1505 or MPL16 groups (Figure 2). The four immunomodulatory strains increased SELL expression, being L. plantarum MPL16 the most efficient to achieve this effect. The non-immunomodulatory strains CRL681 and CRL576 were not able to induce changes in the expression of chemokines and adhesion molecules (Figure 2). Lactobacillus rhamnosus CRL1505, L. plantarum CRL1506, and L. plantarum MPL16 significantly reduced the expression of IL-15 in poly(I:C)- challenged PIE cells, whereas no effect was observed for the other studied strains (Figure 2). The expressions of PTGS2, PLA2G4A, and PTEGES were enhanced, and PTGER4 was reduced by the four immunomodulatory strains (Supplementary Figure S2). However, L. rhamnosus CRL1505 and L. plantarum MPL16 were more efficient than L. plantarum CRL1506 and L. rhamnosus IBL027 to increase the expression of PTGS2, PLA2G4A, and PTEGES and reduce PTGER4 in poly(I:C)-challenged PIE cells. The non-immunomodulatory strains CRL681 and CRL576 were not able to induce changes in the expression of the enzymes involved in prostaglandins biosynthesis (Supplementary Figure S2). FIGURE 1 | Expression of interferon (IFN)-β, antiviral factors (MX2 and RNASEL), and the negative regulator A20 genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C), analyzed by quantitative polymerase chain reaction. Porcine intestinal epithelial cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 1 | Expression of interferon (IFN)-β, antiviral factors (MX2 and RNASEL), and the negative regulator A20 genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C), analyzed by quantitative polymerase chain reaction. Porcine intestinal epithelial cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent experiments. Letters indicate significant differences (P < 0.05), a < b < c. Modulation of TLR3-Induced Immunotranscriptome Changes in PIE Cells by Lactobacilli April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 5 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. FIGURE 2 | Expression of chemokines [interleukin 15 (IL-15), CCL4, and CXCL5] and adhesion molecules (EPCAM, SELE, and SELL) genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C), analyzed by quantitative polymerase chain reaction. Porcine ntestinal epithelial cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 3 | Heat map analysis of the differentially regulated genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C). FIGURE 2 | Expression of chemokines [interleukin 15 (IL-15), CCL4, and CXCL5] and adhesion molecules (EPCAM, SELE, and SELL) genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C), analyzed by quantitative polymerase chain reaction. Porcine intestinal epithelial cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 2 | Expression of chemokines [interleukin 15 (IL-15), CCL4, and CXCL5] and adhesion molecules (EPCAM, SELE, and SELL) genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C), analyzed by quantitative polymerase chain reaction. Porcine intestinal epithelial cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 3 | Heat map analysis of the differentially regulated genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. Modulation of TLR3-Triggered Respiratory Immune Response in Mice by Lactobacilli y We have previously reported that orally administered L. rhamnosus CRL1505 is able to beneficially modulate the respiratory immune response triggered by TLR3 activation (7) and improve the resistance against influenza virus (10) and RSV (9). We also showed that the capacity of orally administered CRL1505 strain to modulate immunity in distal mucosal sites is not sheared by the immunomodulatory strain L. plantarum CRL1506. Then, taking into considerations the similarities found in this work between the CRL1505 and MPL16 strains, we were interested in finding out whether orally administered L. plantarum MPL16 was able to influence respiratory tract immunity. For this purpose, lactobacilli were given orally to different groups of mice, and the serum and respiratory cytokine profile was evaluated before (basal levels) and after the nasal challenge with poly(I:C). The changes in the profile of cytokines induced in the BAL (Supplementary Figure S6) and serum (Supplementary Figure S7) by lactobacilli indicated a clear strain-dependent effect. When the levels of the different cytokines were analyzed in BAL, it was shown that only L. rhamnosus CRL1505 and L. plantarum MPL16 enhanced the concentrations of IFN-β. In addition, CRL1505, MPL16 and IBL027 increased the basal levels of IFN-γ and IL-10. However, L. rhamnosus IBL027 was less efficient than the CRL1505 and MPL16 to induce the up-regulation of those cytokines (Supplementary Figure S6). The basal levels of respiratory TNF-α were increased by L. rhamnosus CRL1505, L. plantarum MPL16, and L. plantarum CRL1506, whereas the CRL681 and CRL576 treatments induced no changes in any of the cytokines evaluated in the respiratory tract (Supplementary Figure S6). We evaluated the biochemical markers LDH and AST in order to study the inflammatory damage after poly(I:C) administration (Figure 4). As we reported previously (8), the intraperitoneal challenge with poly(I:C) significantly increased LDH and AST activities in serum samples. The four immunomodulatory strains decreased serum LDH and AST, whereas the non- immunomodulatory strains CRL681 and CRL576 did not modify the levels of those markers (Figure 4). g In addition, the intraperitoneal administration of poly(I:C) significantly increased the levels of IFN-β; IFN-γ; the proinflammatory cytokines TNF-α, IL-6, and IL-15; and the regulatory cytokine IL-10 in the intestinal fluid (Figure 5). The four immunomodulatory strains were able to enhance the intestinal levels of IFN-β and IFN-γ after TLR3 activation. Modulation of TLR3-Induced Immunotranscriptome Changes in PIE Cells by Lactobacilli plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C). FIGURE 3 | Heat map analysis of the differentially regulated genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C). FIGURE 3 | Heat map analysis of the differentially regulated genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral molecular–associated pattern poly(I:C). with similar immunomodulatory properties in the context of TLR3 activation. As shown in Figure 3, the treatments with immunomodulatory lactobacilli plus poly(I:C) clustered We performed a cluster analysis to depict the transcriptomic patterns of differentially modulated genes between lactobacilli- treated and control PIE cells, in order to find the strains April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 6 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. Again, we performed a cluster analysis to depict the differentially modulated cytokines and injury markers between lactobacilli-treated and control mice, in order to find the strains with similar immunomodulatory properties in the in vivo mice model. As shown in Figure 6, a clear strain-dependent effect was observed in the ability of lactobacilli to modulate cytokines before and after poly(I:C) challenge. Interestingly, L. rhamnosus CRL1505 and L. plantarum MPL16 clustered together and separated from the other immunomodulatory strains L. plantarum CRL1506 and L. rhamnosus IBL027. These results allow us to speculate that L. plantarum MPL16 would have the ability to differentially regulate the intestinal innate immune response in poy(I:C)-challenged mice and protect against the inflammatory damage (Supplementary Figure S5) in a way comparable to that previously reported for L. rhamnosus CRL1505 (8). together and separated from the non-immunomodulatory strains. Moreover, L. rhamnosus CRL1505 and L. plantarum MPL16 were separated from L. plantarum CRL1506 and L. rhamnosus IBL027. These results indicate that L. plantarum MPL16 would have the ability to differentially regulate the immunotranscriptomic response in poy(I:C)-challenged PIE cells (Supplementary Figure S3) in a way comparable to that previously reported for L. rhamnosus CRL1505 (16, 20). Modulation of TLR3-Triggered Intestinal Immune Response in Mice by Lactobacilli Next, we were interested in finding out whether the differences in the immunomodulatory activities of CRL1505, MPL16, CRL1506, and IBL027 observed in PIE cells could be also found in an in vivo model. Then, lactobacilli were given orally to different groups of mice, and the intestinal cytokine profile was evaluated before (basal levels) and after the intraperitoneal challenge with poly(I:C). As observed in Supplementary Figure S4, a strain- dependent ability in the modulation of the basal levels of intestinal cytokines was detected. The four immunomodulatory strains increased the intestinal levels of IFN-β, IFN-γ, and IL-10; however, L. rhamnosus CRL1505 and L. plantarum MPL16 were more efficient than the other strains to augment IFN-γ and IL- 10. The non-immunomodulatory strains CRL681 and CRL576 did not modify the levels of intestinal IFN-β. Interestingly, L. plantarum CRL681 increased the levels of intestinal IFN-γ and IL-10 (Supplementary Figure S4). All the lactobacilli strains with the exception of L. rhamnosus CRL576 increased TNF-α, whereas the CRL1505, MPL16, IBL027, and CRL681 enhanced the intestinal levels of IL-6 (Supplementary Figure S4). The basal concentration of IL-15 was under the detection limits in all the experimental groups (data not shown). Modulation of TLR3-Triggered Respiratory Immune Response in Mice by Lactobacilli The CRL1505, MPL16, CRL1506, and IBL027 strain were also capable of significantly reducing the concentrations of TNF-α, IL-6, and IL-15 and increasing the levels of IL-10 in the intestine when compared to control mice (Figure 5). Of note, L. rhamnosus CRL1505 and L. plantarum MPL16 were more efficient than the other strains to reduce TNF-α and IL-15. The non-immunomodulatory strains CRL681 and CRL576 did not modify the levels of IFN-β, IFN-γ, TNF-α, IL-6, IL-15, or IL-10 when compared to controls (Figure 5). All the immunomodulatory strains were capable of enhancing the concentrations of IFN-β, IFN-γ, TNF-α, and IL-10 in serum when compared to controls. However, L. rhamnosus CRL1505 and L. plantarum MPL16 were more efficient than the other immunomodulatory strains to increase the basal levels of serum IFN-γ, TNF-α, and IL-10. Lactobacillus rhamnosus CRL576 and L. plantarum CRL681 did not induce significant April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org Frontiers in Immunology | www.frontiersin.org 7 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. FIGURE 4 | Levels of serum injury markers [lactate dehydrogenase (LDH) and aspartate aminotransferase (AST)] in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day for five consecutive days) and then challenged by the intraperitoneal route with 30 µg of the viral molecular–associated pattern poly(I:C). Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Serum injury markers were evaluated on day 2 after poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 4 | Levels of serum injury markers [lactate dehydrogenase (LDH) and aspartate aminotransferase (AST)] in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day for five consecutive days) and then challenged by the intraperitoneal route with 30 µg of the viral molecular–associated pattern poly(I:C). Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Serum injury markers were evaluated on day 2 after poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. Modulation of TLR3-Triggered Respiratory Immune Response in Mice by Lactobacilli FIGURE 5 | Levels of intestinal interferons (IFN-β and IFN-γ), proinflammatory cytokines [TNF-α and interleukin 6 (IL-6)] and IL-10 in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day for 5 consecutive days) and then challenged by the intraperitoneal route with 30 µg of the viral molecular–associated pattern poly(I:C). Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Immune factors were evaluated on day 2 after poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 5 | Levels of intestinal interferons (IFN-β and IFN-γ), proinflammatory cytokines [TNF-α and interleukin 6 (IL-6)] and IL-10 in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day for 5 consecutive days) and then challenged by the intraperitoneal route with 30 µg of the viral molecular–associated pattern poly(I:C). Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Immune factors were evaluated on day 2 after poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. levels of IFN-β, IFN-γ, TNF-α, and IL-10. Lactobacillus rhamnosus CRL1505 and L. plantarum MPL16 enhanced the levels of IFN-β and IFN-γ in both serum and BAL, whereas L. rhamnosus IBL027 was capable of increasing only BAL IFN-γ. The four immunomodulatory strains were capable of reducing serum and BAL levels of TNF-α, however; the CRL1505 and MPL16 strains were more effective to down-regulate this inflammatory cytokine in the respiratory tract (Figure 8). In addition, the four immunomodulatory strains increased IL-10 in serum (Supplementary Figure S8), but only L. rhamnosus CRL1505 and L. plantarum MPL16 enhanced the levels of this immunoregulatory cytokine in the respiratory tract (Figure 8). changes in serum cytokines when compared to controls (Supplementary Figure S7). We also evaluated the levels of the biochemical markers albumin and LDH in BAL as indicators of lung injury (7, 9, 10). Frontiers in Immunology | www.frontiersin.org Modulation of TLR3-Triggered Respiratory Immune Response in Mice by Lactobacilli The nasal challenge of mice with poly(I:C) significantly altered lungs function and induced lung injuries as demonstrated by the increased levels of BAL albumin and LDH (Figure 7), reflecting alteration of the alveolar–capillary barrier and local cellular damage. Only L. rhamnosus CRL1505 and L. plantarum MPL16 treatments were able to significantly reduce the levels of BAL LDH and albumin when compared to controls (Figure 7). We performed a cluster analysis to depict the differentially modulated serum and BAL cytokines and lung injury markers The nasal administration poly(I:C) significantly increased serum (Supplementary Figure S8) and respiratory (Figure 8) April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 8 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. FIGURE 6 | Heat map analysis of the differentially regulated intestinal immune factors and serum injury markers before (basal) and after poly(I:C) challenge. Mice were orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681, and then challenged by the intraperitoneal route with the viral molecular–associated pattern poly(I:C). FIGURE 6 | Heat map analysis of the differentially regulated intestinal immune factors and serum injury markers before (basal) and after poly(I:C) challenge. Mice were orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681, and then challenged by the intraperitoneal route with the viral molecular–associated pattern poly(I:C). FIGURE 7 | Levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day for five consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for 3 consecutive days. Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage injury markers were evaluated on day 2 after the last poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 6 | Heat map analysis of the differentially regulated intestinal immune factors and serum injury markers before (basal) and after poly(I:C) challenge. Mice were orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. Modulation of TLR3-Triggered Respiratory Immune Response in Mice by Lactobacilli rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681, and then challenged by the intraperitoneal route with the viral molecular–associated pattern poly(I:C). FIGURE 7 | Levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day for five consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for 3 consecutive days. Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage injury markers were evaluated on day 2 after the last poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 7 | Levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day for five consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for 3 consecutive days. Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage injury markers were evaluated on day 2 after the last poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. between lactobacilli-treated and control mice. As shown in Figure 9, a clear strain-dependent effect was observed in the ability of lactobacilli to modulate immunity in the respiratory tract. Of note, L. rhamnosus CRL1505 and L. plantarum MPL16 clustered together and separated from the other immunomodulatory strains. These results allow us to speculate that L. plantarum MPL16 would have the ability to differentially regulate the systemic and respiratory innate immune response in poy(I:C)-challenged mice and protect against the lung inflammatory damage (Supplementary Figure S9) in a way comparable to that previously reported for L. rhamnosus CRL1505 (7). April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org Frontiers in Immunology | www.frontiersin.org 9 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. Modulation of TLR3-Triggered Respiratory Immune Response in Mice by Lactobacilli plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day for 5 consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for three consecutive days. Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage immune factors were evaluated o day 2 after the last poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. The MPL16 and CRL1505 strains significantly increased the respiratory levels of TNF-α, being L. rhamnosus CRL1505 more effective than L. plantarum MPL16 to achieve this effect (Figure 11). Enhancement of the Resistance Against RSV Infection by L. plantarum MPL16 The MPL16 and CRL1505 strains significantly increased the respiratory levels of TNF-α, being L. rhamnosus CRL1505 more effective than L. plantarum MPL16 to achieve this effect (Figure 11). y p Finally, we aimed to test whether the oral administration of L. plantarum MPL16 was able to confer protection against a respiratory virus challenge. For this purpose, mice were fed the MPL16 strain and then nasally challenged with RSV. Lactobacillus rhamnosus CRL1505 and L. plantarum CRL1506 were used as positive and negative controls, respectively, according to our previous work demonstrating their different ability to protect against this viral pathogen (9). As shown in Figure 10, both L. rhamnosus CRL1505 and L. plantarum MPL16 were equally effective in reducing RSV lung titers, whereas the CRL1506 strain did not induce changes when compared to control mice. In addition, the MPL16 and CRL1505 strains significantly reduced the levels of the markers of lung damage, whereas L. plantarum CRL1506 was not able to achieve this effect (Figure 10). The levels of respiratory IFN- β, IFN-γ, TNF-α, and IL-10 were also evaluated after the challenge with RSV (Figure 11). Both L. rhamnosus CRL1505 and L. plantarum MPL16 enhanced the levels of IFN-β, IFN- γ, and IL-10 in BAL, whereas L. plantarum CRL1506 was not capable of increasing these cytokines when compared to controls. The CRL1506 strain did not induce changes in the levels of BAL TNF-α when compared to the control group. Modulation of TLR3-Triggered Respiratory Immune Response in Mice by Lactobacilli FIGURE 8 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day for 5 consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for three consecutive days. Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage immune factors were evaluated on day 2 after the last poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 8 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day for 5 consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for three consecutive days. Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage immune factors were evaluated on day 2 after the last poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 8 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse per day for 5 consecutive days) and then challenged by the nasal route with 250 µg of the viral molecular–associated pattern poly(I:C) for three consecutive days. Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Bronchoalveolar lavage immune factors were evaluated on day 2 after the last poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 8 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. DISCUSSION Moreover, MPL16-treated mice also showed higher levels of intestinal IFN-γ as observed by L. rhamnosus CRL1505. It was reported that infection with rotavirus in suckling mice induces a significant up-regulation of different types of IFNs in the intestine including IFN-γ by T cells and type I IFNs by dendritic cells (DCs) and IECs (30). Interferons binding to their cognate cell surface receptors activate positive feedback loops that amplify the expression of IFNs as well as more than 300 different IFN-stimulated genes (31). This IFNs release then efficiently amplify the expression of antiviral proteins targeting a variety of viral replication steps in uninfected bystander cells. It was also shown in in vitro studies that the addition of purified exogenous IFNs after rotavirus infection of human IECs does not significantly hamper around the world to reduce the incidence and severity of intestinal and pulmonary infections caused by viruses. Such selection, in addition to being efficient, should be performed using in vitro systems in order to minimize the use of experimental animals. Bifidobacterium infantis MCC12 (15) increased the expression of IFN-β and antiviral factors by reducing the expression of A20. The down-regulation of A20 gene expression in poly(I:C)- challenged PIE cells results in the improved activation of IRF3 and NF-κB signaling pathways, which increase the expression of not only IFN-α, IFN-β, MX2, OAS1, and RNASEL but in addition several other antiviral factors including OASL, MX1, OAS2, RNASE4, IFIT1, IFIT3, IFIT2, and IFIT5 (Supplementary Figure S3) (16). The in vivo experiments in mice performed here also demonstrated that L. plantarum MPL16 is able to enhance the intestinal levels of IFN-β. Moreover, MPL16-treated mice also showed higher levels of intestinal IFN-γ as observed by L. rhamnosus CRL1505. It was reported that infection with rotavirus in suckling mice induces a significant up-regulation of different types of IFNs in the intestine including IFN-γ by T cells and type I IFNs by dendritic cells (DCs) and IECs (30). Interferons binding to their cognate cell surface receptors activate positive feedback loops that amplify the expression of IFNs as well as more than 300 different IFN-stimulated genes (31). This IFNs release then efficiently amplify the expression of antiviral proteins targeting a variety of viral replication steps in uninfected bystander cells. DISCUSSION In middle- and low-income countries, intestinal and respiratory viral infections are the most common and deadly diseases in children (26–28). The use of functional foods such as those containing immunomodulatory probiotic lactobacilli has been proposed to stimulate the intestinal and the respiratory immune system, improving the outcome of viral diarrhea and pneumonia simultaneously. An example of the high probability of success of this strategy is the “Yogurito Nutritional Program” implemented in Argentina (2, 29). The program uses a probiotic yogurt containing the immunobiotic strain L. rhamnosus CRL1505 to prevent respiratory and gastrointestinal diseases by enhancing the immunological system of children attending public schools. Then, the selection of new immunobiotic strains that have different biotechnological properties but the same or better immunomodulatory capacities than L. rhamnosus CRL1505 could enhance the development of various types of functional foods that could be used April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 10 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. FIGURE 9 | Heat map analysis of the differentially regulated serum and bronchoalveolar lavage (BAL) immune factors and BAL injury markers before (basal) and after poly(I:C) challenge. Mice were orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and then challenged by the nasal route with the viral molecular–associated pattern poly(I:C) for three consecutive days. FIGURE 9 | Heat map analysis of the differentially regulated serum and bronchoalveolar lavage (BAL) immune factors and BAL injury markers before (basal) and after poly(I:C) challenge. Mice were orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and then challenged by the nasal route with the viral molecular–associated pattern poly(I:C) for three consecutive days. Bifidobacterium infantis MCC12 (15) increased the expression of IFN-β and antiviral factors by reducing the expression of A20. The down-regulation of A20 gene expression in poly(I:C)- challenged PIE cells results in the improved activation of IRF3 and NF-κB signaling pathways, which increase the expression of not only IFN-α, IFN-β, MX2, OAS1, and RNASEL but in addition several other antiviral factors including OASL, MX1, OAS2, RNASE4, IFIT1, IFIT3, IFIT2, and IFIT5 (Supplementary Figure S3) (16). The in vivo experiments in mice performed here also demonstrated that L. plantarum MPL16 is able to enhance the intestinal levels of IFN-β. Frontiers in Immunology | www.frontiersin.org DISCUSSION Respiratory syncytial virus titers and injury markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 10 | Lung respiratory syncytial virus (RSV) titers, lung wet-to-dry ratio, and levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse per day for five consecutive days) and then challenged by the nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. Respiratory syncytial virus titers and injury markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 10 | Lung respiratory syncytial virus (RSV) titers, lung wet-to-dry ratio, and levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse per day for five consecutive days) and then challenged by the nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. Respiratory syncytial virus titers and injury markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. viral replication; however, IFN treatment of cells prior to viral challenge is required to achieve an efficient restriction of rotavirus replication (32). intestinal mucosa can contribute to the local damage mediated by the inflammatory and oxidative stress (35). In addition, it was reported that purified dsRNA from rotavirus is able to induce severe intestinal damage in mice through the activation of TLR3 signaling pathway (36). Moreover, it was also demonstrated that the intraperitoneal administration of the synthetic dsRNA poly(I:C) to mice mimics the inflammatory intestinal immune response elicited by rotavirus and induce mucosal erosion, villous atrophy, intestinal wall attenuation, and diarrhea (8, 36, 37). Frontiers in Immunology | www.frontiersin.org DISCUSSION It was also shown in in vitro studies that the addition of purified exogenous IFNs after rotavirus infection of human IECs does not significantly hamper In this work, we demonstrated that the study of biomarkers expression in poly(I:C)-challenged PIE cells is a very effective tool for the selection of immunobiotics with the ability to modulate intestinal and respiratory antiviral immunity. The transcriptional profiling performed in vitro in poly(I:C)-challenged PIE cells in this work allowed us to select a new immunobiotic strain, L. plantarum MPL16, with the ability to stimulate in vivo the local (intestinal) and distal (respiratory) mucosal immune systems. Lactobacillus rhamnosus CRL1505 and L. plantarum MPL16 similarly modulated gene expression in poly(I:C)-challenged PIE cells inducing significant increases of both IFN-α and IFN-β and in the antiviral factors MX2, OAS1, and RNASEL. Our previous studies in PIE cells showed that rotavirus can be detected by this cell line through TLR3, inducing the expression of IFN-β and up- regulating the antiviral genes MxA and RNASEL (15). Moreover, those studies demonstrated that immunobiotics strains with the ability to enhance IFN-β, MxA, and RNASEL were also capable of reducing rotavirus replication. We demonstrated that immunobiotic strains such as L. rhamnosus CRL1505 (16) and April 2020 | Volume 11 | Article 543 11 Albarracin et al. Selection of Antiviral Immunobiotics in PIE Cells FIGURE 10 | Lung respiratory syncytial virus (RSV) titers, lung wet-to-dry ratio, and levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse per day for five consecutive days) and then challenged by the nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. Respiratory syncytial virus titers and injury markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 10 | Lung respiratory syncytial virus (RSV) titers, lung wet-to-dry ratio, and levels of bronchoalveolar lavage (BAL) injury markers [albumin and lactate dehydrogenase (LDH)] in mice orally treated with Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse per day for five consecutive days) and then challenged by the nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. DISCUSSION Immune markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. lymphocytes (IELs) and promote epithelial destruction through the RAE1–NKG2D interaction (Supplementary Figure S5) (38). We reported previously that L. rhamnosus CRL1505 is able to significantly reduce the expression of IL-15 and RAE1 in poly(I:C)-challenged PIE cells (16) and to reduce the levels of intestinal TNF-α and IL-15 and diminish the gut damage mediated by CD3+NK1.1+CD8αα+ IELs in mice after TLR3 activation (8). Here, we found that L. plantarum MPL16 is able to modulate the cytokine profile expression triggered by TLR3 activation in PIE cells as well as in mice intestinal mucosa, in a way similar to that observed for the CRL1505 strain. Then, it is tempting to speculate that L. plantarum MPL16 would have the ability to beneficially regulate intestinal inflammation in the context of TLR3 activation; however, more detailed studies using viral challenges are necessary to demonstrate this effect. Our results allow us to speculate that L. plantarum MPL16 would be capable to modulate IECs innate immune response, improve the resistance to rotavirus infection, and reduce the severity of inflammatory-mediated damage, as we have previously demonstrated in vitro (16, 20), in vivo (8), and in clinical trials (2, 29) for the CRL1505 strain. lymphocytes (IELs) and promote epithelial destruction through the RAE1–NKG2D interaction (Supplementary Figure S5) (38). We reported previously that L. rhamnosus CRL1505 is able to significantly reduce the expression of IL-15 and RAE1 in poly(I:C)-challenged PIE cells (16) and to reduce the levels of intestinal TNF-α and IL-15 and diminish the gut damage mediated by CD3+NK1.1+CD8αα+ IELs in mice after TLR3 activation (8). Here, we found that L. plantarum MPL16 is able to modulate the cytokine profile expression triggered by TLR3 activation in PIE cells as well as in mice intestinal mucosa, in a way similar to that observed for the CRL1505 strain. Then, it is tempting to speculate that L. plantarum MPL16 would have the ability to beneficially regulate intestinal inflammation in the context of TLR3 activation; however, more detailed studies using viral challenges are necessary to demonstrate this effect. We also demonstrated here that orally administered L. plantarum MPL16 is able to differentially modulate the respiratory antiviral immune response. DISCUSSION Interestingly, it was shown that the intestinal damage triggered by dsRNA-TRL3 interaction is mediated by the increased expression of IL-15 and retinoic acid early inducible 1 (RAE1) in IECs, which induce the activation of CD3+NK1.1+CD8αα+ intraepithelial The excessive activation of the inflammatory response or the failure in the mechanisms that control it significantly contributes to the injury of the infected tissue during viral infections. Intestinal epithelial cells produce a variety of cytokines and chemokines in response to the viral attack, including IL-6, IL-8, TNF-α, and granulocyte-macrophage colony-stimulating factor. The production of those inflammatory factors is important for the protection against the viral infection through their direct antiviral effects (33) or the recruitment and activation of phagocytes (34). However, infiltration of immune cells to the April 2020 | Volume 11 | Article 543 12 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. FIGURE 11 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse per day for five consecutive days) and then challenged by the nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. Immune markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 11 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse per day for five consecutive days) and then challenged by the nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. Immune markers were evaluated on day 2 after viral infection. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE 11 | Levels of bronchoalveolar lavage (BAL) interferons (IFN-β and IFN-γ), TNF-α, and interleukin 10 (IL-10) in mice orally treated with Lactobacillus rhamnosus CRL1505, Lactobacillus plantarum CRL1506, or L. plantarum MPL16 (108 cells/mouse per day for five consecutive days) and then challenged by the nasal route with RSV. Mice with no lactobacilli treatment and infected with RSV were used as controls. Frontiers in Immunology | www.frontiersin.org DISCUSSION plantarum MPL16 significantly reduced the respiratory injury markers after RSV challenge and differentially modulated the levels of respiratory proinflammatory and anti-inflammatory cytokines induced by the viral infection. Those effects were similar to the previously described for the CRL1505 strain (Supplementary Figure S9) (7, 9, 10, 39). different immune cell populations such as DCs and macrophages, as well as more detailed molecular and genomic characterization of both lactobacilli strains, could contribute significantly to the understanding of the molecular mechanisms involved in the ability of immunobiotics to stimulate distant mucosal sites such as the respiratory tract. Of note, the biotechnological properties of the two strains are different. Whereas L. rhamnosus CRL1505 has been used mainly in the development of dairy functional products (2, 44), the MPL16 strain has shown a remarkable ability to growth and ferment wakame (Undaria pinnatifida) that is the most popular and economically important edible brown algae in Asian countries (24, 45). Then, the different biotechnological properties of L. plantarum MPL16 could potentiate the development of non-dairy functional foods or feeds with the ability to improve antiviral immunity in the intestine and the respiratory tract. AUTHOR CONTRIBUTIONS JV and HK designed the study and manuscript writing. LA, VG-C, YI, and MI did the laboratory work. LA, MI, and YS did the statistical analysis. AG-C, HA, HT, JV, and HK contributed to data analysis and interpretation. All authors read and approved the manuscript. The results of this work confirm that new immunobiotics strains with the ability of stimulating both local and distal antiviral immune responses when orally administered can be efficiently selected by evaluating the expression of appropriate biomarkers of the transcriptomic profile of poly(I:C)-challenged PIE cells. The comparison of the transcriptomic patterns of differentially modulated genes in PIE cells treated with different lactobacilli allowed us to select the MPL16 strain that clustered together with the immunobiotic strain L. rhamnosus CRL1505, which has been proved to differentially modulate the intestinal and the respiratory antiviral responses and protect against enteric and respiratory viruses (2, 7, 9, 10). The in vivo studies performed here conclusively demonstrated that L. plantarum MPL16 modulated the profiles of intestinal, serum, and respiratory cytokines; reduced the inflammatory damage triggered by TLR3 activation in both the intestinal and respiratory mucosa; and improved the resistance to RSV infection. The immunological changes induced by L. plantarum MPL16 were not different from those previously reported for the CRL1505 strain. Further mechanistic studies evaluating comparatively the effects of CRL1505 and MPL16 strains in DISCUSSION We reported previously that the improvement of IFN-β production by CD11c+SiglecF+ alveolar macrophages and IFN-γ by CD3+CD4+ T cells is related to the ability of immunobiotic treatments to enhance resistance to respiratory virus (39, 40), in line with studies demonstrating that these immune cell populations are the main producer of IFNs during pulmonary viral infections (36, 37). The increased levels of respiratory IFN-γ and IFN-β found in L. plantarum April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org Frontiers in Immunology | www.frontiersin.org 13 Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. MPL16–treated mice correlated with the improved resistance of mice to RSV infection. On the other hand, we have extensively used a mice experimental model of lung inflammation based on the nasal administration of poly(I:C) in order to mimic the respiratory innate antiviral immune response triggered by RSV and to evaluate the beneficial effects of immunobiotic bacteria (7, 9, 10, 39, 40). The respiratory priming with the TLR3 agonist induces a marked inflammatory damage characterized by impaired alveolar–capillary barrier function and epithelial cell death as well as increased levels of TNF-α, IL-6, IL-8, and MCP-1. Prominent improvements of the IL-8, MIP-1, RANTES, MCP-1, TNF-α, and IL-6 have been reported in both experimentally RSV-infected mice and naturally RSV-infected children (41). The increase in the respiratory levels of those inflammatory factors, especially TNF-α, contributes to clearance of the virus during the early stages of RSV infection; however, their continued production exacerbates lung injuries during the late stages of infection (41, 42). Then, the appropriate regulation of the respiratory immune response is also essential for the protection of RSV-infected hosts. In this regard, it was demonstrated that IL-10 has a crucial role in regulating the severity of RSV infection (42, 43). The deficiency of IL-10 does not affect RSV load in lungs, but significantly enhances the inflammatory cells influx into the lung, promotes lung damage, and increases weight loss of infected mice (42, 43). The results of this work demonstrated that orally administered L. plantarum MPL16 is able to reduce the levels of inflammatory factors, increase IL-10, and significantly diminish the markers of lung tissue damage after the nasal administration of poly(I:C). Moreover, we also demonstrated here that orally administered L. ETHICS STATEMENT The animal study was reviewed and approved by the Ethical Committee of Animal Care CERELA-CONICET, Tucuman, Argentina. DATA AVAILABILITY STATEMENT The datasets generated for this study are available on request to the corresponding author. Frontiers in Immunology | www.frontiersin.org REFERENCES 8. Tada A, Zelaya H, Clua P, Salva S, Alvarez S, Kitazawa H, et al. Immunobiotic Lactobacillus strains reduce small intestinal injury induced by intraepithelial lymphocytes after Toll-like receptor 3 activation. Inflamm Res. (2016) 65:771– 83. doi: 10.1007/s00011-016-0957-7 1. WHO/UNICEF. Ending Preventable Deaths from Pneumonia and Diarrhoea by 2025. New York, NY: UNICEF. (2013). doi: ISBN978-92-415-0523-9 1. WHO/UNICEF. Ending Preventable Deaths from Pneumonia and Diarrhoea by 2025. New York, NY: UNICEF. (2013). doi: ISBN978-92-415-0523-9 9. Chiba E, Tomosada Y, Vizoso-Pinto MG, Salva S, Takahashi T, Tsukida K, et al. Immunobiotic Lactobacillus rhamnosus improves resistance of infant mice against respiratory syncytial virus infection. Int Immunopharmacol. (2013) 17:373–82. doi: 10.1016/j.intimp.2013.06.024 2. Villena J, Salva S, Núñez M, Corzo J, Tolaba R, Faedda J, et al. Probiotics for everyone! The novel immunobiotic Lactobacillus rhamnosus CRL1505 and the beginning of social probiotic programs in Argentina. Int J Biotechnol Wellness Ind. (2012) 1:189–98. doi: 10.6000/1927-3037/2012.01.03.05 3. Kitazawa H, Villena J. Modulation of respiratory TLR3-anti-viral response by probiotic microorganisms: lessons learned from Lactobacillus rhamnosus CRL1505. Front Immunol. (2014) 5:201. doi: 10.3389/fimmu.2014.00201 10. Zelaya H, Tsukida K, Chiba E, Marranzino G, Alvarez S, Kitazawa H, et al. Immunobiotic Lactobacilli reduce viral-associated pulmonary damage through the modulation of inflammation-coagulation interactions. Int Immunopharmacol. (2014) 19:161–73. doi: 10.1016/j.intimp.2013.12.020 4. Villena J, Vizoso-Pinto MG, Kitazawa H. Intestinal innate antiviral immunity and immunobiotics: beneficial effects against Rotavirus infection. Front Immunol. (2016) 7:563. doi: 10.3389/fimmu.2016.00563 11. Parashar UD, Gibson CJ, Bresee JS, Glass RI. Rotavirus and severe childhood diarrhea. Emerg Infect Dis. (2006) 12:304–6. doi: 10.3201/eid1202.050006 12. Greenberg HB, Estes MK. Rotaviruses: from pathogenesis to vaccination. Gastroenterology. (2009) 136:1939–51. doi: 10.1053/j.gastro.2009.02.076 5. Villena J, Oliveira MLS, Ferreira PCD, Salva S, Alvarez S. Lactic acid bacteria in the prevention of pneumococcal respiratory infection: future opportunities and challenges. Int Immunopharmacol. (2011) 11:1633–45. doi: 10.1016/j. intimp.2011.06.004 13. Villena J, Kitazawa H. Modulation of intestinal TLR4-inflammatory signaling pathways by probiotic microorganisms: lessons learned from Lactobacillus jensenii TL2937. Front Immunol. (2014) 4:512. doi: 10.3389/fimmu.2013. 00512 6. Zelaya H, Alvarez S, Kitazawa H, Villena J. Respiratory antiviral immunity and immunobiotics: beneficial effects on inflammation-coagulation interaction during influenza virus infection. Front Immunol. (2016) 7:633. doi: 10.3389/ fimmu.2016.00633 14. Hosoya S, Villena J, Shimazu T, Tohno M, Fujie H, Chiba E, et al. Immunobiotic lactic acid bacteria beneficially regulate immune response triggered by poly(I:C) in porcine intestinal epithelial cells. Vet Res. (2011) 42:111. doi: 10.1186/1297-9716-42-111 7. SUPPLEMENTARY MATERIAL FIGURE S5 | Global overview of the effect of L. rhamnosus CRL1505 and L. plantarum MPL16 on the intestinal inflammatory injury induced by poly(I:C) and mediated by the activation of CD3+NK1.1+CD8αα+ intraepithelial lymphocytes (IELs) that promote epithelial destruction through the RAE1–NKG2D interaction. Detailed immunomodulatory mechanisms were previously studied for L. rhamnosus CRL1505 (8). The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fimmu. 2020.00543/full#supplementary-material FIGURE S6 | Levels of bronco-alveolar lavages (BAL) interferons (IFN-β and IFN-γ), TNF-α and IL-10 in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse/day for five consecutive days). Mice with no lactobacilli treatment were used as controls. Immune factors were evaluated on day 6. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE S1 | Expression of interferon (IFN)-α, and antiviral factors (TLR3, RIG-1 and OAS1) genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarumC RL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral molecular associated pattern poly(I:C), analyzed by qPCR. PIE cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE S1 | Expression of interferon (IFN)-α, and antiviral factors (TLR3, RIG-1 and OAS1) genes in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarumC RL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral molecular associated pattern poly(I:C), analyzed by qPCR. PIE cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE S1 | Expression of interferon (IFN)-α, and antiviral factors (TLR3, RIG-1 and OAS1) genes in porcine intestinal epithelial (PIE) cells treated with FIGURE S7 | Levels of serum interferons (IFN-β and IFN-γ), TNF-α and IL-10 in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse/day for five consecutive days). Selection of Antiviral Immunobiotics in PIE Cells Selection of Antiviral Immunobiotics in PIE Cells Albarracin et al. SUPPLEMENTARY MATERIAL plantarum MPL16 and challenged with poly(I:C). Detailed immunomodulatory mechanisms were previously studied for L. rhamnosus CRL1505 (16, 20). FIGURE S4 | Levels of intestinal interferons (IFN-β and IFN-γ), proinflammatory cytokines (TNF-α and IL-6) and IL-10 in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse/day for five consecutive days). Mice with no lactobacilli treatment were used as controls. Immune factors were evaluated on day 6. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE S9 | Global overview of the effect of L. rhamnosus CRL1505 and L. plantarum MPL16 on the respiratory innate immune response triggered by poly(I:C). Detailed immunomodulatory mechanisms were previously studied for L. rhamnosus CRL1505 (7, 9). FIGURE S9 | Global overview of the effect of L. rhamnosus CRL1505 and L. plantarum MPL16 on the respiratory innate immune response triggered by poly(I:C). Detailed immunomodulatory mechanisms were previously studied for L. rhamnosus CRL1505 (7, 9). (108 cells/mouse/day for five consecutive days). Mice with no lactobacilli treatment were used as controls. Immune factors were evaluated on day 6. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. SUPPLEMENTARY MATERIAL Mice with no lactobacilli treatment were used as controls. Immune factors were evaluated on day 6. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE S2 | Expression of genes involved in prostaglandins biosynthesis (PTGS2, PLA2G4A, PTGER4 and PTGES) in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral molecular associated pattern poly(I:C), analyzed by qPCR. PIE cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE S2 | Expression of genes involved in prostaglandins biosynthesis (PTGS2, PLA2G4A, PTGER4 and PTGES) in porcine intestinal epithelial (PIE) cells treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 and challenged with the viral molecular associated pattern poly(I:C), analyzed by qPCR. PIE cells with no lactobacilli treatment and stimulated with poly(I:C) were used as controls. The results represent data from three independent experiments. Letters indicate significant differences (P < 0.05), a < b < c. FIGURE S8 | Levels of serum interferons (IFN-β and IFN-γ), TNF-α and IL-10 in mice orally treated with Lactobacillus rhamnosus CRL1505, L. rhamnosus IBL027, L. rhamnosus CRL576, Lactobacillus plantarum CRL1506, L. plantarum MPL16, or L. plantarum CRL681 (108 cells/mouse/day for five consecutive days), and then challenged by the nasal route with 250 µg of the viral molecular associated pattern poly(I:C) for three consecutive days. Mice with no lactobacilli treatment and challenged with poly(I:C) were used as controls. Serum immune factors were evaluated on day 2 after the last poly(:C) administration. The results represent data from three independent experiments (n = 6 per group). Letters indicate significant differences (P < 0.05), a < b < c. FIGURE S3 | Global overview of the signaling pathways and immune genes differentially regulated in PIE cells treated with L. rhamnosus CRL1505 or L. plantarum MPL16 and challenged with poly(I:C). Detailed immunomodulatory mechanisms were previously studied for L. rhamnosus CRL1505 (16, 20). FIGURE S3 | Global overview of the signaling pathways and immune genes differentially regulated in PIE cells treated with L. rhamnosus CRL1505 or L. FUNDING This study was supported by ANPCyT–FONCyT Grant PICT- 2016-0410 to JV, Grant-in-Aid for Scientific Research (A) (19H00965), and Open Partnership Joint Projects of JSPS Bilateral Joint Research Projects from the Japan Society for the Promotion of Science (JSPS) to HK. This research was also supported by grants from the project of NARO Bio-oriented Technology Research Advancement Institution (research program on the development of innovative technology, No. 01002A) to HK and JSPS Core-to-Core Program, A. Advanced Research Networks entitled Establishment of international agricultural immunology research-core for a quantum improvement in food safety. 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(2017) 7:37–61. doi: 10.1080/2157930X. 2017.1281206 Copyright © 2020 Albarracin, Garcia-Castillo, Masumizu, Indo, Islam, Suda, Garcia-Cancino, Aso, Takahashi, Kitazawa and Villena. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). REFERENCES The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Copyright © 2020 Albarracin, Garcia-Castillo, Masumizu, Indo, Islam, Suda, Garcia-Cancino, Aso, Takahashi, Kitazawa and Villena. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). 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Interferons and viruses: an evolutionary arms race of molecular interactions. Trends Immunol. (2015) 36:124–38. doi: 10.1016/j.it.2015.01.004 April 2020 | Volume 11 | Article 543 Frontiers in Immunology | www.frontiersin.org 16
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Genome-Based Approach Delivers Vaccine Candidates Against Pseudomonas aeruginosa
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Genome-Based Approach Delivers Vaccine Candidates Against Pseudomonas aeruginosa Irene Bianconi 1†, Beatriz Alcalá-Franco 1†, Maria Scarselli 2†, Mattia Dalsass 2,3, Scilla Buccato 2, Annalisa Colaprico 2, Sara Marchi 2, Vega Masignani 2‡ and Alessandra Bragonzi 1*‡ 1 Infection and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy, 2 GSK, Siena, Italy, 3 Dipartimento di Scienze Cliniche e Biologiche, Universitá degli Studi di Torino, Turin, Italy PA5340 combined with PA3526-MotY gave the maximum protection. Both proteins were surface exposed by immunofluorescence and triggered a specific immune response. Combination of these two protein antigens could represent a potential vaccine to prevent P. aeruginosa infection Edited by: Pedro A. Reche, Complutense University of Madrid, Spain Reviewed by: Paola Massari, Tufts University School of Medicine, United States Giampiero Pietrocola, University of Pavia, Italy *Correspondence: Alessandra Bragonzi bragonzi.alessandra@hsr.it †These authors have contributed equally to this work and share first authorship ‡These authors have contributed equally to this work and share senior authorship Specialty section: This article was submitted to Vaccines and Molecular Therapeutics, a section of the journal Frontiers in Immunology Specialty section: This article was submitted to Vaccines and Molecular Therapeutics, a section of the journal Frontiers in Immunology Keywords: Pseudomonas aeruginosa, reverse vaccinology, vaccine, respiratory infection, mouse model Received: 17 September 2018 Accepted: 06 December 2018 Published: 09 January 2019 ORIGINAL RESEARCH published: 09 January 2019 doi: 10.3389/fimmu.2018.03021 High incidence, severity and increasing antibiotic resistance characterize Pseudomonas aeruginosa infections, highlighting the need for new therapeutic options. Vaccination strategies to prevent or limit P. aeruginosa infections represent a rational approach to positively impact the clinical outcome of risk patients; nevertheless this bacterium remains a challenging vaccine target. To identify novel vaccine candidates, we started from the genome sequence analysis of the P. aeruginosa reference strain PAO1 exploring the reverse vaccinology approach integrated with additional bioinformatic tools. The bioinformatic approaches resulted in the selection of 52 potential antigens. These vaccine candidates were conserved in P. aeruginosa genomes from different origin and among strains isolated longitudinally from cystic fibrosis patients. To assess the immune-protection of single or antigens combination against P. aeruginosa infection, a vaccination protocol was established in murine model of acute respiratory infection. Combinations of selected candidates, rather than single antigens, effectively controlled P. aeruginosa infection in the in vivo model of murine pneumonia. Five combinations were capable of significantly increase survival rate among challenged mice and all included PA5340, a hypothetical protein exclusively present in P. aeruginosa. PA5340 combined with PA3526-MotY gave the maximum protection. Both proteins were surface exposed by immunofluorescence and triggered a specific immune response. Combination of these two protein antigens could represent a potential vaccine to prevent P. aeruginosa infection High incidence, severity and increasing antibiotic resistance characterize Pseudomonas aeruginosa infections, highlighting the need for new therapeutic options. Vaccination strategies to prevent or limit P. aeruginosa infections represent a rational approach to positively impact the clinical outcome of risk patients; nevertheless this bacterium remains a challenging vaccine target. To identify novel vaccine candidates, we started from the genome sequence analysis of the P. aeruginosa reference strain PAO1 exploring the reverse vaccinology approach integrated with additional bioinformatic tools. The bioinformatic approaches resulted in the selection of 52 potential antigens. These vaccine candidates were conserved in P. aeruginosa genomes from different origin and among strains isolated longitudinally from cystic fibrosis patients. To assess the immune-protection of single or antigens combination against P. aeruginosa infection, a vaccination protocol was established in murine model of acute respiratory infection. Combinations of selected candidates, rather than single antigens, effectively controlled P. aeruginosa infection in the in vivo model of murine pneumonia. Five combinations were capable of significantly increase survival rate among challenged mice and all included PA5340, a hypothetical protein exclusively present in P. aeruginosa. Keywords: Pseudomonas aeruginosa, reverse vaccinology, vaccine, respiratory infection, mouse model P. aeruginosa Antigens Selection by Genome-Wide Screening P. aeruginosa Antigens Selection by Genome-Wide Screening Genome Wide Screening Among 5,570 open reading frames (ORFs) encoded by P. aeruginosa PAO1 strain (5), we predicted a total of 2,430 surface or membrane-associated proteins by using high throughput bioinformatics localization prediction tools. In particular, subcellular localization was predicted by PsortB software. In the case of predicted non-cytoplasmic polypeptides the presence of signal peptide and localization of cleavage site were predicted with SignalP. N-terminal signatures predictive of lipoproteins were identified by using the LipoP server and putative transmembrane regions were predicted with Tmpred. Among them, 307 were classified as outer membrane proteins or lipoproteins, 583 as periplasmic proteins, and 2,109 as inner membrane proteins. The remaining 2,562 ORFs were predicted to encode cytoplasmic proteins. Since inner membrane proteins are barely exposed on the outside of the bacterium and are difficult to express and purify, all were discarded from selection except those with sequence similarities to known virulence factors or extracellular proteins from other bacterial pathogens. The final selection totaled 950 ORFs (Figure 1). In recent years, remarkable progress has been made in the identification of P. aeruginosa virulence factors and their variations among different infection processes. It has been more accurately recognized that P. aeruginosa is an antigenically variable microorganism that adapts easily to different growth conditions and escapes host immune recognition. The high variability of the proteins among different P. aeruginosa strains and within the same strain, grown in diverse environmental conditions, may represent a serious obstacle to the development of a globally effective anti–P. aeruginosa vaccine (10). So far, P. aeruginosa vaccine candidates have been found by classical approach—by identifying more abundant surface proteins and oligosaccharides or by selecting specific virulence factors, according to their relevance in the disease outcome. Integrated genomics and proteomics approaches have been recently used to predict vaccine candidates against P. aeruginosa (11). Although several vaccine formulations have been tested clinically, none has been licensed (10, 12). P. aeruginosa vaccines tested so far in humans consisted of antigens targeting single rather than multiple virulence mechanisms—OprF- OprI fusion (13), flagella (14), O antigen-conjugated vaccines (15), high molecular weight alginate (16). Further success in P. aeruginosa vaccine development may require a different approach, including bacterial genome evaluation to identify novel antigen combinations potentially addressing multiple virulence mechanisms, such as initial bacterial colonization, immune evasion, colony aggregation and cytotoxicity. Citation: Bianconi I, Alcalá-Franco B, Scarselli M, Dalsass M, Buccato S, Colaprico A, Marchi S, Masignani V and Bragonzi A (2019) Genome-Based Approach Delivers Vaccine Candidates Against Pseudomonas aeruginosa. Front. Immunol. 9:3021. doi: 10.3389/fimmu.2018.03021 P. aeruginosa infections are among the most severe public health issues. This opportunistic bacterium belongs to the multi-drug resistant (MDR) ESKAPE pathogens, along with Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter. According to data from Centers for Disease Control, P. aeruginosa is responsible for millions of infections each year in the community, 10–15% of all healthcare-associated infections, with more than 300,000 cases annually in the EU, USA and Japan (1). Patients hospitalized in intensive care units (ICU) run a high risk of acquiring P. aeruginosa as they January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org P. aeruginosa Vaccine Bianconi et al. may develop ventilator-associated pneumonia (VAP) and sepsis (2–4). Other risk groups are patients with a compromised immune system, either from immunosuppressive therapies and underlying diseases such as cancer, AIDS or hereditary cystic fibrosis (CF). This high prevalence is partly due to the vast arsenal of virulence factors that facilitates acute infections and the propensity of P. aeruginosa to form highly structured biofilm communities that cause chronic infections (5). serogroup B Neisseria meningitidis (MenB), now licensed in several countries worldwide (19, 20). Reverse vaccinology aims at identifying surface exposed proteins, ideally playing a relevant role in pathogenesis, which can serve as targets of the host immune system. This approach has not yet been implemented for P. aeruginosa. In this study, reverse vaccinology approach was combined with advanced genomic technologies to select new protein antigens against P. aeruginosa. We report that combinations of selected candidates, more than single antigens, effectively control P. aeruginosa infections in a mouse model of acute pneumonia. Taking the severity of the illness into account, current treatment guidelines for the management of bacterial infection recommend single antibiotic or combination therapy. Despite the wide arsenal of drugs for P. aeruginosa infections available on the market, inefficacy of these treatments is commonplace. Resistance rapidly emerges, usually linked to intrinsic bacterial resistance mechanisms, development of new antibiotic resistance, and/or limited penetration of antibiotics into biofilms (3, 6). Development of antibiotics with a novel mode of action and/or alternative therapies remains an urgent need for patients. Citation: Antibacterial agents launched in recent decades were modifications of existing molecules; the development of entirely new classes of antibiotics has been largely abandoned (7). Immunotherapy for preventing pulmonary infection has also been tested (8), but clinical efficacy has been disappointing (9, 10). Immunization strategies do not cover P. aeruginosa infection in healthcare practices. Frontiers in Immunology | www.frontiersin.org P. aeruginosa Antigens Selection by Genome-Wide Screening g In a second step of prioritization and to avoid selection of potential self-antigens, we excluded all proteins containing domains with sequence similarity (E-value>1e-10) to human and/or mouse proteins, narrowing the selection to 824 proteins. To identify proteins more directly related to P. aeruginosa pathogenesis and fitness, and to avoid widespread bacterial housekeeping factors, sequence comparison to E. coli K12 whole proteome was performed; we discarded P. aeruginosa proteins sharing more than 40% sequence similarity over at least 70% of the length of the E. coli counterpart. As sequence conservation is highly desirable for broad-spectrum vaccine candidates, a comparative analysis was performed with the genome sequence of seven published P. aeruginosa strains including clinical isolates of different origins (PA14, LESB58, PA7, 2192, C3719, PACS2, RP73); only proteins belonging to the core genome were kept. Candidate selection was also refined by removing short peptides (<150 aa long), eventually leading to a total of 531 hits. To further prioritize the candidates and reduce the final pool of proteins for experimental testing, a PSI-Blast analysis was conducted; results were manually curated to remove any residual protein putatively involved in intermediate metabolism, DNA synthesis, translation During the past two decades, reverse vaccinology has revolutionized the approach to vaccine research (17, 18), ultimately leading to the development of new generation vaccines based on antigens previously unrecognized by other approaches. One is 4CMenB, the first universal vaccine against January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org 2 Bianconi et al. P. aeruginosa Vaccine FIGURE 1 | Schematic workflow of antigen selection in silico. The complete PAO1 proteome has been analyzed as described in the text. Distribution of ORFs according to predicted sub-cellular localization using Psort is summarized at the top. Below, selection steps succession is reported, indicating the number of candidates (hits) selected after each step. C: cytoplasm; IN: inner membrane; P: periplasm; OM: outer membrane. FIGURE 1 | Schematic workflow of antigen selection in silico. The complete PAO1 proteome has been analyzed as described in the text. Distribution of ORFs according to predicted sub-cellular localization using Psort is summarized at the top. Below, selection steps succession is reported, indicating the number of candidates (hits) selected after each step. C: cytoplasm; IN: inner membrane; P: periplasm; OM: outer membrane. challenged intratracheally (i.t.) with 5 × 106 CFU/lung of P. P. aeruginosa Antigens Selection by Genome-Wide Screening aeruginosa reference strain PAO1 and monitored twice a day for 1 week for health parameters indicative of animal wellness. In this model, all mice immunized with Alum alone (negative control group) consistently showed symptoms of a severe clinical disease and died within 48 h, whereas mice immunized with whole cell inactivated PAO1 bacteria were consistently protected by homologous challenge in a dose-dependent manner. Of the 30 antigens tested, 10 showed a modest increase in survival compared to the negative control (up to 20% at day 5) and were investigated further (Table 1 and Figure 2). The other 20 proteins tested did not differ substantially from the negative control and were discarded (data not shown). Survival of mice vaccinated with OprF-OprI fusion (10.7%) was comparable to that observed by vaccination with the 10 selected proteins. and repair, protein synthesis and transport, and more generally, in any cellular process confined to the bacterial cytoplasm. The final pool of in silico selected candidates included 52 antigens— 31 proteins of known and 21 of unknown functions (Figure 1 and Table S1). The presence of well-known virulence factors like ExoA and ExoT, as well as relevant outer membrane proteins like OprF and OprH in the final list of candidates confirmed the reliability of the selection strategy. When tested against an extended panel of 104 P. aeruginosa complete genomes, it emerged that all candidates share a mean identity/coverage ratio ranging from 0.78 to 1.00 (Figure S1) confirming that a vast proportion of epitopes potentially presented by each candidate to the immune system is conserved across the natural P. aeruginosa population. Frontiers in Immunology | www.frontiersin.org Evaluation of Combinations of Candidates in a Murine Model of Pneumonia C57Bl/6 male mice were challenged with PAO1 (5*106 cfu) 2 weeks after last vaccination with ten single antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1 heat-inactivated (h.i.) groups (positive control). An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at FIGURE 2 | Survival curves of groups of mice immunized with single antigens selected as vaccine candidates. C57Bl/6 male mice were challenged with PAO1 (5*106 cfu) 2 weeks after last vaccination with ten single antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1 heat-inactivated (h.i.) groups (positive control). An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at least two/three independent experiments (n = 16–40). Results are represented as Kaplan–Meier survival curves and analyzed by the Mantel-Cox test against negative control group. N refers to the number of animals. FIGURE 2 | Survival curves of groups of mice immunized with single antigens selected as vaccine candidates. C57Bl/6 male mice were challenged with PAO1 (5*106 cfu) 2 weeks after last vaccination with ten single antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1 heat-inactivated (h.i.) groups (positive control). An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at least two/three independent experiments (n = 16–40). Results are represented as Kaplan–Meier survival curves and analyzed by the Mantel-Cox test against negative control group. N refers to the number of animals. PA0328-AaaA, PA2407-FpvC, PA3526-MotY, PA4082- CupB5, PA4765-OmlA, PA5047, and PA5340) the antisera obtained immunizing with recombinant proteins were used in Western Blot and immunofluorescence microscopy (Table 1 and Figure 4). All the antisera recognized the recombinant proteins, the homologous P. aeruginosa strain PAO1 and the heterologous clinical isolate MDR-RP73; this demonstrates the capacity of the vaccine candidates to induce specific antibody production that can recognize the native proteins. PA0328-AaaA, PA2407-FpvC, PA3526-MotY, PA4082- CupB5, PA4765-OmlA, PA5047, and PA5340) the antisera obtained immunizing with recombinant proteins were used in Western Blot and immunofluorescence microscopy (Table 1 and Figure 4). All the antisera recognized the recombinant proteins, the homologous P. aeruginosa strain PAO1 and the heterologous clinical isolate MDR-RP73; this demonstrates the capacity of the vaccine candidates to induce specific antibody production that can recognize the native proteins. Evaluation of Combinations of Candidates in a Murine Model of Pneumonia 0.015, and 0.015, respectively) and mean survival time (one-way ANOVA p-value < 0.01) when compared with negative controls (Figure 3 and Figure S2). The best antigens combination was PA5340+PA3526-MotY, with survival increased up to 50%. Three combinations described above, PA5340+PA3526-motY, PA5340+PA5112-EstA, and PA5340+PA0328-AaaA, increased survival significantly when compared with OprF-OprI (Mantel- Cox test 0.0091, 0.0009, and 0.012, respectively). Interestingly, an increase in survival rate was also observed (though not statistically significant) when OprF-OprI was combined with PA5340, going from 10.7% of the fusion alone to 40% when tested in combination (Mantel-Cox test 0.058). To determine whether the selected proteins were effectively expressed and exposed on the surface of bacterial cells, a double immunofluorescence was carried out with the murine antisera and a specific antibody for P. aeruginosa anti-cell wall as initial characterization. Co-localization of the two signals could suggest that the proteins were present at the bacterial cell surface. As expected, sera of naïve mice did not recognize antigens while antisera of mice immunized with whole cell inactivated Evaluation of Combinations of Candidates in a Murine Model of Pneumonia Of 52 P. aeruginosa vaccine candidates (Table S1), 30 ORFs (57.7%) were successfully expressed in E. coli BL21 as His-tag fusions. OprF-OprI fusion, designed according to the known construct used in the recent clinical trial (21), was included in this study. Ability of these antigens to protect against P. aeruginosa infection was tested in a mouse model of acute pneumonia (22). C57Bl/6 mice were immunized intraperitoneally (i.p.) with 10 ug of each protein formulated with aluminum hydroxide (Alum) as adjuvant at 0, 21, and 35 days. At day 50, mice were In order to increase the survival rate of vaccinated mice, proteins conferring higher protection were pooled in group of two, and 22 combinations were tested. Five combinations, all containing the antigen candidate PA5340, were the most promising (PA5340+PA1178-OprH, PA5340+PA3526-motY, PA5340+PA5112-EstA, PA5340+PA5047, PA5340+PA0328- AaaA). These combinations showed a significant increase in both survival curves (Mantel-Cox test p < 0.0002, 0.0019, 0.0027, January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org 3 P. aeruginosa Vaccine Bianconi et al. TABLE 1 | Top line vaccine candidates of P. aeruginosa. Locus_tag Protein annotation Surface exposure(a) Antigenic potential(b) Sequence conservation(c) Sequence conservation(d) PA0328 arginine-specific autotransporter AaaA Yes Yes 99.3% ± 0.2% 99.2% ± 0.3% PA1178 outer membrane protein OprH precursor Yes Yes 100% ± 0% 99.9% ± 0.2% PA1248 outer membrane protein AprF precursor Yes Yes 99.6%± 0.3% 99.2%± 4.6% PA2407 putative adhesion protein FpvC Yes Yes 100% ± 0% 98.3% ± 10.4% PA3526 outer membrane protein precursor MotY Yes Yes 99.1% ± 0.8% 99.7% ± 0.5% PA4082 adhesive protein CupB5 Yes Yes 98.8% ± 0.5% 98.5% ± 2.9% PA4765 outer membrane lipoprotein OmlA precursor Yes Yes 99.7% ± 0.3% 98.9% ± 7.2% PA5047 putative Zn-dependent protease Yes Yes 99.9% ± 0.1% 99.2% ± 7.1% PA5112 esterase EstA No Yes 99.8% ± 0.2% 99.1% ± 7.2% PA5340 hypothetical protein Yes Yes 98.8% ± 0.3% 99.2% ± 0.3% aSurface exposure suggested by immunofluorescence microscopy co-localization (see text). bEvaluated by Western Blot against recombinant proteins, P. aeruginosa strain PAO1 and clinical isolate MDR-RP73 (see text). Sequence conservation expressed as mean percentage of amino acid identity ± standard deviation calculated among a collection of CF clinical strains cand on the public collection of 104 completed P. aeruginosa genomes available in GenBank (see text)d. TABLE 1 | Top line vaccine candidates of P. aeruginosa. Evaluation of Combinations of Candidates in a Murine Model of Pneumonia | p g Locus_tag Protein annotation Surface exposure(a) Antigenic potential(b) Sequence conservation(c) Sequence conservation(d) PA0328 arginine-specific autotransporter AaaA Yes Yes 99.3% ± 0.2% 99.2% ± 0.3% PA1178 outer membrane protein OprH precursor Yes Yes 100% ± 0% 99.9% ± 0.2% PA1248 outer membrane protein AprF precursor Yes Yes 99.6%± 0.3% 99.2%± 4.6% PA2407 putative adhesion protein FpvC Yes Yes 100% ± 0% 98.3% ± 10.4% PA3526 outer membrane protein precursor MotY Yes Yes 99.1% ± 0.8% 99.7% ± 0.5% PA4082 adhesive protein CupB5 Yes Yes 98.8% ± 0.5% 98.5% ± 2.9% PA4765 outer membrane lipoprotein OmlA precursor Yes Yes 99.7% ± 0.3% 98.9% ± 7.2% PA5047 putative Zn-dependent protease Yes Yes 99.9% ± 0.1% 99.2% ± 7.1% PA5112 esterase EstA No Yes 99.8% ± 0.2% 99.1% ± 7.2% PA5340 hypothetical protein Yes Yes 98.8% ± 0.3% 99.2% ± 0.3% aSurface exposure suggested by immunofluorescence microscopy co-localization (see text). bEvaluated by Western Blot against recombinant proteins, P. aeruginosa strain PAO1 and clinical isolate MDR-RP73 (see text). Sequence conservation expressed as mean percentage of amino acid identity ± standard deviation calculated among a collection of CF clinical strains cand on the public collection of 104 completed P. aeruginosa genomes available in GenBank (see text)d. FIGURE 2 | Survival curves of groups of mice immunized with single antigens selected as vaccine candidates. C57Bl/6 male mice were challenged with PAO1 (5*106 cfu) 2 weeks after last vaccination with ten single antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1 heat-inactivated (h.i.) groups (positive control). An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at least two/three independent experiments (n = 16–40). Results are represented as Kaplan–Meier survival curves and analyzed by the Mantel-Cox test against negative control group. N refers to the number of animals. Surface exposure(a) Antigenic potential(b) Sequence conservation(c) Sequence conservation(d) aSurface exposure suggested by immunofluorescence microscopy co-localization (see text). bEvaluated by Western Blot against recombinant proteins, P. aeruginosa strain PAO1 and clinical isolate MDR-RP73 (see text). Sequence conservation expressed as mean percentage of amino acid identity ± standard deviation calculated among a collection of CF clinical strains cand on the public collection of 104 completed P. aeruginosa genomes available in GenBank (see text)d. FIGURE 2 | Survival curves of groups of mice immunized with single antigens selected as vaccine candidates. January 2019 | Volume 9 | Article 3021 In vitro Characterization of Selected Antigens To characterize antigenic potential and cellular localization of selected antigens (PA1178-OprH, PA1248-AprF, PA5112-EstA, January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org 4 P. aeruginosa Vaccine Bianconi et al. FIGURE 3 | Survival curves of groups of mice immunized with combined antigens selected as vaccine candidates. C57Bl/6 male mice were challenged with PAO1 (5*106 cfu) 2 weeks after last vaccination with combined antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1 heat inactivated (h.i.) groups (positive control). An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at least two/three independent experiments (n = 17–33). Results are represented as Kaplan–Meier survival curves and analyzed by the Mantel-Cox test against negative control group: *p < 0.05, **p < 0.01, ***p < 0.001. N refers to the number of animals. FIGURE 4 | Cellular localization of vaccine candidates PA5340 and PA3526-MotY and controls by immunofluorescence microscopy. Immunofluorescence staining with confocal microscopy shows the localization of antigens (green) (A–E) and the PAO1 cell wall (red) (F–J). For antigens localization the antisera of naïve mice (A) or immunized with PA3526-MotY (B), PA5340 (C), OprF-OprI (D) or heat inactivated PAO1 (E) were used. Merged images show the co-localization of the two signals (yellow) (K–O) suggesting that proteins could be surface exposed. Detailed co-localization of antigens of interest is shown in the magnification (L, M, N). FIGURE 3 | Survival curves of groups of mice immunized with combined antigens selected as vaccine candidates. C57Bl/6 male mice were challenged with PAO1 (5*106 cfu) 2 weeks after last vaccination with combined antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1 heat inactivated (h.i.) groups (positive control). An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at least two/three independent experiments (n = 17–33). Results are represented as Kaplan–Meier survival curves and analyzed by the Mantel-Cox test against negative control group: *p < 0.05, **p < 0.01, ***p < 0.001. N refers to the number of animals. FIGURE 3 | Survival curves of groups of mice immunized with combined antigens selected as vaccine candidates. C57Bl/6 male mice were challenged with PAO1 (5*106 cfu) 2 weeks after last vaccination with combined antigens. Comparisons were performed with mice immunized with Alum alone (negative control) and PAO1 heat inactivated (h.i.) groups (positive control). In vitro Characterization of Selected Antigens An additional group was vaccinated with OprF-OprI, tested as clinical vaccine candidate. Data were pooled from at least two/three independent experiments (n = 17–33). Results are represented as Kaplan–Meier survival curves and analyzed by the Mantel-Cox test against negative control group: *p < 0.05, **p < 0.01, ***p < 0.001. N refers to the number of animals. FIGURE 4 | Cellular localization of vaccine candidates PA5340 and PA3526-MotY and controls by immunofluorescence microscopy. Immunofluorescence staining with confocal microscopy shows the localization of antigens (green) (A–E) and the PAO1 cell wall (red) (F–J). For antigens localization the antisera of naïve mice (A) or immunized with PA3526-MotY (B), PA5340 (C), OprF-OprI (D) or heat inactivated PAO1 (E) were used. Merged images show the co-localization of the two signals (yellow) (K–O) suggesting that proteins could be surface exposed. Detailed co-localization of antigens of interest is shown in the magnification (L, M, N). FIGURE 4 | Cellular localization of vaccine candidates PA5340 and PA3526-MotY and controls by immunofluorescence microscopy. Immunofluorescence staining with confocal microscopy shows the localization of antigens (green) (A–E) and the PAO1 cell wall (red) (F–J). For antigens localization the antisera of naïve mice (A) or immunized with PA3526-MotY (B), PA5340 (C), OprF-OprI (D) or heat inactivated PAO1 (E) were used. Merged images show the co-localization of the two signals (yellow) (K–O) suggesting that proteins could be surface exposed. Detailed co-localization of antigens of interest is shown in the magnification (L, M, N). PAO1 showed a strong co-localization signal. The same staining was performed with the antisera of mice immunized with the 10 selected antigens and OprF-OprI (Table 1 and Figure 4). According to immunofluorescence microscopy results, all the selected antigens co-localized with the cell surface antibody, with the exception of PA5112-EstA. In particular, a similar January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org 5 P. aeruginosa Vaccine Bianconi et al. co-localization pattern was observed with antisera of PA5340, PA3526-MotY, and OprF-OprI. co-localization pattern was observed with antisera of PA5340, PA3526-MotY, and OprF-OprI. is an antigenically variable microorganism and can undergo phenotypic variation under changing environmental conditions, such as the airways in CF patients (23). In particular, the adaptation process generates unique lineages of P. aeruginosa pathogenic variants that differ systematically from environmentally-acquired strains and can escape immune recognition (24). In vitro Characterization of Selected Antigens We considered this question worthy of investigation and expanded the comparative sequence analysis on a collection of 19 clinical strains isolated from CF patients at the onset of infection and after years of chronic colonization (25, 26). The selected antigens were conserved among CF clinical isolates indicating that the corresponding genes were not under positive selection and these antigens could be useful for targeting both the initial infecting strains and those promoting progression toward chronic infection. Considering the epidemiology of P. aeruginosa infection, both environmental-to-host and patient- to-patient transmission have been described and it appears likely that highly conserved not-adapted antigens might have superior clinical relevance. Frontiers in Immunology | www.frontiersin.org Conservation Profile of Selected Antigens Among a Collection of CF Clinical Isolates Conservation of the selected antigens among P. aeruginosa genomes was initially considered as selection criteria and the candidates were checked in the ensemble of publicly available complete genome sequences. Moreover, we investigated the sequence conservation of the ten most protective antigens in a collection of 19 clinical strains isolated from CF patients at the onset of infection and after years of chronic colonization (Figure S3). Full-length sequences of the ten genes were obtained by PCR from most of the 19 strains. Nucleotide sequences were translated into the amino acid (aa) sequences and compared with PAO1 protein sequence. Overall, identity conservation levels were higher than 98% (Table 1 and Table S2), confirming a strong potential of these proteins to induce effective and cross- protective immunity among P. aeruginosa circulating strains. Previous studies that tested P. aeruginosa antigens provided valuable information on the feasibility of vaccination but were limited by either the number of antigens tested and by redundancy in their selection (10). Abundant surface proteins and oligosaccharides, particular virulence factors have been previously considered. However, none of these started from a large scale screening, performed comparative analysis of the P. aeruginosa protein antigens and tested in animal models for preclinical studies. Our screening identified 52 antigens distributed as having known (31) or unknown functions (21). The presence of known virulence factors in the final list of candidates confirmed the reliability of this general selection strategy. We identified a number of proteins, like ExoA and ExoT, as well as relevant outer membrane proteins, like OprF, and OprH, already shown to be required for virulence in P. aeruginosa. The outer membrane protein PscC precursor (PA1716) identified in this study was previously identified by integrated genomics and proteomics approach (11). Furthermore, different proteins involved in the chaperone/usher pathways (CupA-E) were identified in this study and Rashid et al. (11). Half of the candidate antigens identified belonged to the functional category of hypothetical, unknown, and unclassified genes (21 genes, 35.8% of the total), suggesting that there is still a large proportion of potentially immunogenic antigens to be discovered within the unexplored part of the P. aeruginosa. DISCUSSION As an alternative treatment to antibiotics, immunotherapy should represent an option to prevent MDR infections by P. aeruginosa. A universal protein-based vaccine against P. aeruginosa remains a critical unmet medical need. To identify possible antigens suitable for the development of a P. aeruginosa vaccine, we explored the reverse vaccinology approach integrated with additional genomic and bioinformatic approaches. This strategy involved an initial screening of target antigens on the basis of their putative cellular localization; this identified a large number of proteins (2,430 ORFs) predicted to be surface or membrane-associated to various extents. Note that the P. aeruginosa genome is larger than most sequenced bacteria (6.3 Mb) (5) and the resulting high number of 5,570 predicted protein encoding genes challenges this approach. Hence, additional criteria were included for antigen selection, with the aim of reducing the pool to a reasonable number of candidates and to rationalize the subsequent experimental steps. In particular, the absence of sequence similarity to proteins encoded by the commensal E. coli K12 strain, as well as sequence similarity to proteins involved in primary house-keeping and cell metabolism functions have been used as cutting edge to narrow the shortlist of antigens. Proteins displaying epitopes very similar to those present in widely-conserved proteins from human and mouse origin were also excluded as candidates, as they might be poorly immunogenic and have a high probability of behaving as self-antigens. Several diverse animal models have been used in preclinical studies of vaccination to evaluate in vivo protection against P. aeruginosa infection. Mouse models, including burned animals, those with immunocompromised intraperitoneal infection, or with acute pneumonia, have primarily been used in the past. These models were used for preclinical evaluation of candidates like the flagellum, the alginate exopolysaccharide conjugated to tetanus toxoid, polysaccharides, and outer membrane protein such as OprF and OprI. (27–31). Based on our previous experience we consider respiratory infection in immunocompetent mice a highly robust and appropriate model to predict efficacy of vaccine candidates for further clinical testing in patients at risk of respiratory infection, Considering that large sequence diversity characterizes P. aeruginosa genome, we tested the conservation of selected candidates among the P. aeruginosa complete genome sequences available on public databases. This analysis confirmed the presence and conservation of selected antigens in the core genome. Further genomic analysis considered sequence intraclonal diversity of selected antigens in clinical strains isolated from CF patients. It is recognized that P. Gene Sequencing Reference strain PAO1 (5) and 19 P. aeruginosa clinical strains isolated from CF patients attending the Medizinische Hochschule Hannover and described previously (25, 26) were used to sequence the genes of vaccine candidates. PCR genes amplification was carried out using the list of primers detailed in the Supplementary Information. Cloning, Expression, and Purification of P. aeruginosa Recombinant Proteins Polypeptides antigens from P. aeruginosa PAO1 were PCR- amplified using specific oligonucleotides and P. aeruginosa chromosomal DNA as templates. Resulting PCR products were cloned in pET15b (Novagen) using the PIPE method (44). To express cloned proteins, BL21(DE3)T1r clones containing pET15b constructs were grown in LB medium containing 100 µg/ml Ampicilin at 37◦C until OD600 = 0.5. Protein expression was induced by adding 1 mM IPTG and growing at the same temperature for additional 3 hrs. Conventional protein extractions and SDS-Page were performed to check protein expression. Western Blot was used to confirm proper expression of tested P. aeruginosa antigens. Protein purification has been performed as reported previously (45). Briefly, bacteria cells undergone to mechanical or chemical lysis and recombinant polypeptides were recovered from crude cell extracts by immobilized-metal ion affinity chromatography (IMAC) using His MultiTrapTM HP 50 mL NiSepharose High-Performance 96 well-vacuum plates (GE Healthcare). Polypeptides expressed as insoluble inclusion bodies were solubilized in 50 mM Tris–HCl elution buffer, pH 8.8 containing 8 MUrea, 1 mM TCEP-HCl, and 250 mM imidazole. Renaturation was performed by dialysis in 50 mM NaH2PO4, pH 8.8 containing 10% (v/v) glycerol, 0.5 M arginine, 5.0 mM of reduced glutathione, 0.5 mM of oxidized glutathione in the presence of 4, 2, or 0 M urea. Protein concentration was determined using the Micro BCA protein assay reagent kit (Pierce). Protein purity was checked by SDS-PAGE CRITERION XT Precast Gel (Biorad) followed by Coomassie blue staining. DISCUSSION In this work, C57Bl/6 mice succumbed following infection with high dose of PAO1 virulent P. aeruginosa strain. Vaccination with whole cell inactivated P. aeruginosa induced an effective immunological response as demonstrated by full protection of the mice. Conversely, mice immunization with the adjuvant alone did not provide any protection as all mice showed severe clinical disease. These data strongly support the choice of this robust mouse model for screening and selecting the best vaccine candidates. Vaccination with the ten purified soluble proteins on our short list demonstrated distinct disease phenotypes, ranging from severe pneumonia to partial protection from a lethal dose of P. aeruginosa infection. We report that half of the vaccine candidates screened in this study were more effective when compared to OprF/OprI. It is worth noting that OprF/OprI fusion was one of the treatments evaluated in clinical trial although clinical efficacy has been disappointing (36). Given that vaccines containing several antigens have been shown to confer better protection than those containing only one antigen (20, 37), we decided to assess antigen combinations. Selection of antigens to combine was made from the shortlist of the ten most promising antigens and tested to further increase the vaccine efficacy and survival rate in murine models. This systematic screening identified five combinations, capable of significantly increasing the survival rate among challenged mice. All combinations included PA5340, a hypothetical protein exclusively present in P. aeruginosa. The maximum proportion of mice protected against challenge was 50%, achieved with PA5340 combined with PA3526-MotY. These two proteins were capable of triggering a specific immune response and initial characterization could indicate surface exposure. Nevertheless, as their function is still undetermined, it is unlikely that either protein would ever be selected by a traditional approach. Overall this study confirms the capability of reverse vaccinology to give new impetus in the research of vaccines against P. aeruginosa infection through the rapid identification of novel vaccine candidates. analysis against the sequenced genomes was performed using BLAST. The amino acid sequence of strain PAO1 was aligned against the protein translation of complete genome sequences with BLASTp (BLAST 2.2.26+) and against the genome of human and mouse with VAXGEN (http://www.violinet.org/ vaxgen/index.php) (43). Ethics Statement Animal studies adhered to the Italian Ministry of Health guidelines for the use and care of experimental animals (protocol #443). The use of the clinical data is in line with study no. 3739 that was approved by the Ethics Commission of Hannover Medical School. DISCUSSION aeruginosa January 2019 | Volume 9 | Article 3021 6 P. aeruginosa Vaccine Bianconi et al. such as VAP or CF (22, 32). The mouse model of acute infection has been extensively employed as the standard in P. aeruginosa pathogenesis and efficacy studies (24, 33–35). In this work, C57Bl/6 mice succumbed following infection with high dose of PAO1 virulent P. aeruginosa strain. Vaccination with whole cell inactivated P. aeruginosa induced an effective immunological response as demonstrated by full protection of the mice. Conversely, mice immunization with the adjuvant alone did not provide any protection as all mice showed severe clinical disease. These data strongly support the choice of this robust mouse model for screening and selecting the best vaccine candidates. Vaccination with the ten purified soluble proteins on our short list demonstrated distinct disease phenotypes, ranging from severe pneumonia to partial protection from a lethal dose of P. aeruginosa infection. We report that half of the vaccine candidates screened in this study were more effective when compared to OprF/OprI. It is worth noting that OprF/OprI fusion was one of the treatments evaluated in clinical trial although clinical efficacy has been disappointing (36). Given that vaccines containing several antigens have been shown to confer better protection than those containing only one antigen (20, 37), we decided to assess antigen combinations. Selection of antigens to combine was made from the shortlist of the ten most promising antigens and tested to further increase the vaccine efficacy and survival rate in murine models. This systematic screening identified five combinations, capable of significantly increasing the survival rate among challenged mice. All combinations included PA5340, a hypothetical protein exclusively present in P. aeruginosa. The maximum proportion of mice protected against challenge was 50%, achieved with PA5340 combined with PA3526-MotY. These two proteins were capable of triggering a specific immune response and initial characterization could indicate surface exposure. Nevertheless, as their function is still undetermined, it is unlikely that either protein would ever be selected by a traditional approach. Overall this study confirms the capability of reverse vaccinology to give new impetus in the research of vaccines against P. aeruginosa infection through the rapid identification of novel vaccine candidates. such as VAP or CF (22, 32). The mouse model of acute infection has been extensively employed as the standard in P. aeruginosa pathogenesis and efficacy studies (24, 33–35). FUNDING whole cell heat-inactivated PAO1 strain at different doses (105- 107 CFU). To obtain the antisera, mice were bled at day - 1, 34, and 49. At day 50, mice were challenged with 5 × 106 CFU of P. aeruginosa PAO1 strain by acute infection and monitored every 12 h for general wellness as detailed in the Supplementary Information. This work was sponsored by Novartis Vaccines and Diagnostics Srl; in March 2015 the Novartis non-influenza Vaccines business was acquired by the GSK group of companies. The sponsor was involved in all stages of the study conduct and analysis. This work was supported in part by the Italian Cystic Fibrosis Research Foundation (FFC#08/2006 and FFC#10/2009) to AB with the contribution of the Delegazioni FFC of Como, Catania, Vittoria Ragusa, Latina and LIFC onlus Associazione regionale siciliana, in memory of Simone. This work was sponsored by Novartis Vaccines and Diagnostics Srl; in March 2015 the Novartis non-influenza Vaccines business was acquired by the GSK group of companies. The sponsor was involved in all stages of the study conduct and analysis. This work was supported in part by the Italian Cystic Fibrosis Research Foundation (FFC#08/2006 and FFC#10/2009) to AB with the contribution of the Delegazioni FFC of Como, Catania, Vittoria Ragusa, Latina and LIFC onlus Associazione regionale siciliana, in memory of Simone. SUPPLEMENTARY MATERIAL AB and VM: conceiving and designing the experiments. BA-F, IB, MS, SB, SM, AC, and MD: performing experiments. AB, AB and VM: conceiving and designing the experiments. BA-F, IB, MS, SB, SM, AC, and MD: performing experiments. AB, BA-F, IB, MS, and VM: analyzing data and interpretation of the experiments results. AB, BA-F, IB, MS, and VM: writing the manuscript. IB, MS, SB, SM, AC, and MD: performing experiments. AB, BA-F, IB, MS, and VM: analyzing data and interpretation of the experiments results. AB, BA-F, IB, MS, and VM: writing the manuscript. The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fimmu. 2018.03021/full#supplementary-material Western Blot and Immunofluorescence Microscopy Specific antisera from immunized mice were used to confirm protein expression by Western Blot and surface localization of antigens by immunofluorescence as detailed in the Supplementary Information. In silico Analysis and Computational Tools In silico Analysis and Computational Tools PSORTb (38) was used for the subcellular localization prediction, SingnalP (39) to predict the SPs and their probable cleavage site in secreted proteins, the TatP prediction server to predict the presence of bacterial Tat signal peptides (40), LipoP (41) predict lipoproteins, TMpred to predict transmembrane segments (42). C57BL/6NCrlBR 5 week-old male mice (Charles River) were immunized i.p. at day 0, 21, and 35 with recombinant proteins formulated with Alum, either individually or as a combination of proteins. The formulations were optimized for pH and osmolarity. Each antigen was used at 10 µg/formulation/animal. The final concentration of Alum was 2 mg/ml in 10 mM histidine buffer (pH 6.5). Negative control mice were immunized with Alum alone, while positive control mice were boosted with To check presence and conservation of vaccine candidates in other P. aeruginosa genomes, comparative protein sequence January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org 7 P. aeruginosa Vaccine Bianconi et al. REFERENCES 13. Westritschnig K, Hochreiter R, Wallner G, Firbas C, Schwameis M, Jilma B, et al. A randomized, placebo-controlled phase I study assessing the safety and immunogenicity of a Pseudomonas aeruginosa hybrid outer membrane protein OprF/I vaccine (IC43) in healthy volunteers. Hum Vacc Immunother. (2014) 10:170–83. doi: 10.4161/hv.26565 1. Boucher HW, Talbot GH, Bradley JS, Edwards JE, Gilbert D, Rice LB, et al. Bad bugs, no drugs: no ESKAPE! an update from the infectious diseases society of america. Clin Infect Dis. (2009) 48:1–12. doi: 10.1086/595011 1. Boucher HW, Talbot GH, Bradley JS, Edwards JE, Gilbert D, Rice LB, et al. 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Vaccination against Pseudomonas aeruginosa pneumonia in immunocompromised mice. Clin Vacc Immunol. (2008) 15:367–75. doi: 10.1128/CVI.00419-07 Conflict of Interest Statement: MS, SM, SB, AC, and VM were employees of Novartis Vaccines and Diagnostics Srl at the time of the study (now part of the GSK group of companies). They are now employees of the GSK group of companies. MD is a student at the University of Torino and participated in a post graduate studentship program at GSK. 32. Kukavica-Ibrulj I, Facchini M, Cigana C, Levesque RC, Bragonzi A. Assessing Pseudomonas aeruginosa virulence and the host response using murine models of acute and chronic lung infection. Methods Molecul Biol. (2014) 1149:757–71. doi: 10.1007/978-1-4939-0473-0_58 The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. 33. Lore NI, Cigana C, De Fino I, Riva C, Juhas M, Schwager S, et al. Cystic fibrosis-niche adaptation of Pseudomonas aeruginosa reduces virulence in multiple infection hosts. PLoS ONE (2012) 7:e35648. doi: 10.1371/journal.pone.0035648 34. De Simone M, Spagnuolo L, Lorè NI, Rossi G, Cigana C, De Fino I, et al. Host genetic background influences the response to the opportunistic Pseudomonas aeruginosa infection altering cell-mediated immunity and bacterial replication. PLoS ONE (2014) 9:e106873. doi: 10.1371/journal.pone.01 06873 Copyright © 2019 Bianconi, Alcalá-Franco, Scarselli, Dalsass, Buccato, Colaprico, Marchi, Masignani and Bragonzi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). Frontiers in Immunology | www.frontiersin.org January 2019 | Volume 9 | Article 3021 35. Cigana C, Bernardini F, Facchini M, Alcalá-Franco B, Riva C, De Fino I, et al. Efficacy of the novel antibiotic POL7001 in preclinical models REFERENCES The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. 35. Cigana C, Bernardini F, Facchini M, Alcalá-Franco B, Riva C, De Fino I, et al. Efficacy of the novel antibiotic POL7001 in preclinical models January 2019 | Volume 9 | Article 3021 Frontiers in Immunology | www.frontiersin.org 9
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* S. Robinson sarah.robinson09@gmail.com Pastoralists as Optimal Foragers? Reoccupation and Site Selection in the Deserts of Post-Soviet Kazakhstan S. Robinson1,2 & C. Kerven1 & R. Behnke1 & K. Kushenov3 & E. J. Milner-Gulland1,4 Published online: 24 December 2016 # The Author(s) 2016. This article is published with open access at Springerlink.com Published online: 24 December 2016 # The Author(s) 2016. This article is published with open access at Springerlink.com Published online: 24 December 2016 # The Author(s) 2016. This article is published with open access at Springerlink.com Keywords Pastoralism . Kazakhstan . Optimal foraging . Central place . Grazing Keywords Pastoralism . Kazakhstan . Optimal foraging . Central place . Grazing Abstract This study explores the drivers of site selection amongst livestock owners under conditions of increasing an- imal numbers following a low point in the 1990s. Our major goal was to understand whether livestock owners are acting as ‘optimal foragers,’ targeting areas of highest forage availabil- ity as they colonise previously empty areas. The results pre- sented here suggest that they do not. Initially, distance from home settlement was the dominant determinant of site occu- pancy, with closer sites occupied earlier regardless of other characteristics. Some owners remained on depleted vegetation for longer than would be predicted under conditions of opti- mal foraging, indicating that distance-related costs constrained resource matching. In the latter period, increases in livestock wealth encouraged the occupation of distant sites exhibiting higher vegetation density and water quality, but some owners still occupied highly depleted sites. Improved transport and water supply infrastructure are needed if pasto- ralists are to optimise resource use across the landscape. 1 Imperial College London, Silwood Park, Buckhurst Road, Ascot, Berks SL5 7PY, UK Hum Ecol (2017) 45:5–21 DOI 10.1007/s10745-016-9870-5 Hum Ecol (2017) 45:5–21 DOI 10.1007/s10745-016-9870-5 2 La Cousteille, 09400 Saurat, France 3 Centre for Livestock and Veterinary Research, Dzhandosov Str. 31, Almaty, Kazakhstan 480035 Electronic supplementary material The online version of this article (doi:10.1007/s10745-016-9870-5) contains supplementary material, which is available to authorized users. 4 Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK Introduction The country as a whole suffers from a winter feed deficit (Government of Kazakhstan and the World Bank 2004) and in semi-arid areas, which comprise 80% of total grazing lands, supplementary fodder cannot be grown. It is here, particularly in key wintering areas, that optimal use of natural forage resources would bring the greatest benefits. In an equilibrium environment, in which all patches are occupied, optimal foraging results in an ideal free distribution, which predicts that the ratio of individuals between two for- aging sites will match the ratio of resources in those two sites, i.e., a matching of foragers and forage resources at the popu- lation level (Fretwell and Lucas 1970). Our study area is one of the most important winter pastures in Kazakhstan and access brings significant economic benefits through a reduction in winter feed costs (Milner-Gulland et al. 2006). It is thus important to understand what is driving, and constraining, the process of re-colonization of such key pas- tures. The second issue of interest is pasture degradation. This is of concern in Central Asia because, although animal num- bers are now low, mobility has declined, leading to high local- ised stocking densities with severe impact on soils and vege- tation (Alimaev et al. 2008; Robinson 2016). We are interested in whether our human agents respond to forage-related factors as the primary criteria for site selection in order to maximise food intake of their livestock, or whether other factors such as water availability or costs related to dis- tance from the home settlement may be more important. The predictions of MVT are thus a convenient starting point from which to explore the factors determining herder decision making. Most grazing systems in Kazakhstan contain multiple veg- etation types, and these pastures are used at different seasons (Zhambakin 1995). Our study system is no exception and consists of four seasonal pasture types located in different ecological zones. Large scale movement between these zones is discussed elsewhere (Kerven et al. 2016a; Robinson et al. 2016). Here, we investigate the re-colonization of well-based sites by livestock herds and flocks across a large desert pasture in one of these ecological zones. The case constitutes an un- usual natural experiment in which people retracted from a fully exploited landscape to concentrate their herds around settlements and then moved back out over a period of decades. Introduction 1 Operation of the classic marginal value theorem. As animals forage for longer in a given patch, intake is assumed to increase at a decreasing rate. The optimal residency time within a patch (Topt) depends on the relationship between travel time and the slope of the curve relating intake to foraging time. Where the marginal rate of intake (slope of the curve) is equal to the slope of the cost (travel time between patches), it is optimal for the animal to leave for the next patch. Therefore when travel time is longer (t2) the animal should spend longer in the patch than when the travel time is shorter (t1). Adapted from Charnov (1976) and De Boer and Prins (1989) Fig. 1 Operation of the classic marginal value theorem. As animals forage for longer in a given patch, intake is assumed to increase at a decreasing rate. The optimal residency time within a patch (Topt) depends on the relationship between travel time and the slope of the curve relating intake to foraging time. Where the marginal rate of intake (slope of the curve) is equal to the slope of the cost (travel time between patches), it is optimal for the animal to leave for the next patch. Therefore when travel time is longer (t2) the animal should spend longer in the patch than when the travel time is shorter (t1). Adapted from Charnov (1976) and De Boer and Prins (1989) Introduction Extensive pastoralism is a key livelihood strategy in arid re- gions where few other forms of land use are feasible (Thornton et al. 2002), and relies on the ability of animals to exploit spatial and temporal variation in forage resources, traditionally achieved through mobile animal husbandry systems. Yet glob- ally livestock mobility is declining (Boone et al. 2008; Dong et al. 2011). Kazakhstan is no exception to this pattern and has suffered from a particularly extreme contraction in livestock mobility (Kerven et al. 2006) following the collapse of collec- tive agriculture and a 75% drop in livestock numbers associated with the end of the Soviet Union (Behnke 2003). Economic conditions remain difficult - the costs of moving livestock now fall on individual households rather than large institutions, lead- ing to loss of economies of scale. Although Kazakhstan has the fifth largest grazing resource in the world (FAOSTAT 2015), it has been estimated that only around 30% is currently grazed (Tazhibaev et al. 2014). Livestock numbers are now increasing. By 2013, total live- stock numbers (in sheep equivalents) had risen by 80% from their nadir in 1999, but still lie at around half of Soviet-era inventories (FAOSTAT 2015). Whilst this increase has not, in the few cases documented, brought about a full scale return to mobile pastoralism, some migrations including high mountain pastures have persisted (Ferret 2013) and re-colonization of abandoned desert areas is now occurring in some areas (Kerven et al. 2016b). This is not the result of state planning, but of individual decision making. The Kazakh government would like to encourage the increased use of remote pastures, seeing these as a way of reducing supplementary feed costs * S. Robinson sarah.robinson09@gmail.com 4 Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK Hum Ecol (2017) 45:5–21 6 compared to landscape averages). They will leave a patch when the marginal intake rate drops to the average for the habitat. This type of individual-level behaviour is captured in the marginal value theorem (MVT) (Charnov 1976): The richer the occupied patch is compared to the landscape aver- age, the longer the patch residence time should be. (Ministry of Agriculture of the Republic of Kazakhstan 2013, 2014). Introduction One similar case is the re-colonisation of the Longone flood plain in Cameroon, in which re-flooding resulted in an influx of pastoralists, shown by the authors to occur roughly in pro- portion to increasing grazing resources (Scholte et al. 2006). In our case, pastoralists started from a central point (the set- tlement) from which they re-colonized sites defined by avail- ability of water. We explore the factors underlying site selec- tion by observing this re-colonization experiment over time. Given the related phenomena of pasture overstocking and abandonment that have been documented in Kazakhstan, we are particularly interested in whether herders are ‘optimal for- agers’, targeting areas of highest forage availability as they colonise previously empty areas. In order to understand this process, we use theoretical frameworks from the discipline of ecology, which predict how animals make decisions about where to forage in space and time. Bringing costs of accessing patches into the equation changes the predicted behaviour. For example, as travel time between patches increases, the time spent in a given patch is predicted to increase, because the costs of leaving are higher (Fig. 1). Such a relationship would suggest that greater travel times would lead to higher depletion of resources as animals spend more time on patches. If there are two sites, one rich in resources but further from the settlement, and one poor in resources but close by, then two processes are operating to retain animals in the richer patch. As well as higher travel costs leading to higher residency time, the higher initial resource density means that the site will be grazed for longer before it reaches the landscape average resource density. Thus, Fig. 1 Operation of the classic marginal value theorem. As animals forage for longer in a given patch, intake is assumed to increase at a decreasing rate. The optimal residency time within a patch (Topt) depends on the relationship between travel time and the slope of the curve relating intake to foraging time. Where the marginal rate of intake (slope of the curve) is equal to the slope of the cost (travel time between patches), it is optimal for the animal to leave for the next patch. Therefore when travel time is longer (t2) the animal should spend longer in the patch than when the travel time is shorter (t1). Adapted from Charnov (1976) and De Boer and Prins (1989) Fig. Optimal Foraging It has long been suggested that animals primarily concerned with maximising their food intake will behave as ‘optimal foragers’. In an unconstrained space within which resources are patchy and travel costs are negligible, these foragers will firstly target resources of highest value (resource density Hum Ecol (2017) 45:5–21 7 and Prins 1989; Moritz et al. 2010; Rozen-Rechels et al. 2015; Shrader et al. 2012; Turner et al. 2005). and Prins 1989; Moritz et al. 2010; Rozen-Rechels et al. 2015; Shrader et al. 2012; Turner et al. 2005). foragers will travel further (bear more costs) for a richer patch where higher initial resource density compensates for the time travelled. This study looks at site selection, not around camps, but between multiple camps distributed at distances of several kilometres across a total area of hundreds of square kilometres, from year to year. We are therefore working at the landscape scale – or Bailey et al.’s Bhome range.^ Only a few studies have mapped or modelled herded livestock at this scale (Boone et al. 2008; McCarthy 2007; Moritz et al. 2014; Scholte et al. 2006; Vanselow et al. 2012). Some (e.g., Moritz et al. 2014) have tested for an ideal free distribution (IFD) at the population level. An IFD would be the predicted result of optimal foraging decisions by individual herders in an equilibrium environment where the ratio of gain to cost is the same across the landscape. But our expanding non- equilibrium environment means that an ideal free distribution is unlikely to have yet emerged. We are thus able to expose the processes involved in site selection over time in a way that is not possible in an equilibrium situation. Our study system is also rather different to those to which MVT is usually applied. Its defining characteristics are common in pastoral systems but rarely appear in ecological studies on wildlife (Table 1). This theory helps us to investigate resource depletion and the potential for pasture degradation, because resource density metrics (e.g., vegetation cover or NDVI) are often easier to measure than forage intake by animals. For this reason, giving up density (GUD), the resource density at which animals leave a patch, is often measured in studies of MVTas an indicator of the intake rate at which patches are left (Brown 1988). Scale Bailey et al. (1996) have defined six scales at which the for- aging behaviour of large herbivores may be studied: bite, feeding station, patch, feeding site, camp, and home range. Most studies of herbivore foraging behaviour are conducted at the lower end of this scale, over minutes or hours and between individual patches of vegetation. It is only recently that studies have been up-scaled to look at seasonal move- ments over landscapes (Owen-Smith et al. 2010). Most stud- ies at the upper end concern wildlife; few deal with herded livestock under human decision making. Optimal Foraging For this study, GUD is interesting in itself – because very low GUDs may be associated with high levels of resource depletion and pasture degradation. Key MVT predictions have been validated in domestic animals under controlled conditions (Laca et al. 1993; Utsumi et al. 2009), in wildlife (Astrom et al. 1990; Fryxell et al. 2004), and in human foragers such as hunter gatherers and fruit pickers (Hill et al. 1987; Wolfe 2013). As predicted, these authors found that total intake rate decreases as distance between patches increases, and that patch residence time in- creases with patch size (a proxy for resource density) and with distance between patches. De Boer and Prins (1989) found that these predictions also partially apply to herders of domes- tic animals, reporting that herders tended to evaluate trade-offs between travel time, foraging time and intake over the day rather than on a patch by patch basis, but that over a longer time frame they did optimise forage intake within the limits imposed by the need to return to the homestead at night. This brings up issues of spatial and temporal scale and of the effects of having a central place to return to, both of which we will now examine in more detail. The study area has an added advantage in that ‘patches’ are self-defining. MVT describes resource consumption in a patchy habitat. But patchiness is a relatively difficult concept to pin down in grassland habitats in which resources may be continuously distributed in space and time (Fryxell 2008). In our case, each well and its associated grazing radius may be construed as a discrete ‘patch.’ This makes it conceptually simple to define both patch occupation and patch abandon- ment as presence and absence at wells. Wells may be used for the whole year or just part of the year. Livestock owners may use several wells in the same year, or one alone, but the set of wells to be used over the year is decided in advance because rental contracts for sites must be made at the beginning of the year or earlier. Thus, decision making events occur in advance and the temporal scale at which site selection must be studied is multi-annual. Central Place Considerations Costs of bringing supplies are incurred many times over grazing period Group foraging effects Larger herd sizes likely to reduce costs of movement per animal Predation Possibly a factor, but not of high significance between sites within the desert Group foraging effects Predation (ii) Considering the expanding nature of site selection over time and ignoring the cost of travel, we predict that sites occupied earlier have a higher resource density than those occupied later, or at least this would have been true during the early stages of re-occupation. distance and environmental quality – e.g., if forage is denser further out from central points. In our system, patch quality is indeed likely to be positively correlated with distance from settlements. Large distance-related costs in a central place foraging scenario could delay leaving times of patches closer to the settlement and decrease the GUD of those patches, despite denser patches further out, contrary to the expectations of MVT when there is no central patch to return to. This would result in a situation much like that of a piosphere, in which closer sites would become depleted and distant sites would become relatively richer, resulting in positive correlations between distance from settlement, total in- take, and environmental quality. If travel costs are much higher than the MOC of not mov- ing, then livestock will deplete resources to far below the average level for the landscape, leading to very low GUDs. In such cases, we would expect to see that hypotheses (i) and (ii) would be refuted. In addition we would expect to observe the following conditions: In such cases, we would expect to see that hypotheses (i) and (ii) would be refuted. In addition we would expect to observe the following conditions: (iii) Higher levels of relative depletion (not absolute re- source density) outwards from wells at occupied sites than unoccupied sites; Close to home, GUD and forage intake rates when the patch is left are low because the short distances compensate for the high missed opportunity costs (MOC) of the better forage in distant patches. Once MOC become larger than distance-related costs, it is worth changing patches. Herd size is likely to offset distance by reducing costs through econo- mies of scale. We use this model to set up our hypotheses. Central Place Considerations Our theory so far would predict that total intake increases with environmental quality but that the GUD is the same for all patches, unless costs are higher at some patches than at others. Although we are not addressing grazing patterns within piospheres, our system also exhibits certain central place char- acteristics. In terms of primary family residence, livestock owners are based in three settlements. Those using several wells over the year may try to ensure that these are located close to each other, but it seems likely that the primary con- sideration will be distance from the home settlement. Within a landscape we would expect to find a relationship between distance and total intake if there is a relationship between Studies of foraging amongst domestic livestock in semi- arid environments often concern herds or flocks congregating around central places, to which they return at night and which represent water or shelter, rather than food resources. This results in the generation of a piosphere or grazing gradient around the central point (Lange 1969). Most studies concerning the foraging patterns of domestic animals (herded or not) concern daily movements around these central points, corresponding to the camp level (Coppolillo 2000; De Boer Hum Ecol (2017) 45:5–21 8 Table 1 Defining characteristics of the study site relevant to studies of foraging cteristics to studies Currency to be optimised Profit Spatial scale Landscape or home range Patch definition Wells, to which livestock are restricted at a radius of around 6 km Temporal scale Multi-annual: the set of wells to be used is decided in advance on an annual basis. Grazing periods at wells usually last months Central place effects The distance from home villages to wells is more likely to influence site selection than distance between wells used by the same livestock owner Costs Most costs co-vary with distance. Metabolic costs are incurred once a year during migration. Central Place Considerations (iv) Lower depletion levels at more recently occupied sites than sites occupied for several years or occupied and then abandoned; (v) An overriding role for distance in the system: sites close to our putative central point, the village, would be colonized first regardless of forage availability considerations; (vi) Amongst occupied sites and over time we would expect to see a positive relationship between vegetation density and distance from villages, as the ratio of gain to cost should start to equalise over the landscape. We would also find negative relationships between forage deple- tion and distance as forage is depleted closer to villages; Table 1 Defining characteristics of the study site relevant to studies of foraging Hypotheses The non-equilibrium situation means that there is unlikely to be a direct relationship between resource density and stocking rate, but the situation of expansion across a single zone is suitable to test the following two hypotheses, which relate to the beginning of the expansion process and would hold if gain is strongly correlated with resource density and if travel- related costs are low: (vii) Lastly, if herd sizes have a mitigating effect on costs, we would expect to see a positive relationship between herd size and distance from the central point. These hypotheses may be tested straightforwardly in an environment in which patch quality (before grazing) is distrib- uted randomly. Yet patch quality distribution is not random, but exhibits gradients across the landscape. Moreover, forage density is certainly not the only site characteristic of possible (i) Resource density may be higher at occupied sites than unoccupied sites if herders are targeting higher vegetation density under optimal foraging conditions and have not yet depleted patches to the landscape average. Hum Ecol (2017) 45:5–21 9 interest to herders. Water quality (salinity) and accessibility (depth) have been shown to influence site selection, whilst snow cover and relief affect vegetation and site accessibility (Kerven et al. 2016b) and also exhibit gradients across the study area. We also explore how the spatial distribution of these additional factors influences site selection. (Fig. 2), most owners now base their livestock along the river Chu or in the Moiynkum desert, and use one or both of these areas over the year. The study area includes three former sovkhoz (Soviet era state collective farms), Chu, Moiynkum and Baital, whose populations were concentrated in the settlements of Ulan bel’, Malye Kamkale, and Sary Ozek respectively (Fig. 3a). Chu and Moiynkum have today been merged to form a single administrative sub-district (Chu), whilst Baital now forms half of the adjacent Karabuget sub-district to the east. Methods We take an interdisciplinary approach using qualitative data from interviews with herders, local officials and livestock pro- fessionals, quantitative data on stocking metrics and a set of bio-physical variables to examine each hypothesis. By the 1980s, the Moiynkum desert was highly degraded, with severe deflation around wells (Bizhanova 1999; Dzhanpeisov et al. 1990). Today, livestock numbers are around only 15–20% of Soviet-era levels, and pasture condi- tion is likely to have recovered to some extent. Since the collapse of the sovkhoz, some herders have established long- term bases around wells. In spring and summer, users may move animals from these bases to temporary encampments in open access areas along the Chu river and in Betpak-dala. By contrast, the bases in the Moiynkum are located on formal- ly leased pasture and often have investments in infrastructure such as barns and houses (Kerven et al. 2016b). Base sites may be occupied for many years, and yet site abandonment and re-occupation was also common during our study. The sample of occupied and unoccupied wells is large enough The Study Area 3 Site occupation and resource density in the Moiynkum desert, (a) Well distribution and occupation in 2003 and 2011–2014 (b) Mean NDVI in 2012 across the study area (c) Relationship between mean annual for basic statistical investigation but not for multi-variate anal- ysis, so the role of resource density and other factors that possibly determine site selection was examined separately. for basic statistical investigation but not for multi-variate anal- ysis, so the role of resource density and other factors that possibly determine site selection was examined separately. was available for 80 owners in 2003 and 84 in 2012 (58 appeared in both years). According to the census data, 49 owners used the Moiynkum desert at some period of the year in 2002-2003, and 30 in 2011–2012 (note that due to the practice of collective herding several owners may use the same sites, just as one owner may use more than one site). The information on stock type, numbers, water source, and monthly location name were entered into a database. Numbers were converted to standard livestock units (LU) often used by pasture scientists in Central Asia and similar to cattle-sheep ratios used on rangelands elsewhere (USDA/NRCS 2003): one sheep or goat is one LU; one cow, horse or camel is five LU. These units were multiplied by the number of days at the The Study Area The Moiynkum is a sandy desert located in Dzhambul prov- ince of south-central Kazakhstan just south of the river Chu (Fig. 2). It originally constituted the wintering pasture of a much larger migratory system in which livestock spent the summer over 300 km north of the river Chu (Fig. 3a), along which the human population and associated settlements are based. Today, although some livestock are moved a reduced distance to the north into the clay desert of Betpak-dala Fig. 2 Location of Moiynkum desert in Kazakhstan Fig. 2 Location of Moiynkum desert in Kazakhstan Fig. 2 Location of Moiynkum desert in Kazakhstan Hum Ecol (2017) 45:5–21 10 for basic statistical investigation but not for multi-variate anal- ysis, so the role of resource density and other factors that possibly determine site selection was examined separately. Data Collection and Processing was available for 80 owners in 2003 and 84 in 2012 (58 appeared in both years). According to the census data, 49 owners used the Moiynkum desert at some period of the year in 2002-2003, and 30 in 2011–2012 (note that due to the practice of collective herding several owners may use the same sites just as one owner may use more than one site) Fig. 3 Site occupation and resource density in the Moiynkum desert, (a) Well distribution and occupation in 2003 and 2011–2014 (b) Mean NDVI in 2012 across the study area (c) Relationship between mean annual NDVI at 6km radius from wells and distance from Chu valley settlements at used and unused sites: b1 = 2.676e-04 (se = 1.893e-05); R2 = 0.49; p < 0.0001 10 Hum Ecol (2017) 45:5 21 Fig. 3 Site occupation and resource density in the Moiynkum desert, (a) Well distribution and occupation in 2003 and 2011–2014 (b) Mean NDVI NDVI at 6km radius from wells and distance from Chu valley settlements at used and unused sites: b1 = 2 676e-04 (se = 1 893e-05); NDVI at 6km radius from wells and distance from Chu valley settlements at used and unused sites: b1 = 2.676e-04 (se = 1.893e-05); R2 = 0.49; p < 0.0001 Fig. Data Collection and Processing Outside these bound- aries, false absences are possible as the knowledge of our informants regarding these outlying areas may have been in- complete, and some wells may have been used for herds from other administrative areas. Livestock from Sary Ozek make little use of the desert and so the dynamic process of site occupation examined in this study principally concerns Chu and Moiynkum, corresponding to modern Chu sub-district. Therefore, some analyses were also performed on this subset of sites alone, concerning 102 potential sites. Most of these have been re-occupied from Ulan bel’ village as Malye Kamkale is virtually abandoned. During interviews conducted in 2013 and in spring 2014 a number of additional occupied wells were recorded, including some which were newly occupied and a small number missed during the original census, but exact dates of use and livestock numbers were not recorded. Thus, livestock presence data were available for wells occupied in 2002–03 and between the end of 2011 and the start of 2014 (concerning mainly the years 2012 and 2013), whilst density (stocking rate) informa- tion was available on a monthly basis for two single year periods running from the months of October 2002 and 2011. Concerning the exact locations of used sites, many of the surveys and interviews were conducted at grazing sites, re- corded by GPS. Livestock owners and other knowledgeable interviewees identified additional used locations on a set of 1:50,000 Soviet era topographical maps. The majority of these sites were then visited by vehicle with key informants and recorded by GPS. The locations of those sites that could not be visited were digitised directly from the georeferenced to- pographical maps on which all wells are shown, many with names. Most such locations were verified on the maps by more than one interviewee. All locations, with their coordi- nates, were inputted into a relational database, thus providing exact locations for every site listed in the livestock survey table. Overall, livestock were present at 26 locations in 2002/ 2003 and 40 during the full fieldwork period of 2011–2014 (of which 37 were within former sovkhoz boundaries and 30 in Chu sub-district). Twenty-seven of these were recorded with full livestock number information for our specific census pe- riod October 2011–October 2012. The rest were recorded as having livestock presence at some point between October 2011 and April 2014. Data Collection and Processing Livestock Data Formal questionnaire censuses were conduct- ed with all livestock owners present in the study area in 2003 and 2012. The census asked owners to list pasture locations and water sources used by their large stock and small stock (separately) over 12 month periods starting from October 2002 and October 2011. Overall, 118 unique livestock owners were recorded. Of these, full livestock ownership information 11 Hum Ecol (2017) 45:5–21 major sites likely to have been used as bases in the past; others consisted of isolated wells and may have been occupied for shorter periods on a temporary basis. Both sets of sites were used in analysis for comparison, but the set of sites with in- frastructure was considered to be the most conservative esti- mate of potential livestock locations existing during the later Soviet period (Fig. 3a). Not all of these have working water supply facilities today, many having been destroyed, dried up or become too expensive to exploit. location during the relevant time period to give a single com- parable figure for each location expressed in ‘livestock unit years’ (LUY). This metric is equivalent to one head of sheep grazing at a location for one year. location during the relevant time period to give a single com- parable figure for each location expressed in ‘livestock unit years’ (LUY). This metric is equivalent to one head of sheep grazing at a location for one year. Open-ended interviews were conducted with 97 individuals (many interviewed more than once) during five fieldwork pe- riods between 2012 and 2014. Interviewees included livestock owners, shepherds, village mayors, veterinary officers, former employees of the state livestock farm, and employees of the state forestry department. Interviews were used to gather livestock owners’ perceptions on site selection and to identify important variables affecting decision-making. The results are discussed in detail elsewhere (Kerven et al. 2016b) and summarised here briefly in relation to our hypotheses and findings. In addition to the set of 282 potential sites, a number of geographical subsets were used during analysis including the restricted set of 130 sites1 within former sovkhoz boundaries, where we can be virtually certain that we have no false ab- sences - i.e., any users of these wells from outside were also recorded and included in the census. 1 All potential site numbers concern those with infrastructure on the maps. Well and Livestock Distributions in the Moiynkum Desert Wells with infrastructure in the sand desert portion of our three sovkhoz territories were located on average 3.5 km apart (well below the radius at which animals graze) so the area was essentially ‘full up’ with potential sites in Soviet times. The distribution of wells (with infrastructure) mapped within all sovkhoz boundaries is close to a distributed regular pattern (n = 130, nearest neighbour ratio = 1.7, z-score = 1.72, p = 0.08) and within Chu sub-district alone follows a highly distributed pattern (n = 102, nearest neighbour ratio = 1.14, z- score = 2.7, p < 0.01). The equivalent analysis using all wells reveals a random pattern, suggesting that a planned effort was made to regularly space sites with infrastructure and confirming that the presence of infrastructure might be the best metric to define absences (potential yet unoccupied sites). These findings also suggest that either underlying environ- mental factors did not influence well distribution, or that these factors do not display a spatial gradient or clustering pattern. Resource Depletion In many arid areas of Central Asia, for- age is relatively homogeneous around wells; wells and shelter are located in the same place and forage availability tends to increase, and grazing pressure to decrease, away from this single central point (Alimaev et al. 2008; Kanchaev et al. 2003; Nechaeva et al. 1979). Differences between NDVI at 0-2 km and 3-5 km from wells, or NDVI gradients, were measured using the annual average NDVI data for 2003 and 2012. These gradients may be interpreted as a measure of resource depletion and have been shown to be closely related to stocking density metrics elsewhere in the region (Behnke et al. 2016). Water Availability Both well depth and salinity have been found to influence site selection, the influence of depth acting through the cost of pumping (Kerven et al. 2016b). Water quality was estimated by livestock owners as good, average, or salty for a subset of 41 wells, and interviewees also provid- ed depth information for 39 wells. Today, large areas of the Moiynkum desert are unoccupied but the number of occupied sites has risen from 26 in 2002–3 to 40 in 2012–13, with 15 sites occupied in both periods. Some sites are occupied all year but others only seasonally. Well and Livestock Distributions in the Moiynkum Desert Seasonal use is now highly variable, ranging from one to four seasons rather than in spring/autumn (north of the desert) and winter (southern desert) which characterised the Soviet period (Fig. S2, supplementary materials 3). Other Variables Affecting Site Selection It was assumed that travel costs to occupied sites from home settlements were proportional to distance, which was measured using the ARCMAP point distance tool. Products from the MODIS in- strument were processed to produce multi-annual snow cover images at a resolution of 5 degrees (see supplementary mate- rials 1). Relief, in the form of sand dunes, was mapped at a 30 m resolution using visual enhancement and interpretation of an ASTER Digital Elevation Model (DEM). Data Collection and Processing Statistical Analysis Relationships between distance from set- tlement and NDVI, date of first occupation and NDVI, stock- ing rate and NDVI gradient, and well depth and first date of occupation were explored by ordinary least squares linear re- gression. Differences in mean NDVI, NDVI gradient, distance from settlement, well depth and snow cover between locations with stock presence and absence were assessed using Welch’s t-test; differences in these variables between the four site stocking categories (used in 2003 alone, 2011–14 alone, both periods or unused) were assessed using one-way ANOVA. All statistical analyses were carried out in R (R Core Team 2014). Image processing and analysis were carried out using the Raster package for R (Hijmans and van Etten 2013) and ARCGIS (ESRI 2011). We have not attempted to match the season of use of the Moiynkum desert to NDVI values at time of use. In the mi- gratory system as a whole movements are partly influenced by seasonal variations in vegetation availability which occur be- tween vegetation zones (Robinson et al. 2016). However, within the Moiynkum vegetation types are more homoge- neous. These sites constitute primary bases from which other, more temporary moves may be made. By integrating NDVI over the year, we are looking at the overall attractiveness of a site as a ‘base’ regardless of the season in which it was used at the time of the study. Data Collection and Processing These data represent two snapshots of well occupation in a complex 20 year-long process of well occupation and abandonment. Our data do not include infor- mation on the exact dates and length of occupation periods between the two study periods. However, the year of first occupation since the collapse of the sovkhoz was obtained for a subset of 29 wells for more detailed investigation of site sequencing. The sets of occupied sites are different in the two time periods, altering the choice of unoccupied sites. This is addressed by explicitly comparing site characteristics between sites occupied in 2011–2014 alone, occupied in 2003 and then abandoned, and occupied in both periods. Livestock presences were recorded as locations having any stock presence over the year, whilst absences were defined as locations having wells that existed in the Soviet era, but which were not recorded as occupied either in 2002–3, or between 2011 and 2014. These may be considered potential sites, and were digitised from the topographic maps (which show all wells and outbuildings existing during the 1980s, after which no new infrastructure was built). Over the past few years, livestock owners whose animals are based at settlements along the Chu have started to move them to wells outside former sovkhoz boundaries. For this reason the maximum extent of our analysis was set to cover an area stretching up to 30 km from these boundaries. Within this area, of the total of 445 occupied and potential sites, 282 had infrastructure (buildings, barns) and were considered to be Resource Density The remote-sensing derived Normalised Difference Vegetation Index (NDVI) is used worldwide as an indicator of green biomass (Pettorelli et al. 2011). We 12 Hum Ecol (2017) 45:5–21 employed a gapless 250 m 16 day NDVI dataset generated from the MODIS MOD13Q1 product (Vuolo et al. 2012) for the years 2001–2012, from which we extracted annual aver- ages both over the entire period and for the years 2003 and 2012 alone (see supplementary materials 1). Average NDVI values were extracted around each location (usually where the livestock were watered or spent the night) at a radius of 6 km, shown to be the typical extent of grazing impact around desert wells in Kazakhstan (Karnieli et al. 2008). Vegetation compo- sition was also investigated using a vegetation map (Fig. S1 supplementary materials 2) generated from a MODIS-based classification (see supplementary materials 1). Resource Density Our first hypothesis was that occupied sites may be those with higher long term average resource density. We examined this by comparing average annual NDVI (2001–2012) at occupied and unoccupied wells. Taking livestock occupancy during the 2011–2014 period, there was no significant difference in mean NDVI values between the 37 occupied and 93 unoccupied locations within the three former sovkhoz boundaries at a 6 km radius from the well (t = 0.87, p = 0.39). But at a radius of 1 km, where grazing pressure is greatest, occupied sites had significantly lower NDVI (t = 2.46, p < 0.05). The 2003 set of occupied sites exhibits very strong differences in NDVI when compared with sites unoccupied at that time, even at 6 km radius from wells, with occupied sites having significantly lower NDVI (n = 130 wells of which 26 occupied; t = 4.2, p < 0.0005). These differences were also noted using NDVI in the year of use instead of 12 year annual average NDVI. Thus site selection decisions made in individual years are unlikely to depend on resource density characteristics in that specific year, and resource densities in a given year do not differ rad- ically from long term averages. Biomass NDVI appears to increase towards the east of the study area and in some parts of the southeast (Fig. 3b). This follows a precipitation gradient. Average annual precipitation ranges from 150 mm close to the Chu river to 180–200 mm in the central Moiynkum (Kurochkina and Osmanova 1973) and 294 mm in the south (Bizhanova and Kurochkina 1989). The existence of a biomass gradient independent of resource de- pletion by grazers is evident (Fig. 3c), which indicates a strong relationship between NDVI and distance (to the south) from settlements, not only for occupied sites, but also for sites un- occupied in either study period. Water and Snow Our sample of wells, representing those for which respondents had knowledge, exhibited decreasing sa- linity towards the south from settlements, a factor identified as important in site selection by herders (Kerven et al. 2016b and supplementary materials Table S1). Those wells having aver- age or good quality water tend to be deeper close to Ulan bel’ and shallower to the south and east (Fig. S3). Characterising Resource Gradients across the Study Area The occupation of new sites has occurred mostly to the south and east (Fig. 3a). There are large groups of sites, particularly to the south of Ulan Bel’ and northern parts of former sovkhoz Moiynkum, which are unoccupied. We discuss how forage 13 Hum Ecol (2017) 45:5–21 resources, and other natural factors possibly influencing site selection, vary across the desert. resources, and other natural factors possibly influencing site selection, vary across the desert. higher precipitation, snow cover is also lower to the south and east, probably influenced by higher temperatures, partic- ularly in early spring (Fig. S4, supplementary materials 5). Vegetation and Soils The north of the desert, which has clay takyr-like soils, has few wells because the ground water is salty. This area is covered by vegetation dominated by Artemisia and Haloxylon spp. (see vegetation type 1, Fig. S1, supplementary materials). This pasture makes poor grazing outside the autumn and only two occupied wells were located here. Further south, the soil becomes progressively sandier (Fig. 3b). Transitional areas dominated by Ceratoides (vegetation type 2 in Fig. S1) give way to vegeta- tion dominated by shrubs such as Calligonum, Haloxylon, Astragalus spp. which, together with an understory including Ceratoides, Kochia and Atriplex spp., provide good forage all year round. By far the majority of wells are located in this vegetation type on sandy soils (south of the clay/sand border in Fig. 3b and corresponding to type 3 in Fig. S1), which is rather homogeneous, apart from areas affected by fire, visible as patches of low NDVI in the southeast of Fig. 3b. The increasingly sandy soils to the south present transport difficul- ties as deeper sand combined with higher dune size increase both fuel costs and the risk of vehicles becoming stuck, thus requiring heavier and more expensive transportation. Distance The role of distance from settlements as a constraint to site occupation is evident (Fig. 3a). More recently occupied sites appear to be located further away from settlements, a phenomenon even more exaggerated when we consider that in fact most expansion is from the settlement of Ulan bel’ alone. However, the expansion appears rather directional to- wards the south and east, so distance, whilst important, must interact with other factors. We now turn to a more formal analysis of relationships between these factors and site occupation. Resource Density Post hoc com- parisons using the Tukey HSD test indicated that the difference in mean NDVI gradient between newly occupied sites (2011–14) verses sites oc- cupied in both periods is significant (p < 0.001); difference between sites occupied in 2003 alone and in 2011–14 alone is insignificant (p = 0.9); difference between sites used in both years and sites never used is signif- icant (p < 0.0001). Note: boxplots shown here (and all subsequent boxplots) show median values (horizontal lines in box centre), and the 1st and 3rd quartiles (top and bottom of boxes). The whiskers extend to values of 1.5 x Q3-Q1. Outliers are shown as dots and represent values > Q1–1.5*IQR and < Q3 + 1.5*IQR where IQR = Q3 - Q1. a) Fig. 4 a Regression of annual average NDVI (2001–2012) against year of first re-occupation after collapse of the sovkhoz (n = 29): β1 = 0.001 (se = 0.00028); R2 = 0.327; p < 0.005. b NDVI at sites used in 2003, 2011–14, both periods and unused sites, within sovkhoz boundaries (n = 11, 22, 15, 82). There was a significant difference in group means (F = 4.4; p < 0.01). Post hoc comparisons using the Tukey HSD test indicate no difference between mean NDVI at sites used in 2011–14 and unused sites (p = 0.99); significant differences between unused sites and those used in 2003 (p < 0.05) and near significance between sites used in 2011–2014 and in 2003 alone (p = 0.064). A t-test on these latter two group means is significant: t = −3.1, p < 0.005. c 2012 NDVI gradient at occupied and unoccupied sites within former sovkhoz boundaries in 2011–2012 alone (census year only; present n = 27; absent n = 103). A positive gradient implies that NDVI increases out from the well (a mea- sure of resource depletion); negative gradients imply that NDVI decreases out from the well. The difference in mean gradient is significant: t = −4.8, p < 0.0001. Taking all sites used from 2011 to 2014 (present n = 37, Fig. 4 a Regression of annual average NDVI (2001–2012) against year of first re-occupation after collapse of the sovkhoz (n = 29): β1 = 0.001 (se = 0.00028); R2 = 0.327; p < 0.005. b NDVI at sites used in 2003, 2011–14, both periods and unused sites, within sovkhoz boundaries (n = 11, 22, 15, 82). Resource Density Thus, for a livestock owner based at Ulan bel’, although most nearby wells are relatively shallow, many are of poor quality, while the deeper good quality wells are expensive to use. Further away in former Moiynkum and Baital sovkhozes, those wells known to respondents tended to be both shallow and of good or average quality. These particularly attractive wells are now occupied by owners based at Sary Ozek and Malye Kamkale; others are occupied by owners from Ulan bel’ who have also tended to move greater distances in recent years. Despite Our second hypothesis was that most resource dense sites would be occupied earlier. Here, we regressed annual average NDVI against year of first occupation of sites since the col- lapse of the sovkhoz. Whilst no relationships were evident at 6 km radius, a weak relationship did emerge closer to wells (Fig. 4a), but again the direction of the relationship is the inverse of that predicted by MVT, with those sites occupied first exhibiting lower NDVI than sites occupied later on. Relationships between resource density and the order of site occupation were explored further by comparing NDVI at the sets of sites occupied in 2003 alone, those occupied in 2011–2014 alone, and sites occupied in both years (Fig. 4b). Sites occupied after 2003 (i.e., appearing in the 2011–2014 dataset only) have mean NDVI levels very close to those of unoccupied sites, whilst those occupied in 2003 and during both periods have much lower NDVI values. Hum Ecol (2017) 45:5–21 14 14 Fig. 4 a Regression of annual average NDVI (2001–2012) against year of first re-occupation after collapse of the sovkhoz (n = 29): β1 = 0.001 (se = 0.00028); R2 = 0.327; p < 0.005. b NDVI at sites used in 2003, 2011–14, both periods and unused sites, within sovkhoz boundaries (n = 11, 22, 15, 82). There was a significant difference in group means (F = 4.4; p < 0.01). Post hoc comparisons using the Tukey HSD test indicate no difference between mean NDVI at sites used in 2011–14 and unused sites (p = 0.99); significant differences between unused sites and those used in 2003 (p < 0.05) and near significance between sites used in 2011–2014 and in 2003 alone (p = 0.064). A t-test on these latter two group means is significant: t = −3.1, p < 0.005. Resource Density c 2012 NDVI gradient at occupied and unoccupied sites within former sovkhoz boundaries in 2011–2012 alone (census year only; present n = 27; absent n = 103). A positive gradient implies that NDVI increases out from the well (a mea- sure of resource depletion); negative gradients imply that NDVI decreases out from the well. The difference in mean gradient is significant: t = −4.8, p < 0.0001. Taking all sites used from 2011 to 2014 (present n = 37, absent n = 93) the relationship is weaker as many of these were used for the first time t = −3.0, p < 0.005. The equivalent test for 2003 data (n = 26; 104) is significant: t = −4.1, p < 0.0005. d 2012 NDVI gradients at sites used in 2003, 2011–14, both periods and unused sites, within former sovkhoz boundaries (n = 11, 22, 15, 82). There was a significant difference between group means (F = 10.44; P < 0.0001). Post hoc com- parisons using the Tukey HSD test indicated that the difference in mean NDVI gradient between newly occupied sites (2011–14) verses sites oc- cupied in both periods is significant (p < 0.001); difference between sites occupied in 2003 alone and in 2011–14 alone is insignificant (p = 0.9); difference between sites used in both years and sites never used is signif- icant (p < 0.0001). Note: boxplots shown here (and all subsequent boxplots) show median values (horizontal lines in box centre), and the 1st and 3rd quartiles (top and bottom of boxes). The whiskers extend to values of 1.5 x Q3-Q1. Outliers are shown as dots and represent values > Q1–1.5*IQR and < Q3 + 1.5*IQR where IQR = Q3 - Q1. a) 14 Hum Ecol (2017) 45:5–21 absent n = 93) the relationship is weaker as many of these were used for the first time t = −3.0, p < 0.005. The equivalent test for 2003 data (n = 26; 104) is significant: t = −4.1, p < 0.0005. d 2012 NDVI gradients at sites used in 2003, 2011–14, both periods and unused sites, within former sovkhoz boundaries (n = 11, 22, 15, 82). There was a significant difference between group means (F = 10.44; P < 0.0001). Resource Density There was a significant difference in group means (F = 4.4; p < 0.01). Post hoc comparisons using the Tukey HSD test indicate no difference between mean NDVI at sites used in 2011–14 and unused sites (p = 0.99); significant differences between unused sites and those used in 2003 (p < 0.05) and near significance between sites used in 2011–2014 and in 2003 alone (p = 0.064). A t-test on these latter two group means is significant: t = −3.1, p < 0.005. c 2012 NDVI gradient at occupied and unoccupied sites within former sovkhoz boundaries in 2011–2012 alone (census year only; present n = 27; absent n = 103). A positive gradient implies that NDVI increases out from the well (a mea- sure of resource depletion); negative gradients imply that NDVI decreases out from the well. The difference in mean gradient is significant: t = −4.8, p < 0.0001. Taking all sites used from 2011 to 2014 (present n = 37, absent n = 93) the relationship is weaker as many of these were used for the first time t = −3.0, p < 0.005. The equivalent test for 2003 data (n = 26; 104) is significant: t = −4.1, p < 0.0005. d 2012 NDVI gradients at sites used in 2003, 2011–14, both periods and unused sites, within former sovkhoz boundaries (n = 11, 22, 15, 82). There was a significant difference between group means (F = 10.44; P < 0.0001). Post hoc com- parisons using the Tukey HSD test indicated that the difference in mean NDVI gradient between newly occupied sites (2011–14) verses sites oc- cupied in both periods is significant (p < 0.001); difference between sites occupied in 2003 alone and in 2011–14 alone is insignificant (p = 0.9); difference between sites used in both years and sites never used is signif- icant (p < 0.0001). Note: boxplots shown here (and all subsequent boxplots) show median values (horizontal lines in box centre), and the 1st and 3rd quartiles (top and bottom of boxes). The whiskers extend to values of 1.5 x Q3-Q1. Outliers are shown as dots and represent values > Q1–1.5*IQR and < Q3 + 1.5*IQR where IQR = Q3 - Q1. Resource Density a) Hum Ecol (2017) 45:5–21 15 The above analyses suggest that differences in resource density between occupied and unoccupied wells, both in space and over time, are related to vegetation depletion caused by grazing at various periods during the 12 years over which the NDVI data are averaged. In this scenario, our theory predicts that when travel costs are high, sites are occupied beyond the point at which the forage acquisition rate drops below the landscape average. In this case, site occupancy determines vegetation density rather than the reverse. Additional evidence for such a scenario is that NDVI differences between occupied and unoccupied sites in 2012 and 2003 are larger (with higher statistical significance) when the full set of sites with wells (not only those having infrastructure) are included in the anal- ysis. Whilst wells with infrastructure are likely to have been occupied in the past, those without infrastructure may have been little or never occupied, thus amplifying the potential difference in accumulated grazing pressure between occupied and unoccupied sites. This also suggests that past grazing effects are detectable for long periods. weedy species may persist for many years after NDVI gradients are no longer detectable. It should be noted that although we have found relationships between livestock presence and resource depletion, relationships were not found between actual livestock density (annualised stocking rate) and the extent or size of the gradient in either 2003 or 2012. This may be because stocking rates are not vari- able enough to cause detectable differences in depletion level. Overall, at least by 2012, site occupation appears more likely to be causing resource depletion than to constitute a response to variability in vegetation density, consistent with the scenario that distance-related costs were the dominant fac- tor determining site selection. However, although the MVT prediction that the most resource dense sites would be occu- pied first has not been shown to be correct, it is difficult to refute convincingly because we are essentially dealing with two temporal ‘snapshots.’ Our dataset does not have the fine temporal detail of occupation and abandonment dates which could perhaps have been used with associated NDVI data at dates of initial occupation to untangle these two factors. If relationships between resource density and date of first occu- pation do exist, they are most likely to be negative, as those sites occupied first are furthest north, where precipitation is lowest. Resource Density Those sites occupied in 2003, but abandoned before the subsequent study period, have low NDVI gradients (little depletion) in 2012 (Fig. 4d), but also have low long-term average absolute NDVI values (Fig. 4b), suggesting that these sites may be generally resource-poor in a way not related to depletion alone. This may also explain why the difference between NDVI at occupied and unoccupied sites was so much greater for the 2003 dataset (significant at 6 km) than for the 2011–14 dataset (non-significant at 6 km). However, we have seen that there is also a north-south gradient in ‘natural’ vegetation density related to climatic fac- tors rather than livestock grazing. Our most recently occupied sites, as well as many unoccupied sites, appear to be located further south. Thus we must examine not only absolute re- source density, but relative depletion levels around wells in order to better understand the process behind the observed patterns. Resource Depletion We now therefore turn to our hypotheses concerning NDVI gradients outwards from wells. As hypothesised, average NDVI gradients were steeper at occupied than at unoccupied sites in both 2003 and 2012 (Fig. 4c). Secondly, we examined average NDVI gradients in 2012, at sites with different occu- pation histories, to address the hypothesis that more recently occupied, or more briefly occupied, sites should exhibit less resource depletion. Within sovkhoz boundaries, sites occupied only in recent times (appearing in the 2011–2014 dataset alone) exhibited no discernible difference in NDVI gradient in 2012 from unoccupied sites, which, as would be expected, have a median gradient of around zero (Fig. 4d). Sites occupied in both periods exhibited high levels of depletion. The difference be- tween sites occupied in both periods and those appearing only in the 2011–2014 dataset is particularly strong. However, de- pletion at sites occupied in 2003 but subsequently abandoned is slight, and mean gradients are statistically indistinguishable from those at sites occupied only recently (Fig. 4d). These results suggest that (i) the effects of depletion require several years of site occupation to become evident as NDVI gradients, and (ii) the impact of past grazing appears to decrease over the timescale at which we are working. We should remember here that NDVI gradients are not measuring the quality of grazing - A second prediction of classical MVT, that movement away from sites would occur once they had been grazed down to the landscape average resource density, appears not to be supported, at least for the 2003 dataset. Even in recent years, although some herders have recently colonised un-depleted sites, others have stayed on patches long past the GUD pre- dicted by MVT, again supporting the idea that costs of move- ment are high. We now turn to hypothesis (v) concerning distance from the home settlement (Table 2). Other Factors Other factors that interviews with herders and local profes- sionals suggested were important determinants of the cost or attractiveness of particular sites were water quality (saline or not), depth and type of the well (which may affect extraction cost), topography (which may affect travel cost), and snow cover (which may impede grazing in winter but provide im- portant moisture in spring) (see Kerven et al. 2016b). As we have seen, the water quality of wells varies with distance from settlements, such that less saline wells are further away (Table S1 in supplementary materials). Of the 41 wells for which salinity scores were given, 24 of the 25 wells listed as good or average were occupied between 2011 and 2014, whilst the 16 saline wells were occupied and unoccupied in equal proportion. In 2003 there was no difference in the pro- portion of occupied saline and non-saline wells, suggesting that selectivity for water quality may have increased over time. Likewise, no relationship was detected between water quality and date of first occupation for our subset of 29 wells for which year of first occupation after collapse of the sovkhoz was available. If costs increase with distance then we would expect GUD to be lower closer to settlements and higher farther away, as the ratio of cost to gain starts to equalise over the landscape (hypothesis vi). By the end of our study period, we would thus expect to see a gradient of resource density outwards from settlements at sites occupied during our study period, but not at unoccupied sites. However, this hypothesis cannot be con- firmed due to the natural north-south increase in resource den- sity evident at both occupied and unoccupied sites (Fig. 2c). It is in 2013 and within sovkhoz boundaries alone that there is most likely to be equalising of cost-gain ratio. We did indeed find a strong positive relationship between distance from the home settlement and NDVI at sites that had been occupied at any time during the study period (n = 48; β1 = 7.2e-04 (se = 6.0e-05); R2 = 0.76, p < 0.0001). However, there is also a strong relationship between NDVI and distance for sites that were not occupied in either period (n = 82; β1 = 7.6e-04 (se = 7.3e-05); R2 = 0.57; p < 0.0001), albeit with a lower slope. Distance According to this hypothesis, if other factors were equal then we would expect the sites closest to villages to be settled first. This question is explored for Ulan bel’ sub-district (former Chu and Moiynkum sovkhoz) alone, as so few stock from Sary Ozek are located outside the settlement. In this sub- district most livestock are coming from the settlement of Ulan bel’. Results confirm that indeed occupied sites were significantly closer to Ulan bel’ than unoccupied sites in 2003 (Table 2). However, by 2012 there was no significant Hum Ecol (2017) 45:5–21 16 Table 2 Distance from Ulan bel’ and livestock presence and absence (for sites within the boundaries of Chu sub-district). Year n (absence) n (presence) Mean distance, km (absence) Mean distance, km (presence) t p 2003 78 24 49.6 37.2 4.3 <0.0001 2012 72 30 46.6 46.9 -0.081 ns (0.9359) difference between occupied and unoccupied sites. It thus ap- pears that either suitable sites closer to Ulan bel’ are all occu- pied or a reduced importance of travel costs (e.g., lower fuel costs or higher returns from meat sales) means that factors other than distance are increasingly important in site selection. Certainly 11 of the sites occupied in 2003 close to Ulan bel’ were subsequently abandoned, and there are still many empty wells throughout the study area, so reduced travel costs may be more important. No relationships between stocking rate and distance from Ulan bel’ were found. related to distance from the village. We explored the relationship between both average herd size over the months each site was occupied, and annualised stocking rate (in LUY) and distance from village for the year 2012. No relationships were apparent here for either variable, however the sample size of sites for which stocking information was available was small (n = 27). The difference in herd size between sites occupied in 2012 and sites occupied in both 2003 and 2012 was also non-significant. Yet the impact of distance on site selection still had conse- quences during the later study period. If we compare sites occupied in 2011–14 with the theoretical larger universe of unoccupied sites across the wider Moiynkum zone, then NDVI values at sites occupied in 2011–14 are significantly lower than those of other sites, even at a radius of 6 km (242 wells of which 40 occupied; t = 4.2, df = 68.12, p < 0.001). Distance This is because there are many unoccupied sites in the highly vegetated south of the sandy massif. These sites are potentially available and indeed a few were occupied by 2013. Other Factors Sites unused in either period not included as sample size n = 3 is too small Fig. 5 a Well depth and year of first occupation (n = 23): β1=-0.8494 (se = 0.2522); R2 = 0.35, p < 0.005. Note: two very deep outliers (80 m) have been removed. b Well depth and use period category. Sites used in 2003 only: mean = 19 m, n = 5. In 2011–2014 only: mean = 13 m, n = 17. In both periods: mean = 24 m; n = 14. T-test for difference in mean depths of wells used in 2003 or both years verses those used in 2011–2014 alone (n = 19; 17, means =22.7 m & 12.7 m) is significant: t = 3.8, p < 0.001. Sites unused in either period not included as sample size n = 3 is too small lower at more recently occupied sites (2011–14 only) compared to those occupied in 2003 alone, but the absolute mean differ- ences are very small (Fig. S6, supplementary materials 7). Moreover, more snow may be positive for spring growth, thus in interviews some herders considered snow to be an important factor determining site selection whilst others did not, depending on season of use. This factor is also likely to be confounded with geographical location, which as we have seen, correlates with other factors varying along the same north-south gradient. those which were in fact occupied later on (hence existence of knowledge about these wells in 2012–2014 interviews). There are very few data for wells unoccupied in either period. This is because herders are unsure about the status of wells that have not been visited for a long time. However, interviews do con- firm that pumping costs increase with well depth and that water quality is an important pull factor in site selection (Kerven et al. 2016b). Lastly, we examined the effect of water source type on live- stock presence. The Soviet-era grazing plan of Ulan bel’ shows all major shaft wells and bore holes (n = 58). Sites having only bore holes may be the least likely to be occupied today as they require the most powerful pumps. Indeed, of the 25 sites at which bore holes alone are indicated, only five were occupied in either 2003 or 2011–14 (of which three have been occupied since 2012). Other Factors We would also expect to find negative relationships between forage depletion and distance from settlement at oc- cupied sites, as forage is depleted closer to settlements (again calculating distances as above). Here although a slightly neg- ative relationship was observed, it is extremely weak (b1 = −9.6e-05 (se = 4.5e-05); R2 = 0.08, p < 0.05). There were no significant differences in well depth be- tween occupied and unoccupied wells in 2011–14, but the sample size of unoccupied wells (8) for which depth data were available was small. In 2003, occupied wells were significant- ly deeper (n = 39; unoccupied n = 20, occupied n = 19; means =12.5 m and 22.7 m; t = −4.06, p < 0.0005). The possible conclusion that shallower wells tend to be occupied later on is supported by weak relationships between well depth and both date of first occupation and use period category (Fig. 5). These data are circumstantial at best – the set of wells for which information could be gathered represents that for which informants had knowledge, and the limit of our research re- sources. Most data for wells unoccupied in 2003 concern Lastly, we expected that if economies of scale could mitigate travel costs, herd size should be positively 17 Hum Ecol (2017) 45:5–21 Fig. 5 a Well depth and year of first occupation (n = 23): β1=-0.8494 (se = 0.2522); R2 = 0.35, p < 0.005. Note: two very deep outliers (80 m) have been removed. b Well depth and use period category. Sites used in 2003 only: mean = 19 m, n = 5. In 2011–2014 only: mean = 13 m, n = 17. In both periods: mean = 24 m; n = 14. T-test for difference in mean depths of wells used in 2003 or both years verses those used in 2011–2014 alone (n = 19; 17, means =22.7 m & 12.7 m) is significant: t = 3.8, p < 0.001. Sites unused in either period not included as sample size n = 3 is too small In both periods: mean = 24 m; n = 14. T-test for difference in mean depths of wells used in 2003 or both years verses those used in 2011–2014 alone (n = 19; 17, means =22.7 m & 12.7 m) is significant: t = 3.8, p < 0.001. Other Factors Of the 33 sites with shaft wells or both types, 18 (54%) were occupied (X2 = 7.1, p < 0.005). Most unoccupied sites lie directly south of Ulan bel’ nearer to the metalled road. The fact that most of them are bore holes may explain why those sites, despite being easily accessed, are rarely occupied (Fig. 2a, Fig. S5, supplementary materials 6). In this area, livestock owners also mentioned transport difficulties related to sand depth and dune height (Kerven et al. 2016b). Sandy soils may increase travel costs related to the occupation of all southern wells, but those in the south west may be particularly hard to reach (sup- plementary materials 6). To summarise, it appears that over time, herders have been increasingly targeting shallower and less saline wells in areas with higher vegetation density. Discussion and Conclusions False in 2012 However, even unoccupied sites may have continued to exhibit depletion from heavy use in the Soviet era; at the start of the study the time scale needed for more recent grazing activity to become detectable was unknown - the effects of grazing in 2012 were not detectable in the NDVI data at 6 km radius. equalise, is only one of the processes occurring here. The other is that the ratio of costs to profit is changing over time, thus the depressing effect of cost on GUD may also lessen over time. This is indeed illustrated by the declining influence of distance on site selection between our two study periods. Livestock have stayed at these sites longer than would be predicted under conditions of optimal foraging, and have thus grazed vegetation to levels lower than would be expected if they were just responding to differences in forage availability between sites. GUDs are low, suggesting that costs of movement are high. These costs tend to co-vary with distance from settlements and were clearly the overriding factor determining site selection, at least during in the initial phase of expansion. Distance imposes costs not only in the one-off movement of livestock at the start of the grazing period, but in the many trips back and forth for supplies and family visits (Kerven et al. 2006). Part of this decrease in costs may be related to an increase in livestock numbers, which operates to decrease economies of scale (Kerven et al. 2004, 2006, 2008). Although we have shown in previous work that herd size is strongly related to the number of ecological zones occupied by migratory livestock (Robinson et al. 2016), we have not been able to demonstrate relationships between herd size and distance within the single zone studied here. However, the number of small stock in our study area roughly doubled from 2003 to 2012. This increase has translated both into a greater number of flocks using the Moiynkum desert, and to an increase in median flock size belonging to individuals, by around 70% over our study peri- od (Kerven et al. 2016b). Higher meat prices and lower pumping costs have also contributed to general increased wealth of herders in recent years. Secondly, sites occupied later on have on average, both higher vegetation densities and lower depletion levels than those occupied at the start of our study period. Discussion and Conclusions A major goal of this paper was to understand whether live- stock owners are acting as ‘optimal foragers,’ targeting areas of highest forage availability as they colonise previously emp- ty areas. The results presented here suggest that they do not follow the classical MVT (hypotheses i and ii, Table 3). Rather, it appears that travel costs are potentially critical de- terminants of site occupation, meaning that animals stay lon- ger at sites than would be expected under classical MVT, leading to resource depletion (hypotheses iii–vi, Table 3). This is despite the continued existence of many unoccupied sites in the study area. Historically, one of the values of the Moiynkum desert as a winter grazing area lay in its relatively low snow cover. Today, although many sites are also occupied in other seasons (Fig. S2, supplementary materials 3), winter is still a key grazing period. Snow cover as measured by satellite imagery is significantly We found that occupied sites have significantly lower veg- etation density and higher NDVI gradients than unoccupied sites. Such a pattern may seem rather predictable in semi-arid systems in which livestock are constrained to water points. Hum Ecol (2017) 45:5–21 18 Table 3 Results of hypothesis testing № Hypothesis Results (i) Resource density is higher at used sites than at unused sites (IFD) False in 2003 & 2012. (ii) Order of site occupation by individual herders since the collapse of the sovkhoz is positively related to resource density (IFD) False (iii) Resource depletion is higher at sites where livestock are present than at those where they are absent. True in 2003 & 2012 (iv) Resource depletion is lower at more recently occupied sites than (a) sites used for many years and (b) sites used and then abandoned. (a) True (b) False (v) Within specified spatial boundaries, sites at which livestock are present are closer to settlements than sites from which they are absent. 2003: True 2012: False (vi) For the later dataset we expect: (a) positive relationship between forage density and distance from villages; (b) negative relationship between forage depletion and distance from settlements (a) True (b) Inconclusive (vii) If larger herd sizes mitigate costs of movement we would expect to find positive relationships between herd size and distance from settlements. Table 3 Results of hypothesis testing References Alimaev, I. I., Kerven, C., Torekhanov, A., Behnke, R., Smailov, K., Yurchenko, V., Sisatov, Z., and Shanbaev, K. (2008). The impact of livestock grazing on soils and vegetation around settlements in Southeast Kazakhstan. In Behnke, R. (ed.), The Socio-economic Causes and Consequences of Desertification in Central Asia, Springer. ( y g ) This study has shown the dominance of economic considerations over forage-related issues in herders’ de- cisions about how best to use resources, in contrast to a pastoral system in Africa which has been subject to sim- ilar analyses (Scholte et al. 2006). Such a situation is likely to be the case in pastoral systems that are increas- ingly subject to sedentarisation of households in a central place and reliance on mechanised transport. In terms of policy, the Kazakh government could intervene in a number of ways to reduce the high costs related to low GUDs and high levels of resource depletion. These in- clude improving transport links, increasing the attractive- ness of distant sites by repairing wells and other infra- structure and ensuring that administrative and other transaction costs of land access are as low as possible. It could also act to incentivise seasonal movement out of the Moiynkum desert, as much of the strongest depletion comes from livestock kept in the desert in the summer. Overall, the government needs to weigh the cost efficien- cy of such policies, in terms of improved access to nat- ural forage, against its current policies which favour the intensification of livestock production. Astrom M., Lunberg P., and Danell K. (1990). Partial Prey Consumption by Browsers: Trees as Patches. Journal of Animal Ecology 59: 287– 300. Bailey D. W., Gross J. E., Laca E. A., Rittenhouse L. R., Coughenour M. B., Swift D. M., and Sims P. L. (1996). Mechanisms that Result in Large Herbivore Grazing Distribution Patterns. Journal of Range Management 49: 386–400. Behnke R. (2003). Reconfiguring property rights in livestock production systems of western Almaty oblast, Kazakstan. In Kerven C. (ed.), Prospects for Pastoralism in Kazakstan and Turkmenistan: From State Farms to Private Flocks, Routledge Curzon, London. Behnke R., Robinson S., and Milner-Gulland E. J. (2016). Governing Open Access: Livestock Distributions and Institutional Control in the Karakum Desert of Turkmenistan. Land Use Policy 52: 103– 119. Bizhanova, G. K. (1999). Discussion and Conclusions Thus over time, depletion may indeed be driving livestock to new sites with high vegetation density, located further from the central point of departure. However, these sites do not just exhibit high levels of un-depleted vegetation. As we noted, they also tend to host sweet and shallow wells. Well salinity and snow cover vary along the same spatial gradient as vegetation density so it is difficult to untangle their relative importance. Herders’ perceptions suggest that water-related factors are impor- tant in site selection and abandonment, with depletion also a notable ‘push factor.’ Absolute vegetation density was less commonly given as a ‘pull factor.’ Whichever predominates, livestock owners have clearly selected more attractive sites in 2012 than in 2003. This may have relaxed constraints originally imposed by distance, allowing livestock owners to target better sites. Such a proposition is supported by the fact that the colonisation of increasing numbers of sites has been accompanied by a simul- taneous process of site abandonment, as evidenced by the group of wells occupied in 2003 alone, and suggesting that the factors favouring the initial choice of certain sites subse- quently changed over time. Resource depletion at early- occupied sites, a suite of positive characteristics of unoccupied sites, and a decrease in distance-related costs may have all led to the observed patterns of site occupation over time. The operation of the MVT, predicting movement from depleted patches to new patches once costs and gains Despite these processes, and the recent colonisation of many new sites with low depletion and high vegetation density, a Hum Ecol (2017) 45:5–21 19 Zharas; Nurgul and Nazgul Zhumasheva. We appreciate the comments and suggestions from two anonymous reviewers. large proportion of sites occupied in 2003 continue to be occu- pied today, and this set of sites in particular still exhibits strong depletion – indicating very low GUDs and high cost to gain ratios. In order to use sites in the Moiynkum, considerable investments must be made to restore wells, winter houses and barns. Even if owners were able to Bsell^ these assets, the costs of rebuilding them at a new and more distant sites is likely to be high. Although recent trends suggest movement out of depleted areas, these have not yet resulted in optimal foraging patterns across the landscape. It remains to be seen whether such pat- terns will emerge as livestock numbers rise still further. Discussion and Conclusions Compliance with Ethical Standards Research reported here was funded by the Leverhulme Trust in an award to Imperial College London, Department of Life Sciences, entitled BExclusion vs Mobility: Limits to Ideal Free Distributions in Pastoralist Systems^ (grant number RPG 251). The authors are solely responsible for the interpretation of the results, and for any errors contained in this paper. Conflict of Interest The authors declare that they have no conflict of interest. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The use of the MVT to structure our investigations has been useful because it allows us to weigh up the opposing ‘pull factors’ of resource density (and other attractive site characteristics) against the constraints im- posed by distance. The relative outcome of these two opposing forces is measured in our specific factor of interest – resource depletion, interpreted in the theory through the concept of GUD. This approach has allowed us to show empirically over a large area what range scientists in Kazakhstan have observed since indepen- dence – an uneven use of rangeland resources leading to a combination of localised overuse and abandonment (Alimaev et al. 2008; Rachkovskaya and Bragina 2012). References Predictive Models of Movement by Serengeti Grazers. Ecology 85: 2429– 2435. Moritz M., Soma E., Scholte P., Xiao N., Taylor L., Juran T., and Saïdou K. (2010). An Integrated Approach to Modeling Grazing Pressure in Pastoral Systems: the Case of the Logone Floodplain (Cameroon). Human Ecology 38: 775–789. Government of Kazakhstan and the World Bank (2004). Supporting Revival of the Livestock Sector in Kazakhstan, Programme for Collaborative Economic Research of the Government of, Kazakhstan, Washington. Moritz M., Hamilton I. A., Chen Y., and Scholte P. (2014). Mobile Pastoralists in the Logone Floodplain Distribute Themselves in an Ideal Free Distribution. 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(eds.), Resource Ecology: Spatial and Temporal Dynamics of Foraging, Springer. Acknowledgements This paper is a contribution to Imperial College’s Grand Challenges in Ecosystems and the Environment initiative. We are very grateful to the following individuals for their support, advice, and assistance: Resgul Adushov; Ilya Ilytch Alimaev; Kydrbai Atabaev and all his family; Cara Kerven; Bulgyn Koitai; Igor Lysenko; Zheksinbai Sisatov; Aidos Smailov; Sayat Temirbekov; Sean Webber; Aigul Brown J. S. (1988). Patch Use as an Indicator of Habitat Preference, Predation Risk and Competition. Behavioural Ecology and Sociobiology 22: 3–47. 20 Hum Ecol (2017) 45:5–21 arid rangelands. In Behnke, R. (ed.), The Socio-Economic Consequences of Desertification in Central Asia, Springer. arid rangelands. In Behnke, R. (ed.), The Socio-Economic Consequences of Desertification in Central Asia, Springer. Charnov E. L. (1976). Optimal Foraging, the Marginal Value Theorum. 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Risk of selection bias in randomized trials: further insight
Trials
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Correspondence: vb78c@nih.gov National Cancer Institute and University of Maryland Baltimore County, Biometry Research Group, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850, USA © 2016 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Background appropriate allocation concealment, but, rather, have (at best) only partial allocation concealment. Cleary, allocation concealment is not a binary phenomenon [2], and its success depends on addressing both threats, direct observation and prediction. In other words, improper randomization constitutes a violation of allocation con- cealment [3]. These are not two distinct dimensions of trial quality, and should not be treated as such. Kahan, Rehal, and Cro [1] are to be congratulated for drawing attention to a rather important problem in trial design, namely how to reduce or eliminate the risk of selection bias. The remedial methods discussed include (1) masking recruiters, (2) the use of unrestricted randomization, (3) not stratifying by site in multicenter trials, (4) avoiding permuted blocks when stratifying by site, and (5) making better use of prognostic covariates. Among the major findings are that 3 % of the trials used unrestricted randomization, 35 % did not specify how they randomized at all, and 58 % of those that stratified by site used permuted blocks. We wish to focus on these findings, and also on another opportunity to curb selec- tion bias, namely post-trial auditing as a disincentive. Berger Trials (2016) 17:485 DOI 10.1186/s13063-016-1597-5 Berger Trials (2016) 17:485 DOI 10.1186/s13063-016-1597-5 Open Access Risk of selection bias in randomized trials: further insight Vance W. Berger Vance W. Berger Abstract The quality of randomization is an under-appreciated facet of trial design. The present piece represents an advance in our collective understanding of how allocation concealment and randomization relate to risk of selection bias in randomized trials, and other measures are also considered. Though the overwhelming majority of the advice given is timely and correct, it is more instructive to focus on the relatively narrow sliver of advice that is incorrect (namely, that trials should not stratify by site, and that unrestricted randomization is a solution to the problem of selection bias), so it is in this context that the comments here must be understood. In no way is this intended to be a rebuttal of the excellent work we have before us. Rather, it is a refinement. Keywords: Allocation concealment, Berger-Exner test, Conditional unrestricted randomization, Maximal procedure Unrestricted randomization: is 3 % too much, or too little? The authors put forth unrestricted randomization as a method to eliminate selection bias, and indeed it is. But when we bear in mind that we can prevent all carpal tunnel syndrome instantly by amputating all hands as a preventative measure, we recognize that eliminating one problem is not enough. The solution must also not intro- duce additional problems. Unfortunately, unrestricted randomization does precisely that, and this is why nobody has ever used it, or ever would use it in an actual trial. The 3 % is not, as suggested, too small a figure; it is, on the contrary, too large a figure. The true nature of allocation concealment It is stated that even with appropriate allocation conceal- ment, prediction may still be possible. This misguided statement represents a misunderstanding of allocation concealment, and needs to be refuted since the notion is so prevalent. As one might guess from the name itself, allocation concealment means that the allocations are concealed. If they can be predicted, then we do not have This may sound like an audacious claim. How can we state that unrestricted randomization has never been used when the authors report that 3 % figure? In fact what is used when authors claim unrestricted randomization is not actually unrestricted randomization, as we shall explain. They instead use a vaguely defined Correspondence: vb78c@nih.gov National Cancer Institute and University of Maryland Baltimore County, Biometry Research Group, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850, USA Berger Trials (2016) 17:485 Page 2 of 5 Page 2 of 5 variation we shall refer to as conditional unrestricted randomization. One major problem with unrestricted randomization is chronological bias, or the possibility of many more early patients ending up in one treatment group and many more later patients ending up in the other treatment group [4, 5]. In fact, this chronological bias is the primary reason that restricted randomization is used (as it should be) [6]. However, we shall focus instead on another issue with unrestricted randomization. Just as a normal distribution for heights means that, sooner or later, we will encounter an individual with a negative height [7], so too is it the case that with true unrestricted randomization we will, sooner or later, see an allocation sequence comprised entirely of only one treatment group. condition) [4, 5, 9]. As it turns out, these MTI procedures are not only expressed more precisely (and honestly) than unrestricted randomization, but they are also far more suitable for actual trials by virtue of controlling chrono- logical bias and eliminating the possibility of unfortunate outcomes of the type we described earlier. So the authors are correct in spirit. We do need randomization procedures with fewer restrictions. But the solution is not to swing the pendulum all the way to the other side. We do still need some restrictions, namely the MTI. But the call should be for no additional restrictions above and beyond this, and also for larger MTI values than those that are typically used in practice, plus dropping the requirement of terminal balance. The true nature of allocation concealment q p y y g p We do not believe that any clinical trial researcher would ever, under any circumstances, accept such an unfortunate outcome. If confronted by this, they would “throw it back” and try again. But this discretion to do that calls into question just which allocation sequences would be considered admissible? We do not get around this consideration by appeal to the fact that we did not have to throw the first one back, nor by the old adage about not being able to define it but knowing it when we see it. In a world of precise definitions, this simply will not cut it. Knowledge of the sampling properties of the randomization procedure is possible only when we actually know what the randomization procedure is. So would we have accepted a split of 95:5? What about 90:10? Where exactly is the line drawn? And even if we are not only OK but also thrilled with the ideal ratio of 50:50, are we still OK with a 50:50 sequence that is segregated, with the first half of the allocations all going to the same group, and then the rest going to the other group to balance out the numbers at the end? No, we are not. Failure to specify how the trial was randomized The authors are correct that failure to specify how the trial was randomized is simply unacceptable. And yet this occurred in 35 % of the trials evaluated. One can only imagine a conversation between a patient (P), a prescribing physician (PP), and a statistician (S): P: Is this treatment you prescribed the best option given my condition? PP: The evidence suggests that it is. P: I understand that medical studies are conducted to the highest and most rigorous standards possible? PP: Yes, they are. The stakes are too high for anything less than the best. P: And this is why the highest level of evidence is reserved for randomized trials? Berger Trials (2016) 17:485 Berger Trials (2016) 17:485 Berger Trials (2016) 17:485 Page 3 of 5 Page 3 of 5 S: That is correct. to recommend its use, given its drawbacks on the other dimension. But that is not the case when stating that the MTI procedures are superior to blocked randomization. Here, the superiority is in an overall sense, and not just in one isolated dimension. There is no compensation by appeal to other dimensions. The MTI procedures match blocked randomization for control of chronological bias, and beat it soundly for control of selection bias, in fact in more ways than one [9]. As such, the use of permuted block randomization is indefensible. P: And instead of calling these authors to account, you just assume that they randomized correctly, and then you act accordingly in your prescribing decisions? Don’t ask, don’t tell? Even if that means that patients may then get exposed to harmful treatments? And this is where our hypothetical dialogue ends, but I would be curious to know how real physicians might respond at this point. The enormous influence on trial quality and the reliability of the precise method of randomization cannot be overstated. The potential for misleading evidence resulting from flawed randomization methods has been well-documented [5]. And yet even given how important this information is, over one third of the trial authors could not be bothered to supply it, and over one third of the journal review teams could not be bothered to insist on it as a condition for publication. The very essence of evidence-based medicine is trust but verify (and that trust part is optional), yet consumers of medical research are put in a position of having to take it on faith that the research teams conducted rigorous research despite the fact that these very same research teams clearly were not rigorous at all in their reporting? This is not even a matter of trust. Trust would be believing the claim, but here, no claim is even offered. They do not even claim to have randomized correctly. Credibility in a sys- tem that allows for this cavalier attitude towards the lives and health of actual patients might be misplaced. Berger Trials (2016) 17:485 One reviewer pointed out that permuted block randomization should be fine in masked trials, since even an occasional unmasked allocation would likely occur after the block is complete, and also for multi- center trials for which no one investigator can keep track of all allocations, since some will occur at other centers. This is, in fact, a widely held view, and likely contributes to the reluctance to switch from permuted block randomization to MTI randomization, so it does merit a thoughtful response. g p First, in multicenter trials, randomization is generally stratified by center, so that in fact an investigator can keep track of how the allocation is progressing, at least at his or her center, but then this is all that is relevant for prediction anyway. Second, even if randomization were not so stratified, investigators can still predict successfully, even without certainty, based on how many patients have so far been randomized to each group. True, this can be done with MTI randomization too, but then it will be less successful than it will be with permuted blocks. Moreover, some unmasking in trials that are planned as masked can be immediate, as with injection site reactions [11]. And even if masking is retained perfectly throughout, so that selection bias of the type we consider is not an issue, there is still no benefit in using permuted block randomization. In that case, it is just as good as, but not better than, MTI randomization [9]. So we are comparing two procedures, one of which is clearly better in one situation and is just as good in the other situation, and we would not know ahead of time which situation we would be in. PP: Exactly. PP: Exactly. PP: Exactly. P: Are all types of randomization equally rigorous, or are some better than others? PP: This is a question for the statistician. S: Some methods of randomization are better than others. The worst ones, such as permuted block randomization, can be easily deciphered and subverted. Hopefully, it is clear that “unrestricted randomization” is a procedure that nobody would ever use in an actual clinical trial and, moreover, it is sufficiently poorly defined that when it is claimed we cannot decipher what proced- ure actually was used. If pressed, then a researcher who claimed to use unrestricted randomization would have to come to grips with just how large an imbalance in group sizes he or she would tolerate. In fact, there is a class of randomization procedures that explicitly takes into account this maximally tolerated imbalance (MTI), namely the MTI procedures, including the big stick (essentially unrestricted randomization until the MTI is reached, at which point the allocation is forced to restore balance) [6], Chen’s procedure (a refinement of the big stick in which a biasing probability is specified so as to encourage a move towards balance without forcing it, at least until the MTI is reached) [8], and the maximal procedure (which selects randomly from among the allocation sequences that adhere to the MTI P: I see! Well, in that case, it’s a good thing that the trials whose results have informed your decision on how to treat me did not use permuted block randomization! p S: Well, they may have. We actually don’t know if they did or didn’t. P: I understand. I would not expect you to memorize all the details of every study. But for my peace of mind, can you please check on that when you go back to your office and have the studies available? S: No, I happen to have the articles right here with me. It is not that I cannot remember. We do not know because the articles did not specify how they randomized. P: So you are telling me that they may have used a valid randomization procedure, and they may not have? We have no way to know? And if they didn’t, then the trial results may bear little or no resemblance to the reality governing how effective this treatment is for my condition? Permuted blocks It is pointed out [1] that 58 % of the stratified trials used permuted blocks. We can all agree that this is way too high, and the ideal proportion would be somewhere close to zero. Even one trial using permuted blocks is one too many. But what about trials that are not strati- fied by center? Are permuted blocks OK in these? The answer is still no. Just as the MTI procedures are far su- perior to unrestricted randomization by virtue of their better ability to handle chronological bias, so too are they far superior to permuted block randomization, but here due to their superior ability to control selection bias [9, 10]. The best randomization procedure for eliminat- ing selection bias is unrestricted randomization, yet for the reasons articulated above, we are still opposed to its use in practice. Might the same argument be offered to justify using permuted block randomization even though the MTI methods are superior? No, it cannot. This discussion makes clear that permuted block randomization should not be used. It does not, however, support the use of MTI randomization, since it would be a false dichotomy to believe that these are the only two options. Clearly, they are not. Proschan [12] discusses some other types of randomization that might be used, and, indeed, these too would be preferable to permuted block randomization. However, in other work we have found MTI randomization to be optimal, so it is these procedures that we focus on, and recommend for use in practice. Future work will extend the MTI procedures to unequal allocation, and more than two treatment groups, but for now, at least we can point out that it does seem The comparison of any two randomization methods, whether we are comparing unrestricted randomization to the maximal procedure or whether we are comparing blocked randomization to the big stick, must necessarily account for both selection bias and chronological bias. The fact that unrestricted randomization wins on only one of these comparisons is, as we have seen, insufficient Berger Trials (2016) 17:485 Berger Trials (2016) 17:485 Page 4 of 5 Page 4 of 5 prudent to replace permuted block randomization with MTI randomization, at least for trials with two arms and a 1:1 allocation. treatment in fact is no more effective than the control (or placebo). Abbreviations MTI: Maximally tolerated imbalance; P: Patient; PP: Prescribing physician; S: Statistician Competing interests The author declares that he has no competing interests. p g The author declares that he has no competing interests. Received: 17 September 2015 Accepted: 11 September 2016 References Permuted blocks So while inertia remains a huge problem in getting researchers to upgrade their methodologies [15], it is not the only problem. There is more at play here, including a perverse system of incentives that works to reward researchers for using flawed research method- ology. What possible incentive do researchers have to get it right when doing so will hurt their bottom line and, moreover, given that it is optional anyway? Why report honest trial results when doing so will put you at a strategic disadvantage relative to your competitors, some of whom may be using blocked randomization and any other trick they can get away with? Post-trial auditing One ideal opportunity to control selection bias was not touched upon, but should have been. It seems pretty close to research malpractice to not specify how the randomization was conducted, and it is just as bad to not formally test for selection bias after the fact. This widespread failure to even consider selection bias allows offending investigators to fly under the radar and to carry on without any fear of any real consequence. There simply is no disincentive to engage in this type of behavior. Clearly, this needs to change if trial results are to remain credible even after the public comes to understand just how easy the results are to manipulate. They will need to be assured that while it is theoretically possible to manipulate trial results, actual trials are immune because only best practices are used. Presently, we are not even close to being able to claim this. Clearly, self-policing does not work. It is time for an external agency to step in and clean up the mess. Only when true accountability is demanded of all medical researchers can we expect, first, better reporting of randomization methods, and second, better randomization methods. The first step has to be zero tolerance for failure to report the randomization method used in a trial, and zero tolerance for failure to audit the trial for selection bias after the fact. Short of these steps, the public has every reason to withdraw whatever trust it has left in the medical establishment. Post-trial auditing needs to be standard and routine. It should not be triggered only when there is some basis for suspicion [13], unless the inherent vested interests the researchers have when conducting the trials them- selves constitute a firm basis for suspicion, as clearly they should. The most reliable method for testing for selection bias in a randomized trial is the Berger-Exner test [14], which is based on a comparative analysis of those patients who could have been anticipated to end up in the active treatment group versus those who ended up there by chance. One can only wonder how many of the trials considered conducted this analysis, although the silence on this issue speaks volumes and we pretty much already know the answer. References h 1. Kahan BC, Rehal S, Cro S. Risk of selection bias in randomised trials. Trials. 2015. In press. Acknowledgements The review team offered helpful comments that greatly improved the presentation. The review team offered helpful comments that greatly improved the presentation. 12. Proschan M. Influence of selection bias on type I error rate under random permuted block designs. Stat Sin. 1994;4:219–31. 13. Berger VW. Do not test for baseline imbalances unless they are known to be present? Qual Life Res. 2009;18:399. 14. Berger VW, Exner DV. Detecting selection bias in randomized clinical trials. Control Clin Trials. 1999;20(4):319–27. 15. Berger VW. Conflicts of interest, selective inertia, and research malpractice in randomized clinical trials: an unholy trinity. Sci Eng Ethics. 2014. in press. Berger Trials (2016) 17:485 Conclusions 2. Berger VW. Is allocation concealment a binary phenomenon? Med J Aust. 2005;183(3):165. There is a major disconnect between the perception of medical research as a pristine beacon of hope working to save us all, and the reality of medical research as a business conducted at least partially to enrich those engage in it. Certain outcomes are more profitable, and the trials are conducted, for the most part, by the very parties who stand to gain or lose based on the trial outcomes. Moreover, these same parties with the vested interests also enjoy almost unfettered discretion to conduct the trials as they see fit, subject to some constraints but, as we have seen, constraints that still allow for discretion in deciding, among other things, to randomize properly or not. This key component of trial quality is left as a personal decision. 3. Berger VW, Do AC. Allocation concealment continues to be misunderstood. J Clin Epidemiol. 2010;63(4):468–70. 4. Berger VW, Ivanova A, Deloria-Knoll M. Minimizing predictability while retaining balance through the use of less restrictive randomization procedures. Stat Med. 2003;22(19):3017–28. 5. Berger VW. Selection bias and covariate imbalances in randomized clinical trials. Chichester: Wiley; 2005. 6. Soares JF, Wu CFJ. Some restricted randomization rules in sequential designs. Commun Stat Theor Methods. 1983;12:2017–34. 7. Perlman P, Possen BH, Legat VD, Rubenacker AS, Bockiger U, Stieben-Emmerling L When will we see people of negative height. Significance. 2013;10(1):46–8. 8. Chen YP. Biased coin design with imbalance tolerance. Communicat Stat Stoch Models. 1999;15:953–75. 8. Chen YP. Biased coin design with imbalance tolerance. Communicat Stat Stoch Models. 1999;15:953–75. 9. Berger VW, Agnor RC, Bejleri K. Comparing MTI randomization procedures to blocked randomization. Stat Med. 2016;35(5):685–94. 10. Zhao W, Weng Y, Wu Q, Palesch Y. Quantitative comparison of randomization designs in sequential clinical trials based on treatment balance and allocation randomness. Pharm Stat. 2012;11:39–48. doi:10.1002/pst.493. Improper randomization, such as permuted block randomization, invites the type of selection bias that can masquerade as a treatment effect even when the 11. Berger VW, Agnor RC. Delayed unmasking and selection bias. Stat Med. 2016;35(12):2111–2. 11. Berger VW, Agnor RC. Delayed unmasking and selection bias. Stat Med. 2016;35(12):2111–2. 15. Berger VW. Conflicts of interest, selective inertia, and research malpractice in randomized clinical trials: an unholy trinity. Sci Eng Ethics. 2014. in press. Berger Trials (2016) 17:485 Page 5 of 5 Berger Trials (2016) 17:485 Berger Trials (2016) 17:485 Page 5 of 5 • We accept pre-submission inquiries • Our selector tool helps you to find the most relevant journal • We provide round the clock customer support • Convenient online submission • Thorough peer review • Inclusion in PubMed and all major indexing services • Maximum visibility for your research Submit your manuscript at www.biomedcentral.com/submit Submit your next manuscript to BioMed Central and we will help you at every step: • We accept pre-submission inquiries • Our selector tool helps you to find the most relevant journal • We provide round the clock customer support • Convenient online submission • Thorough peer review • Inclusion in PubMed and all major indexing services • Maximum visibility for your research Submit your manuscript at www.biomedcentral.com/submit Submit your next manuscript to BioMed Central and we will help you at every step: • We accept pre-submission inquiries • Our selector tool helps you to find the most relevant journal • We provide round the clock customer support • Convenient online submission • Thorough peer review • Inclusion in PubMed and all major indexing services • Maximum visibility for your research Submit your manuscript at www.biomedcentral.com/submit Submit your next manuscript to BioMed Central and we will help you at every step: Submit your next manuscript to BioMed Central and we will help you at every step:
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Effects of the consumption of "multimixture" on nutritional status: a community trial involving children from a slum district on the outskirts of Maceió, State of Alagoas, Brazil
Revista Brasileira de Saúde Materno Infantil
2,008
cc-by
6,737
ARTIGOS ORIGINAIS / ORIGINAL ARTICLES ARTIGOS ORIGINAIS / ORIGINAL ARTICLES Resumo Objectives: to investigate the impact of the consumption of "multimixture" (a bran-based cereal mixture) on the nutritional status of children at risk of malnutrition. Objetivos: verificar o impacto do consumo da multi- mistura sobre as condições de nutrição e saúde de crianças em situação de risco. Métodos: ensaio comunitário envolvendo crianças (6 a 60 meses) de uma favela de Maceió, Alagoas, Brasil, aleatoriamente alocadas para o Grupo Controle (n=50) ou Grupo Multimistura (n=48). Neste, a suplementação consistiu de duas colheres de sopa/dia. Avaliações antropométricas foram realizadas antes e após a fase experimental (10 meses). A incidência de agravos à saúde foi investigada pela realização de inquéritos quinzenais de morbidade. O consumo alimentar foi ana- lisado por inquérito recordatório de 24 horas (três dias alternados). Os níveis de hemoglobina (Hemocue ) e de retinol sérico (HPLC) foram aferidos apenas no final da fase experimental. As medidas de desfecho foram comparadas entre os grupos usando-se testes paramétricos ou não-paramétricos, conforme cada situ- ação. Diferenças foram consideradas como estatistica- mente significativas quando p<0,05. Methods: a community trial involving children (6 to 60 months) from a slum area in the city of Maceió, State of Alagoas, Brazil, randomly assigned to the Control Group (n=60) or to the "multimixture" Group (n=48). The supplement consisted of two tablespoons of "multimixture" per day. Anthropometric measure- ments were taken before and after the experimental phase (10 months). The incidence of health problems was investigated on a biweekly basis. Food consump- tion was assessed by way of 24 hour dietary recall (on three alternate days). Hemoglobin (HemoCue®) and serum retinol (HPLC) were determined at the end of the experimental phase. The resulting measurements for the two groups were compared using parametric or non-parametric statistics in according with the situation. Differences were considerate as significa- tive statistically when p<0.05. Resultados: não foram observadas diferenças (p>0,05) entre os resultados obtidos na avaliação antropométrica, dietética, bioquímica e na incidência de diarréia, vômitos e febre. Todavia, as infecções respi- ratórias incidiram de forma mais intensa sobre as crianças do Grupo Controle (24,3% vs. 16,9%; OR=1,59; IC95%=1,13-2,24; p<0,01). Results: no differences were observed (p>0.05) between the results obtained from anthropometric measurements and dietary intake, between levels of hemoglobin and serum retinol or in the incidence of diarrhea, vomiting or fever. However, there was a higher incidence of respiratory infections among the children in the Control Group (24.3% vs.16.9%; OR=1.59; 95%CI = 1.13-2.24; p<0.01). Efeitos do consumo da multimistura sobre o estado nutricional: ensaio comunitário envolvendo crianças de uma favela da periferia de Maceió, Alagoas, Brasil Haroldo da Silva Ferreira 1 Sybelle de Araújo Cavalcante 2 Cyro Rego Cabral Jr. 3 Adriana Toledo de Paffer 4 Haroldo da Silva Ferreira 1 Sybelle de Araújo Cavalcante 2 Cyro Rego Cabral Jr. 3 Adriana Toledo de Paffer 4 1-4 Faculdade de Nutrição. Universidade Federal de Alagoas. Campus A. C. Simões, BR 104-Norte, Km 97, Cidade Universitária. Maceió, AL, Brasil. CEP: 57.072-970. E-mail: haroldo.ufal@gmail.com 1-4 Faculdade de Nutrição. Universidade Federal de Alagoas. Campus A. C. Simões, BR 104-Norte, Km 97, Cidade Universitária. Maceió, AL, Brasil. CEP: 57.072-970. E-mail: haroldo.ufal@gmail.com Effects of the consumption of "multimixture" on nutritional status: a community trial involving children from a slum district on the outskirts of Maceió, State of Alagoas, Brazil Palavras-chave Palavras-chave Antropometria, Anemia, Alimentação alternativa, Infecções respiratórias Alimentação alternativa, Infecções respiratórias Resumo Conclusões: a suplementação com multimistura não alterou o perfil antropométrico ou a freqüência de anemia e hipovitaminose A entre as crianças. Conclusions: the "multimixture" food supplement did not alter the anthropometric profile or the frequency of anemia or hypervitaminosis A among the children. Métodos Trata-se de um estudo do tipo ensaio comunitário, constituído de um grupo experimental e um grupo controle, envolvendo crianças na faixa etária de 6 a 60 meses, residentes na favela Cidade de Lona, no município de Maceió, Alagoas, Brasil. A favela Cidade de Lona possui aproximada- mente 600 domicílios. A fim de proceder a alocação das crianças em um dos grupos de estudo, dividiu-se a área em dois setores, A e B, tomando como refe- rência uma rua central da localidade. Após uma avaliação antropométrica de todas as crianças da faixa etária-alvo, foi escolhido, para cada setor, um grupo de 50 crianças com menor escore z para o índice peso para idade. Por meio de sorteio, definiu- se que tais crianças dos setores A e B formariam, respectivamente, os grupos controle e multimistura. A investigação foi procedida no período de janeiro a outubro de 2006. Segundo Mahler,5 sendo a desnutrição uma conseqüência da pobreza e da privação, só poderá ser erradicada mediante uma ação política orientada a reduzir as desigualdades entre países e entre os habitantes de um mesmo país. Na ausência dessa política, a sociedade civil organizada busca soluções alternativas para o problema. Todos os pais ou responsáveis foram informados quanto aos detalhes da pesquisa, autorizaram e assi- naram o Termo de Consentimento Livre e Esclarecido, conforme definido no projeto subme- tido e aprovado pelo Comitê de Ética em Pesquisa da Universidade Federal de Alagoas. No contexto dessas ações, surgiu a proposta da alimentação alternativa, tendo por base a premissa que folhas, cascas e sementes descartadas como lixo, seriam potencialmente nutritivas.6 Esse conceito teve como principal desdobramento a elaboração da chamada multimistura (MM), um farelo formulado a partir desses subprodutos e usado como suplemento à alimentação habitual de crianças, o qual vem sendo utilizado por profissionais de saúde em grande número de municípios brasileiros.7 Não foram incluídas no sorteio aquelas crianças que atendessem uma ou mais das seguintes condições: a) não autorização dos pais ou respon- sáveis; b) criança portadora de desnutrição grave (z <-3 para quaisquer dos índices antropométricos formados com as variáveis peso, altura, sexo e idade); e c) criança portadora de malformações ou enfermidades (acamadas, hospitalizadas, com febre no início do estudo, entre outras condições). Key words Key words Anthropometry, Anemia, Alternative feeding, Respiratory tract infections 309 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Ferreira HS et al. Introdução entre os resultados obtidos.7 entre os resultados obtidos.7 Diante do exposto, justifica-se a realização de estudos epidemiológicos controlados que possam avaliar a eficácia das intervenções que vêm sendo adotadas em várias localidades brasileiras, baseadas na utilização da multimistura. Apesar das evidências de que o Brasil passa por um processo de transição nutricional e das reiteradas vezes em que os países membros das Nações Unidas têm reafirmado o compromisso de garantir o direito de todo ser humano em não padecer de fome, a desnutrição infantil continua sendo um grave pro- blema de saúde pública em nosso país.1 O objetivo deste trabalho foi avaliar se o consumo regular da multimistura contribui para a promoção da melhoria das condições de nutrição e saúde de crianças submetidas à situação de risco nutricional. A partir 1974, quando ocorreu o primeiro inquérito nutricional de abrangência nacional, a prevalência de desnutrição em crianças apresentou um declínio da ordem de 72%. No entanto, ainda existem diferenciais importantes entre as regiões geográficas brasileiras. No último inquérito, rea- lizado em 1996, a prevalência de desnutrição obser- vada no Centro-Sul do país foi de 5,6% enquanto que, no Nordeste, essa prevalência era de 17,9% de crianças desnutridas.2 Esses dados, baseados em proporções populacionais, mascaram a gravidade com que a desnutrição acomete determinados grupos, especialmente aqueles submetidos à insegu- rança alimentar. Em estudos conduzidos em favelas de Alagoas, têm-se encontrado quase 50% das crianças com déficit estatural importante3 e mais de 93% acometidas pela anemia.4 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Métodos No entanto, tal proposição tem recebido muitas críticas no meio acadêmico em virtude da alegação de falta de comprovação científica de seus efeitos, ausência de controle sanitário, bem como pela sua inadequação para consumo humano, isso devido à possível existência de toxinas e fatores antinutri- cionais.8-12 Além desses critérios, definiu-se que seriam excluídas do estudo as crianças que, tendo sido intro- duzidas no Grupo Multimistura, tenham durante o transcorrer da coleta de dados: a) deteriorado seu estado nutricional atingindo a condição de desnu- trição grave; b) desenvolvido qualquer agravo que pudesse ser atribuído ao uso da multimistura, ainda No intuito de contribuir para o esclarecimento dessa problemática, várias pesquisas têm sido rea- lizadas; no entanto, ainda existem muitas divergên- cias sobre o assunto em virtude das discrepâncias 310 Efeitos do consumo da multimistura que de forma especulativa; c) a autorização dos pais para participação no estudo fosse retirada; e d) não tenham participado de todas as etapas do estudo. adequação tendo como referencial os valores recomendados nas Recommended Dietary Allowances (RDAs).15 Adicionalmente, comparou- se o percentual de crianças que não atingiram a meta de ingestão individual (RDA), no grupo experi- mental e controle. A multimistura foi preparada e fornecida pela Pastoral da Criança de Maceió. Era composta de farelo de trigo (80%), folha de mandioca (10%) e pó de casca de ovo (10%). Esses ingredientes passavam por um tratamento térmico durante 5 a 10 minutos em fogo baixo, mexendo-se com colher de pau com a finalidade de destruir microrganismos e substân- cias tóxicas. Em seguida, eram trituradas em moinho e depois peneiradas a fim de facilitar a homo- geneização. Embora não fosse objetivo deste trabalho avaliar o padrão alimentar das crianças, houve a necessidade de introdução desse procedimento, visando-se garantir que possíveis diferenças encontradas nos indicadores utilizados no estudo pudessem ser atribuídas à suplementação utilizada e não a discrepâncias na ingestão dietética dos grupos envolvidos. O controle de qualidade do produto final foi efe- tuado pelo Laboratório Central do Estado de Alagoas (LACEN) e, paralelamente, pelo Laboratório de Microbiologia de Alimentos da Faculdade de Nutrição da Universidade Federal de Alagoas. Foram realizadas duas avaliações antropomé- tricas, uma antes do início do seguimento e outra no final da fase experimental. Os dados relativos às variáveis de idade, sexo, massa corporal e estatura foram processados por meio do Epi-Info 3.3.2, de modo a constituir os índices peso-para-idade, peso- para-altura e altura-para-idade. Métodos O referencial antro- pométrico utilizado foi o do Center for Disease Control and Prevention (CDC) do National Center for Health Statistics, 2000, que se encontra incorpo- rado ao programa Epi-info. Obviamente, apenas as crianças do grupo experi- mental (Grupo Multimistura) recebiam o suple- mento. Para cada criança, era fornecida multimistura em embalagem específica, contendo a quantidade aproximada para consumo quinzenal. Ao final deste período, um membro da equipe retornava ao domicílio recolhendo o recipiente com as eventuais sobras, fornecendo novo recipiente com multimis- tura, para consumo na quinzena seguinte. Esses procedimentos tiveram os seguintes objetivos: a) evitar o consumo de multimistura com validade vencida; e b) observar se a mesma estava sendo de fato consumida. A massa corporal foi obtida por meio de balança antropométrica digital portátil, com capacidade para 180 kg e sensibilidade de 100 g (balança Marte PP180 ). O comprimento das crianças menores de dois anos foi verificado na posição de decúbito dorsal sobre um estadiômetro de madeira, dotado de fita métrica, com sensibilidade de 0,1cm. As crianças com idade superior a dois anos foram medidas em posição ortostática em estadiômetro dotado de fita métrica com as mesmas características acima referidas. A Multimistura era oferecida na proporção de duas colheres de sopa por dia, fracionadas na alimentação habitual da criança, durante um período de 10 meses (fase experimental). A ingestão habitual das crianças foi estimada com base na média do consumo obtida em três inquéritos recordatórios de 24 horas aplicados em intervalos não inferiores a 30 dias. As informações foram sempre prestadas pelas respectivas mães. Como recurso para ajudá-las a recordar as porções de alimentos consumidos foi utilizado o álbum de registro fotográfico de alimentos de Zabotto.13 Os dados foram coletados por estudantes do curso de graduação em nutrição, devidamente treinados e supervisionados, seguindo as recomen- dações do Ministério da Saúde.16 O inquérito bioquímico envolveu todas as crianças do estudo (Grupos Controle e Multimistura) e foi constituído de exame de hemoglobina (Hb) e determinação do retinol sérico. Por questões éticas, essas determinações só foram procedidas ao final da fase experimental, de modo a garantir tratamento adequado a todas as crianças que apresentassem anemia e/ou hipovitaminose A. O inquérito bioquímico envolveu todas as crianças do estudo (Grupos Controle e Multimistura) e foi constituído de exame de hemoglobina (Hb) e determinação do retinol sérico. Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Resultados As condições de vida verificadas na localidade estu- dada eram de extrema miséria. Todos os domicílios eram barracos feitos de caibros cobertos com plás- tico ou papelão. O piso não tinha revestimento. Não existia banheiro, de modo que os dejetos eram jogados a céu aberto, juntamente com o lixo em geral. A água era obtida da rede pública, através de algumas torneiras colocadas em pontos estratégicos da favela, sendo armazenada em recipientes como tonéis, baldes ou latões. A maioria dos adultos não estava inserida no mercado de trabalho formal, de modo que os homens faziam "biscaites" e as mulheres, quando trabalhavam, exerciam funções como as de empregada doméstica ou lavadeira, si- tuação em parte explicada pelo baixo nível de esco- laridade vigente (50,7% dos adultos eram analfa- betos). Portanto, a amostra estudada foi retirada de uma população em situação de extrema insegurança alimentar. Na análise, somaram-se todos os eventos ocor- ridos durante o período de avaliação, segundo o tipo de ocorrência e grupo de estudo. As respectivas freqüências foram, então, comparadas. As crianças de ambos os grupos receberam anti- helmíntico polivalente no início do estudo e também ao final do mesmo. Aquelas que, por ocasião dos inquéritos de morbidade, estavam acometidas por diarréia, rece- biam atenção específica baseada na terapia de reidratação oral. Para isso foram distribuídas colheres-medida e as respectivas orientações de como preparar e administrar o soro caseiro. Adicionalmente, foi distribuído hipoclorito de sódio em todos os domicílios, visando melhorar a quali- dade sanitária da água consumida. Ao final do período experimental de dez meses, o grupo controle permaneceu com as 50 crianças que iniciaram o estudo, enquanto o Grupo Multimistura ficou com 48. Neste grupo, duas crianças foram excluídas, em virtude de não terem utilizado a multi- mistura com a regularidade recomendada. Os pacotes estatísticos Epi-Info, versão 3.3.2 e SPSS, versão 14.0, foram usados para as análises estatísticas. Para verificar o atendimento aos pressu- postos paramétricos foram utilizados o teste de Levene (para homogeneidade das variâncias dos erros) e o teste de Shapiro-Wilk (para normalidade na distribuição dos resíduos), admitindo-se para ambos p<0,05. Houve necessidade de ajuste apenas para as variáveis dietéticas, exceto para o ferro e o zinco. A energia e o cálcio foram ajustados por trans- formação logarítmica. Os valores de proteína foram transformados em raiz quadrada mais 0,5. Para a vitamina A não se obteve ajuste em nenhum dos procedimentos testados. Métodos Por questões éticas, essas determinações só foram procedidas ao final da fase experimental, de modo a garantir tratamento adequado a todas as crianças que apresentassem anemia e/ou hipovitaminose A. Para os cálculos da ingestão (média dos três inquéritos) de energia, proteínas, ferro, vitamina A, cálcio e zinco, os dados obtidos foram processados no software NutWin®.14 Objetivando transformar os dados em uma unidade padrão que permitisse a comparação das ingestões do conjunto das crianças, haja vista a impossibilidade de comparação direta em virtude das diferentes recomendações nutricionais segundo as distintas faixas etárias, os respectivos valores de ingestão foram transformados em percentual de A determinação da Hb foi procedida em uma gota de sangue capilar, obtida por punção da polpa digital, em um fotômetro portátil (HemoCuea®). Foram consideradas anêmicas as crianças com níveis de Hb<11g/dl.17 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 311 Ferreira HS et al. Ferreira HS et al. Para a determinação do retinol sérico, após jejum noturno de 12 horas, foram coletados cerca de 3 mL de sangue venoso em seringas descartáveis, trans- ferindo o material para tubos de ensaio. Após centrifugação, o soro foi acondicionado em tubos Eppendorf e mantido sob congelamento até o momento das análises, procedidas por método cromatográfico (cromatografia líquida de alta resolução-HPLC). Durante todas as etapas, tomou-se o cuidado de manter as amostras ao abrigo da luz, em virtude da fotossensibilidade do retinol. Foram consideradas portadoras de hipovitaminose A as crianças com retinol sérico <20 µg/dL.18 pendentes (exceto para a vitamina A que, por não atender aos pressupostos paramétricos, foi analisada por meio do teste de Mann-Whitney). Quando a análise envolvia três ou mais médias, usou-se a análise de variância (ANOVA) pelo Teste F de Snedecor, seguida do Teste de Tukey (HSD; p<0,05) para comparações múltiplas das médias. Na comparação entre as freqüências das variá- veis categóricas usou-se o Teste do Qui-quadrado de Pearson (χ2) para verificação de diferença significa- tiva (p<0,05) e como medida de associação, a razão de chances (Odds ratio). Após três meses do início da fase experimental, procederam-se inquéritos quinzenais de morbidade referida, com auxílio de formulário específico, no intuito de caracterizar a presença de agravos à saúde, tais como diarréia, infecções respiratórias, febre e vômitos. Este inquérito era repetido a cada 15 dias durante o transcorrer da fase experimental e seguiu a metodologia descrita por Cesar et al.19 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 OR=Odds ratio (razão de chances); IC95%=Intervalo de confiança 95%; *=obtido pelo coeficiente de associação phi (ϕ) entre os grupos de estudo; ns=não significativo (p>0,05). **=diferença estatisticamente significativa. Resultados Os resultados referentes aos inquéritos antro- pométricos encontram-se expressos na Tabela 1, enquanto aqueles relativos às determinações de hemoglobina e retinol sérico são apresentados na Tabela 2. Em nenhuma das situações observaram-se diferenças significativas (p>0,05). O consumo da multimistura não alterou a incidência de diarréia, vômito e febre durante a fase experimental, já que as diferenças entre os grupos não foram significativas (p>0,05). Quanto às infecções respiratórias, ocorreu maior incidência sobre o grupo controle (24,3% versus 16,9%; OR=1,59; IC95%=1,1-2,2; p=0,006) conforme Para verificar a existência de diferença significa- tiva (p<0,05) entre as médias obtidas em cada grupo utilizou-se o teste t de Student para amostras inde- 312 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Efeitos do consumo da multimistura Tabela 1 Índices antropométricos (Escores z médios) em crianças de 0 a 60 meses de idade, antes e após a suplementação (Grupo multimistura) ou não com a multimistura (Grupo Controle). Favela "Cidade de Lona", Maceió, Alagoas, 2005. Índice antropométrico Inquérito Grupos de estudo Valor p (ANOVA) Controle Multimistura Altura-para-idade inicial -1,19±1,41 -1,44±1,35 0,46 final -1,17±1,35 -1,53±1,28 Peso-para-idade inicial -1,03±1,18 -1,25±1,11 0,60 final -0,96±1,17 -1,17±1,09 Peso-para-altura inicial -0,32±0,87 -0,44±0,83 0,88 final -0,29±1,05 -0,31±0,92 Tabela 2 Hemoglobina e retinol sérico (Média ± DP) e prevalência de anemia e hipovitaminose A em crianças de 0 a 60 meses após 10 meses de suplementação (Grupo Multimistura) ou não com a multimistura (Grupo Controle). Favela "Cidade de Lona", Maceió, Alagoas, 2005 Grupo Hb (g/dL) Retinol (µg/dL) Anemia* (%) Hipovitaminose A** (%) Controle 12,4±2,3 26,0±5,9 16,1 11,9 Multimistura 12,8±1,7 24,4±4,4 8,3 21,6 Significância estatística pa=0,41ns pa=0,18ns OR=2,12 OR=0,49 IC95%=0,3-17,7 IC95%=0,1-1,9 pb=0,45ns pc=0,24ns *=Hemoglobina <11 g/dL; **=retinol sérico <20 µg/dL; a=Teste t de Student; b =Teste de Fischer; c=teste do qui- quadrado; OR=Odds ratio (razão de chances); IC95%=Intervalo de confiança 95%; ns=não significativo (p>0,05). Índices antropométricos (Escores z médios) em crianças de 0 a 60 meses de idade, antes e após a suplementação (Grupo multimistura) ou não com a multimistura (Grupo Controle). Favela "Cidade de Lona", Maceió, Alagoas, 2005. Índice antropométrico Inquérito Grupos de estudo Valor p (ANOVA) Controle Multimistura Altura-para-idade inicial -1,19±1,41 -1,44±1,35 0,46 final -1,17±1,35 -1,53±1,28 Peso-para-idade inicial -1,03±1,18 -1,25±1,11 0,60 final -0,96±1,17 -1,17±1,09 Peso-para-altura inicial -0,32±0,87 -0,44±0,83 0,88 final -0,29±1,05 -0,31±0,92 Índices antropométricos (Escores z médios) em crianças de 0 a 60 meses de idade, antes e após a suplementação (Grupo multimistura) ou não com a multimistura (Grupo Controle). Favela "Cidade de Lona", Maceió, Alagoas, 2005. Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Tabela 4 Características do consumo alimentar de crianças menores de cinco anos, segundo alocação no Grupo Controle ou no Grupo Multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. Componente dietético Grupo Adequação percentual em relação à Proporção (%) de crianças que recomendação* não atingiram a meta de ingestão individual* mediana (p25-p75) pa (%) pb Energia Controle 67,7 (52,1-84,9) 0,707 88,9 0,35 Multimistura 66,3 (52,9-79,4) 77,4 Proteína Controle 186,2 (140,3-269,8) 0,104 5,6 0,65 Multimistura 237,2 (181,5-341,4) 9,7 Cálcio Controle 51,4 (29,2-96,6) 0,203 77,8 0,09 Multimistura 44,1 (21,8-66,9) 93,5 Ferro Controle 77,6 (56,3-98,4) 0,934 75,0 0,95 Multimistura 75,2 (60,9-92,3) 77,4 Vitamina A Controle 60,3 (29,7-107,0) 0,807 73,5 0,77 Multimistura 49,4 (29,5-92,0) 76,7 Zinco Controle 43,6 (29,4-59,9) 0,147 100,0 0,21 Multimistura 51,3 (37,9-69,2) 93,5 *=RDA=Recommended Dietary Allowances;15 a=teste t de Student para amostras independentes, exceto para vitamina A (Mann-Whitney); b=Teste do qui-quadrado (χ2); p>0,05 (diferença não-significativa). Características do consumo alimentar de crianças menores de cinco anos, segundo alocação no Grupo Controle ou no Grupo Multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. *=RDA=Recommended Dietary Allowances;15 a=teste t de Student para amostras independentes, exceto para vitamina A (Mann-Whitney); b=Teste do qui-quadrado (χ2); p>0,05 (diferença não-significativa). *=RDA=Recommended Dietary Allowances;15 a=teste t de Student para amostras independentes, exceto para vitamina A (Mann-Whitney); b=Teste do qui-quadrado (χ2); p>0,05 (diferença não-significativa). Tabela 2 Tabela 2 Hemoglobina e retinol sérico (Média ± DP) e prevalência de anemia e hipovitaminose A em crianças de 0 a 60 meses após 10 meses de suplementação (Grupo Multimistura) ou não com a multimistura (Grupo Controle). Favela "Cidade de Lona", Maceió, Alagoas, 2005 Grupo Hb (g/dL) Retinol (µg/dL) Anemia* (%) Hipovitaminose A** (%) Controle 12,4±2,3 26,0±5,9 16,1 11,9 Multimistura 12,8±1,7 24,4±4,4 8,3 21,6 Significância estatística pa=0,41ns pa=0,18ns OR=2,12 OR=0,49 IC95%=0,3-17,7 IC95%=0,1-1,9 pb=0,45ns pc=0,24ns *=Hemoglobina <11 g/dL; **=retinol sérico <20 µg/dL; a=Teste t de Student; b =Teste de Fischer; c=teste do qui- quadrado; OR=Odds ratio (razão de chances); IC95%=Intervalo de confiança 95%; ns=não significativo (p>0,05). Hemoglobina e retinol sérico (Média ± DP) e prevalência de anemia e hipovitaminose A em crianças de 0 a 60 meses após 10 meses de suplementação (Grupo Multimistura) ou não com a multimistura (Grupo Controle). Favela "Cidade de Lona", Maceió, Alagoas, 2005 *=Hemoglobina <11 g/dL; **=retinol sérico <20 µg/dL; a=Teste t de Student; b =Teste de Fischer; c=teste do qui- quadrado; OR=Odds ratio (razão de chances); IC95%=Intervalo de confiança 95%; ns=não significativo (p>0,05). Incidência de eventos nosológicos entre crianças de 6 a 60 meses, segundo o consumo ou não da Multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005 Agravos Grupos de estudo OR (IC95%) Valor p* Controle (%) Multimistura (%) Diarréia 10,9 10,5 1,04 0,86ns (0,67-1,62) Infecção respiratória 24,3 16,9 1,59 0,006** (1,13-2,24) Vômito 2,6 2,9 0,89 0,77ns (0,38 - 2,10) Febre 16,7 14,4 1,19 0,35ns (0,81-1,74) OR=Odds ratio (razão de chances); IC95%=Intervalo de confiança 95%; *=obtido pelo coeficiente de associação phi (ϕ) entre os grupos de estudo; ns=não significativo (p>0 05) **=diferença estatisticamente significativa Incidência de eventos nosológicos entre crianças de 6 a 60 meses, segundo o consumo ou não da Multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005 OR=Odds ratio (razão de chances); IC95%=Intervalo de confiança 95%; *=obtido pelo coeficiente de associação phi (ϕ) entre os grupos de estudo; ns=não significativo (p>0,05). **=diferença estatisticamente significativa. 313 Ferreira HS et al. Tabela 4 Figura 1 50,0 40,0 20,0 10,0 0 Frequência (%) Vômito Fase experimental (mês) Multimistura Controle 4 5 6 7 8 9 10 50,0 40,0 20,0 10,0 0 Frequência (%) Febre Fase experimental (mês) Multimistura Controle 4 5 6 7 8 9 10 g Evolução de agravos à saúde de crianças suplementadas (Grupo multimistura) ou não (Grupo Controle) com a multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. Evolução de agravos à saúde de crianças suplementadas (Grupo multimistura) ou não (Grupo Controle) com a multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. 50,0 40,0 20,0 10,0 0 Frequência (%) Vômito Fase experimental (mês) Multimistura Controle 4 5 6 7 8 9 10 50,0 40,0 20,0 10,0 0 Frequência (%) Febre Fase experimental (mês) Multimistura Controle 4 5 6 7 8 9 10 Evolução de agravos à saúde de crianças suplementadas (Grupo multimistura) ou não (Grupo Controle) com a multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. demonstrado na Tabela 3. A Figura 1 ilustra a evolução desses agravos ao longo do experimento, destacando-se a sazonalidade de suas ocorrências. fora discreta, no entanto eliminaram-se as formas graves que antes acometiam 16% das crianças.20 Apesar de o trabalho ter sido descontinuado, pode ter contribuído, em longo prazo, para a redução aos níveis ora observados. A utilização da multimistura, por sua vez, a julgar pelos resultados aqui apresen- tados, parece não ter interferido no sentido de incre- mentar os níveis de hemoglobina e/ou reduzir a prevalência de anemia. O inquérito dietético revelou que os dois grupos tinham consumo alimentar semelhantes, não tendo sido observadas diferenças significativas (p>0,05) na proporção de crianças que não atingiram a meta de ingestão individual para nenhum dos compo- nentes dietéticos analisados, bem como na ade- quação percentual em relação às RDAs (Tabela 4). Resultado semelhante foi obtido em 2002, por Neumann,21 em pesquisa realizada nas creches do município de Pelotas, Rio Grande do Sul. Cerca de 1200 crianças de um a sete anos participaram do estudo, sendo que metade recebeu a multimistura (farelo de trigo: 30%, farelo de arroz: 30%, farinha de milho: 15%, farinha de trigo: 10%, casca de ovo: 5% e sementes de abóbora ou girassol: 5% e pó de folha de mandioca:5%). Ao final de seis meses, não havia diferença quanto à anemia entre as crianças que receberam e as que não receberam a multimis- tura. Figura 1 A partir desse estudo, conduzido por um dos coordenadores da Pastoral da Criança, principal instituição promotora da utilização desse suplemento no Brasil, houve uma reorientação das estratégias de ação dessa Organização em relação à anemia, passando-se ao seu pessoal de campo a seguinte recomendação: "A multimistura não funciona para crianças com anemia e, portanto, não deve ser Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Figura 1 50,0 40,0 20,0 10,0 0 Frequência (%) Diarréia Fase experimental (mês) Multimistura Controle 4 5 6 7 8 9 10 50,0 40,0 20,0 10,0 0 Frequência Infecções Respiratórias Fase experimental (mês) Multimistura Controle 4 5 6 7 8 9 10 g Evolução de agravos à saúde de crianças suplementadas (Grupo multimistura) ou não (Grupo Controle) com a multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. continua Evolução de agravos à saúde de crianças suplementadas (Grupo multimistura) ou não (Grupo Controle) com a multimistura. Favela "Cidade de Lona", Maceió, Alagoas, 2005. Fase experimental (mês) 7 8 continua Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 314 Efeitos do consumo da multimistura Figura 1 Discussão A prevalência geral de anemia observada no conjunto das crianças (12,3%) foi surpreendente- mente baixa considerando-se o contexto ambiental em que vivem. Pesquisa realizada por Ferreira et al.4 nessa mesma comunidade, no ano de 2002, encon- trou uma freqüência de 96,4% entre as crianças da mesma faixa etária. Imediatamente após esse trabalho, iniciou-se um projeto de extensão onde foram desenvolvidas diversas atividades dire- cionadas à prevenção e ao controle do problema, tais como a educação nutricional e tratamento com sulfato ferroso e anti-helmíntico polivalente. Seis meses após a implantação desses procedimentos, verificou-se que a redução da prevalência de anemia 315 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Ferreira HS et al. utilizada com esta intenção."22 utilizada com esta intenção."22 que consumiu a mesma dieta, sem multimistura. Após seis meses de intervenção, verificou-se que as ações gerais de saúde causaram efeito benéfico na condição nutricional das crianças, tendo em vista que melhoraram seus parâmetros hematológicos, independentemente da multimistura. No entanto, os valores médios para o índice estatura para idade foram significantemente mais elevados no grupo submetido à suplementação. Concluíram que a suplementação de dietas deficientes com multimis- tura contribuiu para a melhoria da estatura de crianças. No presente estudo, a multimistura também não se revelou efetiva no sentido de elevar os níveis séricos de retinol e/ou reduzir a prevalência de hipovitaminose A. A World Health Organization23 classifica os indi- víduos, segundo os níveis de retinol, em quatro cate- gorias: Deficiente (<10,0 µg/dL); Baixo (de 10,0 a 19,9 µg/dL); Aceitável (de 20,0 a 29,9 µg/dL); e Normal (>30,0µg/dL). Com base nessa classificação, considera-se que prevalências de 2% a 10% de baixos níveis (10,0 a 19,9 µg/dL) na população representa um problema de saúde pública leve. Quando entre 10,1% a 19,9%, qualifica-se o pro- blema como moderado. Acima dessa freqüência, caracteriza-se a situação como grave problema de saúde pública. Considerando o conjunto das crianças avaliadas neste estudo, a prevalência de crianças com baixos níveis foi de 16,5%. Como a análise estatística indicou que as diferenças observadas entre os grupos não podem ser atribuídas ao consumo da multimistura, pode-se inferir que essa proporção possa ser extrapolada para o conjunto das crianças residentes na favela Cidade de Lona. Assim, a hipovitaminose A representaria um problema de saúde pública em nível moderado nessa comunidade. Discussão Em nosso estudo a utilização da multimistura não alterou a prevalência de agravos à saúde, exceto em relação às infecções respiratórias. Esse dado parece contraditório na medida em que não foram obser- vadas diferenças nos níveis séricos de retinol, fator reconhecidamente protetor contra as infecções.26 Essa observação remete a uma limitação desta inves- tigação, que foi a de não controlar a avaliação do retinol sérico pela presença de infecção, determi- nando-se, concomitantemente, por exemplo, a proteína C reativa.27 Diante da condição ambiental degradante em que viviam as crianças, infecções constantes representa uma rotina entre elas. A presença desse tipo de agravo pode afetar a síntese da Retinol Binding Protein (RBP), contribuindo para a diminuição dos níveis circulantes do retinol, ainda que possam haver reservas hepáticas adequadas desse nutriente, o que determinaria uma classifi- cação errada (falsos-positivos) de hipovitaminose A. Embora o nível de retinol sérico seja um dos indi- cadores mais utilizados atualmente para detectar a carência de vitamina A em nível epidemiológico, admite-se certa limitação em sua utilização pelo fato de que ele não reflete com fidedignidade as reservas orgânicas desse nutriente.28 Tal como ocorreu em relação aos níveis de hemoglobina e de retinol sérico, o consumo da multimistura também não se mostrou efetivo na melhoria do perfil antropométrico das crianças. Resultados semelhantes foram encontrados por Oliveira et al.24 ao avaliaram o impacto da suple- mentação da dieta com multimistura sobre o estado nutricional de pré-escolares matriculados em quatro creches no Estado da Paraíba. As crianças foram dividas em três grupos, cada um recebendo, respecti- vamente, placebo, 5 g e 10 g de multimistura. Concluíram que não houve alteração significativa no estado nutricional após dois meses de suplemen- tação. Gigante et al.25 também concluíram pela inefetividade da multimistura ao conduzirem estudo de intervenção, longitudinal e controlado, incluindo crianças de 24 escolas de educação infantil que foram comparadas antes e depois da intervenção, tendo como indicadores parâmetros antropométricos e o nível de hemoglobina. Esse aspecto pode ter mascarado os possíveis efeitos da multimistura especificamente em relação ao seu potencial em prover quantidades importantes de vitamina A. Estudo realizado em nossos labo- ratórios7 avaliou a efetividade da multimistura como suplemento vitamínico e/ou mineral na recuperação ponderal de ratos submetidos à desnutrição pós- natal, concluindo que a mesma atendeu às necessi- dades de vitaminas, mas apenas parte das necessi- dades de minerais dos animais. Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Discussão Siqueira et al.26 investigaram a efetividade da suplementação dietética com a multimistura, concomitantemente com outras ações destinadas a melhorar a saúde de crianças. Trinta e um estudantes matriculados em uma escola rural foram examinados (antropometria e hematologia), antes e após o consumo da multimistura. Os resultados foram comparados com aqueles do grupo controle (n=26), Estudos bromatológicos têm encontrado altas concentrações de minerais (ferro, cálcio, zinco, cobre, manganês, selênio) e vitaminas (A, B2, B6, C, ácido fólico, ácido pantotênico e biotina) na multi- mistura ou em seus componentes.29 Contudo, existe a possibilidade de uma baixa biodisponibilidade 316 Efeitos do consumo da multimistura acreditam que crianças menores de cinco anos não sejam susceptíveis a um efeito psicológico (efeito placebo) por estarem recebendo uma alimentação adicionada de um determinado suplemento. desses minerais, pelo fato de que o zinco, o ferro, o cobre e o cálcio, em determinadas concentrações relativas, interferirem mutuamente nas suas taxas de utilização. Adicionalmente, a multimistura possui teores importantes de fitatos, oxalatos e de fibra dietética, que podem reduzir a biodisponibilidade dos minerais.30 Diante do exposto, pode-se concluir que a adição de multimistura à alimentação habitual de crianças de uma favela, caracterizada por extrema precariedade ambiental e socioeconômica, não alterou seu perfil antropométrico, a freqüência de anemia ou a de hipovitaminose A. Em relação às morbidades, parece ter reduzido a incidência de infecções respiratórias, resultado este que necessita ser visto com cuidado, considerando a falta de justi- ficativa fisiológica para esse achado. No presente estudo, não foi possível fazer a comparação dos níveis de hemoglobina e de retinol sérico no início e ao final do trabalho, tal como se fez com a antropometria. Por questões éticas, tais procedimentos foram realizados apenas no final da fase experimental, uma vez que os casos de anemia e/ou hipovitaminose A detectados teriam que ser devidamente tratados pelos métodos convencionais (sulfato ferroso e/ou megadose de vitamina A prescritos por médica da equipe e fornecidos pela coordenação do projeto). Assim, embora todo estudo experimental seja longitudinal por natureza, esse procedimento, especificamente, teve caráter trans- versal, de forma que os autores não conheciam a condição inicial das crianças. No entanto, em virtude da homogeneidade das famílias residentes na favela "Cidade de Lona" em termos socioeconômicos e ambientais, é altamente plausível supor que os grupos eram semelhantes entre si no início do estudo. Discussão A alta prevalência de infecções e má-nutrição observada na comunidade deve-se às precárias condições socioeconômicas e péssima qualidade de vida prevalecentes na localidade. A não disponibili- dade de água de boa qualidade, ausência de sanea- mento básico, inadequado destino do lixo e dos dejetos, a baixa escolaridade e profissionalização dos adultos, o difícil ou inexistente acesso à assistência à saúde, entre outros fatores, são pro- blemas que precisam ser resolvidos para que se garanta, efetivamente, um melhor nível de saúde para aquela comunidade, sobretudo, para as suas crianças. Nesta investigação não foi utilizado placebo no Grupo Controle em virtude da dificuldade de encon- trar substrato que mimetizasse a multimistura e que, adicionalmente, não promovesse qualquer incre- mento nutritivo à refeição. Pensou-se em usar farinha de mandioca ou farinha láctea, mas decidiu- se por não fazê-lo, pois esses ingredientes possuem características nutricionais que não permitem considerá-los como "inertes". Além disso, os autores Agradecimentos À Fundação de Amparo à Pesquisa do Estado de Alagoas (FAPEAL) e ao Conselho Nacional de Desenvolvimento Científico e Tecnólogico (CNPq) pela concessão, respectivamente, de bolsa de mestrado (Processo No. 20050230427-7) e de inici- ação científica. 4. Ferreira HS, Assunção ML, Vasconcelos VS, Melo FP, Oliveira CG, Santos TO. Saúde de populações marginal- izadas: desnutrição, anemia e enteroparasitoses em crianças de uma favela do Movimento dos Sem-Teto, Maceió, Alagoas. Rev Bras Saúde Matern Infant. 2002; 2: 177-85. 3. Ferreira HS, Albuquerque MFM, Ataide TR, Morais MGC, Mendes MCR, Siqueira TCA, Silva GJ. Estado nutricional de crianças residentes em invasão do movimento dos Sem- Terra. Fazenda Conceição, Porto Calvo, Alagoas. Cad Saúde Pública. 1997; 13: 137-9. Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 2. Monteiro CA. A dimensão da pobreza, da desnutrição e da fome no Brasil. Est Avançados. 2003;17: 7-20. Referências 1. Monte CMG. Desnutrição: um desafio secular à nutrição infantil. J Pediatr. (Rio de J) 2000; 76 (Supl. 3): S285-S97. 5. Mahler H. Present status of WHO's initiative, health for all by the year 2000. Ann Rev Public Health. 1988; 9: 71-97. 2. Monteiro CA. A dimensão da pobreza, da desnutrição e da fome no Brasil. Est Avançados. 2003;17: 7-20. 6. Brandão CT, Brandão RF. Alimentação alternativa. Brasília: INAN, 1996. 7. Ferreira HS, Assunção ML, França AOS, Cardoso EP, Moura FA. Efetividade da multimistura como suplemento de dietas deficientes em vitaminas e/ou minerais na recu- peração ponderal de ratos submetidos à desnutrição pós- natal. Rev Nutr. 2005; 18: 63-74. 4. Ferreira HS, Assunção ML, Vasconcelos VS, Melo FP, Oliveira CG, Santos TO. Saúde de populações marginal- izadas: desnutrição, anemia e enteroparasitoses em crianças de uma favela do Movimento dos Sem-Teto, Maceió, Alagoas. Rev Bras Saúde Matern Infant. 2002; 2: 177-85. 8. Amâncio OMS, Lajolo FM, Santoro M, Nóbrega FJ, Queiroz SS, Farfan JA. Recuperação nutricional de grupos populacionais de baixa renda: análise crítica. Cad Nutr. 1995; 9: 1-4. 317 Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Ferreira HS et al. 21. Neumann NA. Multimistura de farelos não combate a anemia. J Pastoral Criança.[periódico online] 2005. [acesso em 26 jun 2006] 105: 14. Disponível em: http://www. pastoraldacrianca.com.br/jornal/107/pag14.pdf. 9. Azeredo VB. Multimistura: uma alternativa alimentar? Rio de Janeiro: Universidade Federal Fluminense; 1999. 10. Bittencourt SA. Uma alternativa para a política nutricional brasileira? Cad Saúde Pública. 1998; 14: 629-39. 22. Coordenação Nacional da Pastoral da Criança. Multimistura de alimentos, resgate do conceito original: quanto mais colorido for o prato de comida, melhor! [16 jun 2006] Disponível em: http://www.pastoraldacrianca.org.br/ htmltonuke.php?filnavn=dicas/dicas_multimistura.htm. 11. CFN (Conselho Federal de Nutricionistas). Multimistura: a posição do CFN. Rev Cons Nac Nutr. 2002; 6: 9. 12. Farfan JA. Alimentação alternativa: análise crítica de uma proposta de intervenção nutricional. Cad Saúde Pública. 1998; 14: 205-11. 23. WHO (World Health Organization). Control of vitamin A deficiency and xerophthalmia: Geneva; 1982. (WHO: Technical Report Series, 672). 13. Zabotto CB. Registro fotográfico para inquéritos dietéticos. Goiânia: Ed. UFG; 1996. 14. Anção MS, Cuppari L, Draibe SA, Sigulem D. Programa de Apoio à Nutrição - NutWin, versão 1.5 [CD-ROM]. São Paulo: Departamento de Informática em Saúde da Escola Paulista de Medicina da Universidade Federal de São Paulo; 2002 24. Rev. Bras. Saúde Matern. Infant., Recife, 8 (3): 309-318, jul. / set., 2008 Recebido em 4 de setembro de 2007 Versão final apresentada em 4 de julho de 2008 Aprovado em 7 de julho de 2008 Referências Oliveira SMS, Costa MJC, Rivera MAA, Santos LMP, Ribeiro MLC, Soares GSF, Asciutti LS, Costa SFG. Impacto da multimistura no estado nutricional de pré-esco- lares matriculados em creches. Rev Nutr. 2006; 19: 169-76. 25. Gigante DP, Buchweitz M, Helbig E, Almeida AS, Araújo CL, Neumann NA, Victora C. Ensaio randomizado sobre o impacto da multimistura no estado nutricional de crianças atendidas em escolas de educação infantil. J Pediatr. (Rio J) 2007; 83: 363-9 15. National Research Council. Commission on Life Sciences. Subcommittee on the 10 Edition of the Recommended Dietary Allowances, Food and Nutrition Board. Recommended dietary allowances. 10. ed. Washington, DC: National Academy Press; 1989. 26. Siqueira EMA, Azevedo IT, Arruda SF, Lima SMD, Gonçalves CA, Souza EMT. Regional low-cost diet supple- ment improves the nutritional status of school children in a semi-arid region of Brazil. Nutr Res. 2003; 23: 703-12. 16. Fagundes AA, Barros DC, Duar HA, Sardinha LMV, Pereira MM, Leão MM. Vigilância alimentar e nutricional - SISVAN: orientações básicas para a coleta, processamento, análise de dados e informação em serviços de saúde. Brasília, DF: Ministério da Saúde; 2004. 27. Aukrust P, Müller F, Ueland T, Svardal AM, Berge RK, Frøland SS. Decreased vitamin A levels in common vari- able immunodeficiency: vitamin A supplementation in vivo enhances immunoglobulin production and downregulates inflammatory responses. Eur J Clin Invest. 2000; 30: 252-9. 17. WHO (World Health Organization). Iron deficiency anaemia. Assessment, prevention and control: a guide for programme managers. Geneva; 2001. 18. WHO (World Health Organization). Indicators for assessing vitamin A deficiency and their application in monitoring and evaluating intervention programmes. Geneva; 1996. (Micronutrient Series). 28. Stephensen CB, Gildengorin G. Serum retinol, the acute phase response, and the apparent misclassification of vitamin A status in the III National Health and Nutrition Examination Survey. Am J Clin Nutr. 2000; 72: 1170-8. 19. Cesar CLG, Figueiredo GM, Westphal MF, Cardoso MRA, Costa MZ, Gattás VL. Morbidade referida e utilização de serviços de saúde em localidades urbanas brasileiras: metodologia. Rev Saúde Pública. 1996; 30: 153-60. 29. Madruga MS, Câmara FS. The chemical composition of "multimistura" as a food supplement. Food Chem. 2000; 68: 41-4. 30. Cozollino SMF. Biodisponibilidade de minerais. Rev Nutr. 1997; 10: 87-98. 20. Ferreira HS. Mulheres obesas de baixa estatura e seus filhos desnutridos. Est Avançados. 2006; 20: 159-66. 318
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Deriving expert-driven seismic and wind fragility functions for non-engineered residential typologies in Batanes, Philippines
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OPEN Arvin Hadlos *, Aaron Opdyke  & S. Ali Hadigheh Natural hazards inflict significant damage to dwellings in the Philippines where housing is often the most valued asset of households. Residential fragility functions estimate structural damage to mitigate risk but these are challenging to derive when empirical and analytical data are lacking, as is common in rural areas. Too often, conventional fragility estimates overlook the characteristics of informally built or non-engineered dwellings common in rural areas. We used a heuristic alternative of deriving fragility functions relying on experts’ judgements to understand the housing performance of non-engineered residential typologies in the Province of Batanes in the Philippines. Drawing on field surveys in the Municipality of Itbayat, we identified and defined seven prominent typologies. Based on the Applied Technology Council’s expert-driven method of deriving fragility functions, 18 experts estimated the damage states of these typologies against the impacts of earthquakes and typhoons which are the two most prominent hazards in the region. Our findings provide first-generation fragility functions for Batanes as a step towards more localised risk assessment in the Philippines. More broadly, these functions can be used for typologies identified beyond Batanes where similar structural characteristics are prevalent. Building back safer after disasters has been a consistent mantra for post-disaster reconstruction efforts under the Sendai Framework for Disaster Risk ­Reduction1. Dwellings in low- and middle-income countries are the most valued assets of households but these also tend to be the most disaster-affected2. To safeguard these assets, it is imperative to understand their structural performance against the impacts of hazards. The derivation of fragility functions captures structural performance of a building when it is subjected to an environmental ­excitation3–6. Fragility functions, often depicted graphically as a series of fragility curves, appraise risk by quantifying the rela- tionship between a hazard intensity (e.g., seismic intensity or wind speed) and the probability of a component or structure reaching or exceeding a certain damage ­state3–6.h g g g The availability of fragility functions can support modelling natural hazard impacts and more informed targeting of structural safety programs. For example, deriving these functions can reveal vulnerable structural typologies in a building stock leading to risk prioritisation interventions. Hence, risk and loss estimation methods are usually anchored on deriving these functions, such as those developed by the United States Federal Emergency Management Agency (FEMA)4,7–9. www.nature.com/scientificreports www.nature.com/scientificreports School of Civil Engineering, The University of Sydney, Camperdown, NSW 2006, Australia. *email: arvin.hadlos@ sydney.edu.au Scientific Reports | (2023) 13:22008 www.nature.com/scientificreports/ performance when assessed against competing impacts on structures. Building-level disaster risk reduction (DRR) measures have shown how multi-hazard trade-offs and asynergies complicate building more resilient dwellings. That is, where construction practices may reduce the impact of risk to one hazard, such can exacerbate the risk to another ­hazard13,14. Depending on the available sources of damage data, fragility functions can be derived in various ­ways5,15. When documented post-disaster damage data is available, empirical methods can be used. If resources allow for the simulation or modelling of structural typologies, analytical methods can be employed. When both resources are lacking, a heuristic alternative is to solicit experts’ opinions to derive the functions. A fourth approach is a hybrid of at least two methods. Further discussion about these four methods, including an overview of past studies using specific approaches, can be found in Maio and Tsionis et al.16 and Rossetto et al.17. Previous atten- tion to deriving these functions has primarily focused on a structure’s performance to a single hazard. Recently, there has been a growing emphasis in academic, policy, and practice environments to incorporate multi-hazard approaches to realise effective DRR ­strategies14,18,19.f f Hazards impact a structure differently thereby requiring a combination of strategies and approaches to reduce or mitigate ­risk13,14. Deriving multi-hazard fragility functions can therefore offer insights on how to optimise trade-offs in construction decisions. The scarcity of data and technical resources are, however, roadblocks in rural contexts in low- and middle-income countries. The expert-driven approach is often the only possible method in the absence of empirical and analytical ­data16,20–22. Elicitation of experts’ opinions has been used in various disciplines to produce the fragility functions of components of interests, extending from structural ­engineering20,23–25, ­hydrology10,22, and civil ­engineering26. The ATC-58 project of the Applied Technology Council (ATC) aimed to develop next-generation seismic design assessment standards, and the expert-driven method is adopted among other approaches to derive fragility functions as formalised through a proposed method of solicitation and aggregation of experts’ ­opinions27,28. The main strength of this approach is that experts can include in their assessment all factors affecting the response of a structure against hazards, unlike empirical and analytical methods where these are limited to the quantity and quality of available ­data15. The major drawback of expert-driven methods is the subjectivity associated with experts’ experience and trust in their ­judgement15. www.nature.com/scientificreports/ However, when dealing with non-engineered residential typologies, experts’ experience is beneficial to capture the varied structural performance arising from the inherent variability of the design and construction of these building classes.h g The objective of this study was to derive fragility functions for non-engineered residential typologies in the Province of Batanes—the storm-battered northernmost part of the Philippines. We drew on field surveys in the Municipality of Itbayat to identify relevant typologies for the Province of Batanes. The remote island municipal- ity of Itbayat was home to vernacular stone-and-lime houses, like elsewhere in Batanes, built out of tradition to withstand typhoon impacts. Unfortunately, these dwellings were extensively damaged following the series of destructive earthquakes (magnitudes ­(Mw) 5.4, 5.9, 5.8) in ­201929,30. These disasters redefined the construction practices in the area with a departure from the stone-and-lime character of the building stock. We surveyed the existing building stock three years later and identified the most prominent typologies that households chose to build to replace these vernacular dwellings. Based on the expert-driven approach of deriving fragility functions developed in ATC-58, a pool of experts estimated the seismic and wind performance of both the vernacular and replacement typologies.hh y g The rest of the paper is structured as follows. The Methods section characterises the research procedures and protocols undertaken for this study. Next, under the Results section, we present the identified housing typologies and the derived fragility functions. The Discussion section then provides insights gleaned in using the expert- driven approach in deriving fragility functions. Lastly, in the Conclusion section, we summarise the theoretical and practical implications of this study. Methods B l Below, we outline how we surveyed the housing typologies, followed by the process of soliciting and aggregating experts’ estimates. We then present how we derived the fragility functions. Lastly, we provide information on the research ethics protocols and permits obtained for this study. OPEN However, in the context of resource-constraint communities, the limited data on past disaster damage and unregulated construction practices inhibit the derivation of fragility functions. While these functions are a foundational tool to understand structural safety and are useful for disaster preparedness, they are too often lacking in hazard-prone regions where they are critically ­important10. yt g p g y y p In rural areas in low- and middle-income countries, dwellings built informally by residents are common. These are either patterned from longstanding vernacular practices, borne out of the immediate need to have shelter (e.g., urgent reconstruction due to disaster impacts), or as a compromise to rising construction costs. In these cases, the construction of dwellings is usually non-engineered, with the absence or limited oversight of qualified building ­professionals11. As a result, housing typologies often exhibit a high variance of characteristics compared to conventional building typologies designed and constructed based on prevailing building codes and standards. While these non-engineered structures are not prejudiced to be deficient in structural safety and may, in fact, reveal sound locally developed building ­practices12, their structural performance is less documented and certain. Furthermore, the exposure of dwellings to multiple natural hazards hinders our understanding of their Scientific Reports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 www.nature.com/scientificreports/ Identification of housing typologiesi Identifying a building typology is the first step in building-level risk estimation as this serves as the object of analysis for fragility functions. A typology, usually labelled with a taxonomy (string), characterises a building class from attributes posing vulnerability to the impacts of natural ­hazards4,31. For example, for earthquake risk, structures are classified according to the (i) type of lateral load-resisting system, (ii) material of lateral load- resisting system, (iii) building height, and (iv) seismic code level (or the period of construction of a structure vis-à-vis the enforcement of seismic regulations). Such attributes are the core parameters used in risk analysis by many organisations, such as FEMA for ­HAZUS7 and the Global Earthquake Model (GEM)31. For typhoon risk, the same set of attributes are relevant, but with wind-induced damage concentrated on walls and ­roofs32,33, building envelope materials and roof profile are usually considered in ­conjunction34. In this study, we used all these attributes—except for the seismic code level—to inform the development of a rapid visual survey to assess the attributes of a building stock. The seismic code level was omitted because the housing typologies surveyed were non-engineered, with formal seismic regulations having limited applicability to these types of structures. Th d l d d h fi b ld b h g g g y y The rapid visual surveys were conducted in January 2023 using the five building attributes as the parameters of the assessment. For lateral load-resisting systems, we referred to the expanded classifications and defini- tions of the GEM ­taxonomy35 since their database accounts for the structural characteristics of non-engineered ­construction31. The field study aimed to understand the housing reconstruction strategies of households after Scientific Reports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 Solicitation of experts’ opiniont p p After identifying the predominant housing typologies, we selected a pool of experts to estimate the damage states of these typologies. In qualifying “expertise”, we recognised both the inputs of those who are locally based (“local experts”) and those who are not but with relevant insights on the housing performance of non-engineered typologies in the country (“specialists”). Local experts included the municipal engineers for all six municipalities in Batanes and district engineers at the provincial level. These roles assume building regulatory responsibilities in the targeted jurisdictions encompassing extensive experience with local damage impacts from past earthquakes and typhoons in Batanes. yp For the specialists, their expertise was sought because of their familiarity with the dynamics of the typologies of interest. While the impacts of hazards vary in different geographical contexts, the specialists’ judgements were considered reliable if they were acquainted with the common damage mechanisms or expected performance of these structures in the Philippine setting. We relied on academic publications and technical reports focused on seismic and wind field assessments as the basis for identifying specialists. We identified documents on Google Scholar and Scopus employing a permutation of the following keywords: “housing”, “damage”, “Philippines”, “dis- aster”, “shelter”, “assessment”, “wind OR typhoon”, and “seismic OR earthquake”. From this query, we shortlisted relevant documents, and then conducted literature snowballing to trace other documents not captured by the keyword search. The authors of these documents were then compiled. Finally, we shortlisted those with civil, structural, or construction engineering backgrounds. g g g Porter et al.27 developed a method to systematically solicit and aggregate experts’ opinions to derive fragil- ity functions. This is among the methods of damage analysis developed for the ATC for its next-generation probabilistic assessment of structures adapted from the Pacific Earthquake Engineering Research ­Centre27. Unlike behavioural means of aggregating experts’ opinions wherein participants interact with each other and arrive at a consensus, this proposed method uses a mathematical approach to consolidate distinct inputs of ­participants17. Consultation with experts and combining their individual judgements provide a worthwhile basis for ­assessment41 since consensus-based approaches might reflect mere conformity among experts rather than genuine ­agreement24. While developed for seismic applications, the expert-driven method for ATC explicitly focuses on aggregating experts’ opinions. It can therefore be adaptable if the required information on component types, damage states, and engineering demand parameters (EDPs) are contextualised to the impacts of hazards of interest. Solicitation of experts’ opiniont Hence, we used this method in deriving both the fragility functions against the impacts of earthquakes and typhoons. The procedure asks experts to estimate the (median and lower-bound) values of a specified EDP with respect to the presented component type and damage states, alongside their self-assessed level of expertise. The use of EDP, however, is less relevant when the components of interest are low-rise non-engineered hous- ing typologies. For example, inter-story drift ratio, being one of the most common ­EDPs42,43, is best suited for multi-story components because of the need to analyse relative translational displacement of floor levels. In this regard, it was imperative to substitute EDP with the intensity measure of a hazard. g p y A survey form adapted from Porter et al.27 was developed for this study. For earthquakes, we used the Philip- pine Institute of Volcanology and Seismology (PHIVOLCS) Earthquake Intensity Scale (PEIS) as the intensity measure, ranging from numeral I (weakest, “scarcely perceptible”) to X (strongest, “completely devastating”)44. This intensity scale, developed by PHIVOLCS, considers the common building construction types in the Philip- pines and the population’s perception of shaking strength, thus making it the official intensity scale in the country since ­199645. PEIS is comparable to the widely used Modified Mercalli Intensity (MMI) scale in that intensities I to VII represent the same effect of ground shaking, while PEIS VIII is similar to MMI VIII–IX; PEIS IX to MMI X–XI; and PEIS X to MMI ­XII45,46. We opted to use earthquake intensity instead of Peak Ground Acceleration (PGA) because the local engineers surveyed were more familiar with damage relationships with instrumental intensities. This is due to the lack of localised seismic hazard maps until recently and the limited use of PGA as a design parameter in the current National Structural Code of the Philippines. In addition, instrumental intensi- ties can be converted to PGA when conversion equations of intensities and ground motion become ­available47 with applicability to the geographical context of interest. With the absence of such conversion equations for the Philippines for the time being, using PEIS is logical since building damageability has been long attributed to instrumental intensities within the country. www.nature.com/scientificreports/ www.nature.com/scientificreports/ the 2019 earthquakes in the Municipality of Itbayat, located in the Province of Batanes in the Philippines (see Fig. 1). Hence, we focused the surveys on the emergent (or replacement) typologies constructed by households who were living in vernacular stone-and-lime houses before the earthquakes but were forced to rebuild due to the extensive damage to this typology. This pre-earthquake typology was also surveyed. Out of the 153 households identified from the joint report of the Municipal Disaster Risk Reduction Office (MDRRMO) and the Municipal Planning and Development Office (MPDO) in Itbayat, we were able to survey 101 structures. The remaining houses were not surveyed due to the unavailability of households despite multiple attempts at the time of the survey (n = 35) or where households did not reconstruct their houses and have either migrated to a different municipality or living with relatives (n = 17). In surveying the attributes of the stone-and-lime housing typol- ogy, we relied on households’ recollection about the features of their past dwelling. We also triangulated these features via archival research (e.g., photo documentation from the National Commission on Indigenous Peoples (NCIP)), desk research (e.g., ­publications36–40), and field visits to a few standing archetypes in the municipality. For the emergent housing typologies after the earthquakes, these were surveyed as all the necessary information was observable onsite. 3 Vol (012 ports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 Figure 1. Map of Itbayat, Batanes in the Philippines. Figure 1. Map of Itbayat, Batanes in the Philipp Figure 1. Map of Itbayat, Batanes in the Philippines. https://doi.org/10.1038/s41598-023-49398-2 https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ Solicitation of experts’ opiniont We explained the median as, “What hazard intensity can bring the specified damage state to 50% of the residential structures having the same typology?” For the lower bound, it was explained as, “What hazard intensity can bring the specified damage state to 10% of the residential structures having the same typology?” Lastly, experts were also asked to rate their level of confidence with the range of estimates they provided for each typology, ranging from 1 (low) to 5 (high). Note that we used the term level of confidence instead of level of expertise to emphasise that we were interested in the trust in their estimates and not with their professional standing as this was pre-assessed before invitation using the methods described above.h of the 2019 earthquakes in Itbayat (and the felt intensities in surrounding municipalities)30 was provided to help orient the respondents about the intensity measure used. Similarly, for the third part, information about the known intensities of Typhoon Ferdie (Meranti) in 2016 and Typhoon Yolanda (Haiyan) in 2013 was supplied with a sample of the regional wind hazard map of the Philippines. For both the second and third part, the respective damage states were presented, leading to the assessment section. The experts were asked to estimate what PEIS intensity (for earthquake) and 3-s peak gust wind speed (for typhoon) will yield each of the damage states (DS1 to DS5) for each of the typologies. The experts were asked to provide both median and lower-bound intensities, following the method of Porter et al.27,28. We explained the median as, “What hazard intensity can bring the specified damage state to 50% of the residential structures having the same typology?” For the lower bound, it was explained as, “What hazard intensity can bring the specified damage state to 10% of the residential structures having the same typology?” Lastly, experts were also asked to rate their level of confidence with the range of estimates they provided for each typology, ranging from 1 (low) to 5 (high). Note that we used the term level of confidence instead of level of expertise to emphasise that we were interested in the trust in their estimates and not with their professional standing as this was pre-assessed before invitation using the methods described above. Th d d l f l l h p g p g The surveys were conducted online from May 2023 to July 2023. Solicitation of experts’ opiniont Forcing the use of PGA considering such context would introduce significant, and in our view—unjustified, uncertainty in the fragility functions.hit gi ji y g y The damage states defined by FEMA for earthquake loss ­estimation4,7 were used after contextualising them to the structural properties of the identified typologies. We used these damage states because of their specificity in describing structural conditions. Thus, these well-delineated descriptions of structural failure for each dam- age state helped eliminate ambiguity in assessing stages of structural ­failure6. These are categorised within five damage states (DS), namely: no/very minor (DS1), minor (DS2), moderate (DS3), extensive (DS4), and complete (DS5) (see Table 1). For typhoons, we used 3-s peak gust wind speed in kilometres per hour (km/h) as the intensity measure, rang- ing from 0 to 400 km/h. The maximum value was capped at 400 km/h—a reasonable and realistic upper bound based on the intensity ranges of the strongest typhoons recorded in the country. For example, Typhoon Haiyan (Yolanda), one of the strongest typhoons to hit the country, had an estimated peak gust of 324 to 378 km/h48. The damage states for wind impacts were based on ­FEMA8,9 for the same reason that they have specific delineations of structural conditions. The damage states are categorised into five, namely: no/very minor (DS1), minor (DS2), moderate (DS3), extensive (DS4), and complete (DS5) (see Table 1).h p The content of the expert survey form was divided into three parts: (1) information on the housing typologies, (2) earthquake assessment, and (3) typhoon assessment. For the first part, actual images of the typologies taken onsite were provided, alongside descriptions of the type and materials of their lateral load-resisting systems, building height, wall materials, and roof profile. For the second part, information about the recorded intensities Scientific Reports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 www.nature.com/scientificreports/ www.nature.com/scientificreports/ p Damage State (DS) Earthquake Typhoon DS1–No/very minor damage None or very minor damage None to very minor damage. Roof cover loss of less than 2% with no or limited water penetration DS2–Minor damage Small (≤ 1/8 inch or ≤ 3 mm) cracks or hairline cracks at corners of doors, windows, wall ceiling intersections, connections (e.g., on welds, beam and column joints, etc.), wall surfaces; spalling at a few locations (for typologies with concrete components) Roof cover loss of 2% to 15% of the roof area but can be temporarily cov- ered to prevent water seepage. Solicitation of experts’ opiniont In total, we sent 57 survey invites to the roster of local experts and specialists we identified earlier. Eighteen (18) agreed to participate, five declined, and 34 did not respond. The respondents comprised seven local experts and 11 specialists. Two local experts decided to provide a single response while two specialists expressed confidence in answering only either the earthquake or typhoon assessment. We therefore collected 16 unique responses per assessment. In using expert judgement to quantify scientific uncertainty, it is suggested that 8–15 experts are reasonable, with diminishing returns becom- ing evident from having 20 or more ­participants49. Recent studies that used expert judgement for engineering applications have relied on this range of the number of experts ­involved10,20,24. Additionally, comprehensive insights of experts can be derived despite a limited size of cohort if and when participants are selected system- atically based on their expertise aligning with the context of the ­assessment49. Finally, in the method utilised for this study, fragility functions derived through experts’ estimates are considered to be of medium quality (the highest benchmark specified) when at least three experts have ≥ 3 level of ­confidence27,28. Solicitation of experts’ opiniont Roof structure remains intact. Maximum of one window/door failure. No failure of wall structure but marks/dents are visible which can be repaired by painting/patching DS3 – Moderate damage Large (> 1/8 inch or > 3 mm) cracks at corners of doors and windows, connections (e.g., on welds, beam and column joints, etc.), wall surfaces; permanent rotation at connections are likely; spalling at wall ends (for typologies with concrete components) Roof cover loss of above 15% to 50% of the roof area. Roof structure remains intact. Moderate window breakage. Water penetration causes some interior damage to the structure. No failure of wall structure DS4–Extensive damage Partial collapse, characterised by failed connections/critical elements, permanent lateral movement of floors, roof, beams, etc., extensive large/ through-the-wall cracks (for concrete/masonry components) or out-of- plane failure Roof cover loss of more than 50%. Roof structure remains intact. Major window damage. Water penetration causes extensive damage to the interior of structure. No failure of wall structure DS5–Complete damage Total collapse, or in imminent danger of collapse, due to failed lateral- load resisting system Complete roof failure and/or failure of wall structure Table 1. Damage states for earthquake and typhoon impacts. Adapted from Kircher et al.4, ­FEMA7,8, and Vickery et al.9. Table 1. Damage states for earthquake and typhoon impacts. Adapted from Kircher et al.4, ­FEMA7,8, and Vickery et al.9. of the 2019 earthquakes in Itbayat (and the felt intensities in surrounding municipalities)30 was provided to help orient the respondents about the intensity measure used. Similarly, for the third part, information about the known intensities of Typhoon Ferdie (Meranti) in 2016 and Typhoon Yolanda (Haiyan) in 2013 was supplied with a sample of the regional wind hazard map of the Philippines. For both the second and third part, the respective damage states were presented, leading to the assessment section. The experts were asked to estimate what PEIS intensity (for earthquake) and 3-s peak gust wind speed (for typhoon) will yield each of the damage states (DS1 to DS5) for each of the typologies. The experts were asked to provide both median and lower-bound intensities, following the method of Porter et al.27,28. Plotting of fragility functions l f d fi h b b Fragility functions define the probability of a damage state ds being exceeded or reached for a component, given a particular value of intensity measure im, such that P[DS ≥ ds | IM = im]. In this expression, lowercase notations indicate particular values of the uppercase variables. Fragility functions are most commonly idealised through a lognormal cumulative distribution ­function5,6,50 (see Eq. 5). Each fragility function needs a median value (xm) of the intensity measure representing the threshold and the variability of a damage state, and a logarithmic standard deviation (β) describing the total variability of the damage ­states4. (5) P[DS ≥ds|IM = im] = φ ln(im/xm) β (5) where ds = specific damage state; im = particular value of intensity measure; ϕ = standard normal cumulative distribution function; xm = median value of distribution (as derived in Eq. 1); β = logarithmic standard deviation (as derived in Eq. 3). In plotting the fragility functions, we used the plnorm() function in RStudio which idealises the lognormal cumulative distribution function. We used the calculated xm and β values from Eqs. (1) and (3). For the xm inputs, we first calculated their lognormal values to standardise on the log scale before feeding them into the function. For one typology (LW-B), we encountered a minor crossing of two functions (damage states). Crossing of curves implies a meaningless negative probability and this was addressed using Eqs. (6) and (7) to adjust xm and β values as proposed by Porter et al.27,28. Where functions i and j cross having medians xmj > xmi and βi ≠ βj, the adjusted values x’mi and β’i were calculated. (6) β′ i = 1 N N  i=1 βi for all i (6) (7) x′mi = exp(1.28(β′ −βi) + lnxmi) (7) Aggregation of experts’ opinionh gg g p p The median and lower-bound values of experts’ estimates of hazard intensities and the corresponding levels of confidence were used as inputs for Eqs. (1, 2, 3) which are part of the method developed by Porter et al.27,28. These equations are based on probability encoding and expert qualification and a full transcript of their derivation is found in Porter et al.28. If Eq. (3) produces β < 0.4, either justify the β, or use Eq. 2 and Eq. 4: (1) xm = N i=1 wα i xmi N i=1 wα i (2) xl = N i=1 wα i xli N i=1 wα i (3) β = ln  xm xl  1.28 (1) (2) (3) If Eq. (3) produces β < 0.4, either justify the β, or use Eq. 2 and Eq. 4: If Eq. (3) produces β < 0.4, either justify the β, or use Eq. 2 and Eq. 4: https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ β = 0.4 xm = 1.67xl (4) where N = number of experts providing judgment about a value; i = index of experts, i {1, 2,…N}; xmi = estimated median intensity measure of expert i; xli = estimated lower-bound intensity measure of expert i; wi = level of expertise of expert i; α = 1.5hih These equations weight experts’ estimates based on their levels of confidence. The constant value of α renders that estimates with an assigned level of confidence of 3 are weighted five times more than just a confidence of 1, while a confidence of 5 is weighted around twice as much as 3. The constant values in Eq. (3) and (4) anchor the dispersion between the median and lower-bound values to suggest a reasonable range within these. For this study, we did not use Eq. (4) and instead just used the calculated β. At least for the context of this assessment, there is no plausible argument to have a definitive threshold to maintain a reasonable gap between the solicited median and lower-bound values. For example, a difference of just 1 PEIS intensity can have pronounced implications for housing damage, as with a 0.5 difference, depending on how these structures are built. For wind speeds, a dif- ference of 10 km/h might already bring lower-bound and median probabilities of damage to certain typologies, while for others, higher wind speeds bring more pronounced housing damage. Ethics and inclusion statement All procedures performed involving human subjects were in accordance with the Human Research Ethics Com- mittee of The University of Sydney under the approved protocol 2022/705. The field study site was located on the ancestral domain of the Indigenous people of Itbayat. A free prior-informed consent was obtained from the National Commission on Indigenous Peoples under Certificate of Precondition R2-IKSP-2022–12-21. Identified housing typologies i g Unreinforced masonry Lightweight Lightweight Two variations of lightweight structures were identified, both having post-and-beam lateral load-resisting sys- tems. The first variation (“LW-A”) features timber beams and timber columns for primary (corner) posts, where the columns do not have footings and are only driven underground. The beam-to-column connections vary with the use of bolts, nails, and improvised hooks made from reinforcing steel bars (RSB). The second variation (“LW-B”) of lightweight structures has primary (corner) posts made of 4-inch to 5-inch diameter steel pipes with RC footing and with timber beams. These components are connected via bolts, improvised hooks made from RSB, and in some instances, the beams are notched and clipped inside the steel pipes. Both lightweight typolo- gies are one-story structures having gable roof profiles, where their roof eaves rarely exceed 300 mm. Roof and walls are enveloped by corrugated galvanised iron (CGI) sheets fastened every other one or two corrugations on wooden frames using common wire nails with improvised rubber washers. Additional timber posts as inter- mediate supports are used. CGI or plywood covers for door openings are common and the same for windows alongside jalousie (louvred) glass. Of the surveyed residential building stock, 17% and 25% account for LW-A and LW-B, respectively. www.nature.com/scientificreports/ organisations. Six prominent housing typologies were identified replacing URM which account for 91% of the surveyed building stock. These include variations of lightweight, semi-concrete, and reinforced concrete (RC) dwellings (see Figs. 2 and 3). organisations. Six prominent housing typologies were identified replacing URM which account for 91% of the surveyed building stock. These include variations of lightweight, semi-concrete, and reinforced concrete (RC) dwellings (see Figs. 2 and 3). Unreinforced masonry f y Before the series of earthquakes in 2019, unreinforced masonry (“URM”) dwellings were the vernacular housing archetype in the municipality of Itbayat like elsewhere in the province of Batanes. This typology is characterised by thick (0.80—1 m in width) coral limestone walls bounded by quicklime mortar and roofed with layered cogon. Unique in Batanes, this typology is of Spanish colonial influence adapted by the Ivatans in response to frequent ­typhoons38,40. With wind-induced damages common in this context, features to safeguard the structure include solid wooden panels with shutters to cover openings, a low stature of the structure for better wind resistance, and a blank wall facing the direction where wind blows strongest. Whilst responsive against wind impacts as per locals’ experience, this typology proved vulnerable to ground shaking—evident on the extensive damage experienced following the maximum intensity of PEIS VII from the 2019 ­earthquakes30. A conservative estimate based on field data suggests that there are fewer than ten structures remaining of such typology in Itbayat, though much can still be seen in most municipalities in Batanes. Post-earthquake, the household-led reconstruction resulted in a departure from the vernacular construction styles. New typologies emerged due to regulatory restric- tions affecting traditional resource extraction of building materials (e.g., hardwood, limestones, and cogon), the favourability of contemporary construction methods, and the presence of modern shelter materials donated by https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ Semi‑concrete For semi-concrete structures, two variations were surveyed, both having hybrid lateral load-resisting systems. These typologies have post-and-beam systems in combination with half-height RC walls at the base of the struc- ture providing additional lateral stiffness. The first variation of semi-concrete structure (“SC-A”) has primary (corner) posts made of 4-inch to 5-inch diameter steel pipes with RC footing and with timber beams. The beam- to-column connections vary with the use of bolts, improvised hooks made from RSB, and in some instances, the beams are just notched and clipped inside the steel pipes. The second variation (“SC-B”) has RC columns with RC footing. The columns have dowels on top used to wrap and fasten the timber beams (and sometimes together with roof members). Both semi-concrete typologies are one-story structures having gable roof profiles, where their roof eaves rarely exceed 300 mm. Roof and walls are enveloped by CGI sheets fastened every other one or two corrugations on wooden frames using common wire nails with improvised rubber washers. Additional timber posts as intermediate supports are used. CGI or plywood covers for door openings are common and Figure 2. The surveyed housing typologies in Itbayat. (a) Unreinforced masonry (URM). (b) Lightweight with wooden posts (LW-A). (c) Lightweight with steel posts (LW-B). (d) Semi-concrete with steel posts (SC-A). (e) Semi-concrete with RC posts (SC-B). (f) RC structure with lightweight roofing (RC-A) where in some instances, inside gutters are common to conceal the edges of roofing sheets as shown in (g). (h) RC structure with RC slab roofing (RC-B). Figure 2. The surveyed housing typologies in Itbayat. (a) Unreinforced masonry (URM). (b) Lightweight with wooden posts (LW-A). (c) Lightweight with steel posts (LW-B). (d) Semi-concrete with steel posts (SC-A). (e) Semi-concrete with RC posts (SC-B). (f) RC structure with lightweight roofing (RC-A) where in some instances, inside gutters are common to conceal the edges of roofing sheets as shown in (g). (h) RC structure with RC slab roofing (RC-B). https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ Figure 3. Structural details documented across the typologies surveyed. (a) Roof-to-wall connection where thick logs are embedded in stone walls and (b) layered thatch (cogon) roofing with reed matting are features of URM. (c) Improvised rubber washers for nail fasteners are used for typologies with CGI sheets. For LW-A, common post-and-beam connections are (d) bolted, (e) hooked with reinforcing steel bars, and (f) nailed. Semi‑concrete For LW-B and SC-A, common post-and-beam connections are (g) bolted, (h) notched and clipped, and (i) hooked with reinforcing steel bars. For SC-B, typical post-and-beam connections are (j, k) dowels wrapped around beams and roof members. For RC-A, (l) roof-to-wall connections are common to be via dowels from reinforcing steel bars wrapping the wooden roof members. For RC-B, (m) beams and columns are reinforced concrete supporting the slab roof. Figure 3. Structural details documented across the typologies surveyed. (a) Roof-to-wall connection where thick logs are embedded in stone walls and (b) layered thatch (cogon) roofing with reed matting are features of URM. (c) Improvised rubber washers for nail fasteners are used for typologies with CGI sheets. For LW-A, common post-and-beam connections are (d) bolted, (e) hooked with reinforcing steel bars, and (f) nailed. For LW-B and SC-A, common post-and-beam connections are (g) bolted, (h) notched and clipped, and (i) hooked with reinforcing steel bars. For SC-B, typical post-and-beam connections are (j, k) dowels wrapped around beams and roof members. For RC-A, (l) roof-to-wall connections are common to be via dowels from reinforcing steel bars wrapping the wooden roof members. For RC-B, (m) beams and columns are reinforced concrete supporting the slab roof. the same for windows alongside jalousie (louvred) glass. SC-A has a 17% share of the surveyed building stock, while SC-B has 14%. Reinforced concrete f Two types of RC structures were identified—one with lightweight roofing (“RC-A”) and the other one with RC slab roofing (“RC-B”). RC-A has a gable roof configuration with eaves rarely exceeding 300 mm. The CGI roof panels are fastened to wooden roof members using common wire nails with improvised rubber washers. Mean- while, RC-B has a flat slab with eaves typically exceeding 300 mm. Both RC typologies are one-story structures having RC posts (including footings), beams, and walls. As such, these are considered to have hybrid lateral load-resisting systems characterised by their moment frame connections in combination with RC walls provid- ing additional lateral stiffness. CGI or plywood covers for door openings are common and the same for windows alongside jalousie (louvred) glass. Of the surveyed residential building stock, 9% are RC-A and 9% are RCB.i g j g y g All the typologies identified in this study are considered non-engineered due to limited regulatory building oversight. For URM, building codes and standards were not yet in place, or perhaps limited, when these structures were constructed (circa ~ 1900s). In 2019 after the earthquakes, the housing reconstruction phase coincided with the typhoon season, and although the need for a building permit was not explicitly waived, the sense of urgency dictated the thrust of the household-led rebuilding influenced by the resources available to households. For example, those who chose to build LW-A and LW-B initially envisioned these as temporary, intending to build more permanent dwellings later, but financial limitations precluded this from happening. Nevertheless, building materials were carefully selected in some instances. For example, local hardwood was favoured over commercial timber for main structural elements such as rafters and beams. For those who chose to build concrete typolo- gies, imported commercial aggregates from mainland Luzon were desired for their quality. However, since the Scientific Reports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 www.nature.com/scientificreports/ importation of materials would inflate building costs, households used local aggregates (crushed coral limestones) for walls while commercial aggregates were used for beams and columns. importation of materials would inflate building costs, households used local aggregates (crushed coral limestones) for walls while commercial aggregates were used for beams and columns. Fragility functionsh g y The fragility functions derived in this study, presented in Figs. 4 and 5, are based on the calculated xm and β values shown in Table 2. For seismic impacts, URM has a 27% probability of reaching or exceeding very minor damage (DS1) at PEIS III. This intensity is of weak shaking comparable to the vibration of a passing light truck. 9 Vol (01234 23) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 The fragility functions derived in this study, presented in Figs. 4 and 5, are based on the calculated xm and β values shown in Table 2. For seismic impacts, URM has a 27% probability of reaching or exceeding very minor damage (DS1) at PEIS III. This intensity is of weak shaking comparable to the vibration of a passing light truck. Figure 4. Fragility functions against seismic impacts derived from experts’ estimates. Figure 4. Fragility functions against seismic impacts derived from experts’ estimates. Scientific Reports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 www.nature.com/scientificreports/ Figure 5. Fragility functions against wind impacts derived through experts’ estimates. Figure 5. Fragility functions against wind impacts derived through experts’ estimates. The rest of the typologies have negligible probabilities (almost 0%) to any damage state at this intensity. At PEIS V, described as strong shaking with a rocking effect on buildings, all typologies except for URM show a 45% to 69% probability of meeting or exceeding DS1 and a likelihood of ≤ 30% of DS2 (minor damage) and DS3 (moderate damage). Meanwhile, at a very destructive shaking (PEIS VIII) where many well-built buildings are expected to be considerably damaged, URM structures have a 95% probability of reaching or exceeding DS4 (extensive damage) and 81% for complete damage (DS5). For lightweight typologies, there are 78% (LW-A) and https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ Table 2. xm and β values of the fragility functions. Fragility functionsh Considering a 200 km/h peak gust, URM, RC typologies, and SC-B have very low to negligible probabilities of reaching or exceeding DS5 unlike LW-A, LW-B, and SC-A where there are 22%, 17%, and 8% chances of meeting or exceeding DS5, respectively. This wind intensity corresponds roughly to an estimated 20-year return period in the Province of Batanes, meaning that it has a 5% possibility to happen in a given year, based on the regional severe wind hazard maps for the ­Philippines51. At 300 km/h, corresponding to a 500-year return period (0.2% chance to happen in a given year), URM structures have 87% and 65% probabilities of reaching or exceeding DS4 and DS5, respectively. RC-A is expected to perform similarly with 87% and 69% probabilities of DS4 and DS5, respectively. Meanwhile, RC-B shows an 11% probability of reaching or exceeding DS4 and a 3% probability for DS5. For lightweight typologies, DS4 has a likelihood of 97% (LW-A and LW-B), while DS5 corresponds with 92% (LW-A) and 91% (LW-B). For semi-concrete typologies, DS4 shows 92% (SC-A) and 89% (SC-B) probabilities of exceedance, and 81% (SC-A) to 74% (SC-B) for DS5. At 400 km/h, all typologies have > 99% probability of exceedance for DS5, except for RC-B having a 79% likelihood of reaching or exceeding this damage state. Studies on the derivation of fragility functions in the Philippines are presently very limited. Cross-comparison of our functions to the available studies is challenging given the differences of how typologies and damage states are characterised including the nuanced assumptions considered in deriving these functions. Given these limita- tions, we were only able to draw comparisons to the works of Pacheco et al.52 and Naguit et al.53 on the fragility functions derived for lightweight, wooden-framed structures. This typology is comparable to LW-A (lightweight with wooden posts) in this study characterised by wooden post and beam systems. Other typologies from these studies exhibit different structural characteristics from the ones we surveyed. For example, low-rise concrete- framed typologies described by both studies cannot be used for direct comparison since in their works, these are described as concrete moment-framed structures with (hollow block) masonry walls whereas those surveyed in this study were concrete moment-framed structures with RC walls, adding lateral stiffness to the structure. Fragility functionsh Typology Earthquake Typhoon DS1 DS2 DS3 DS4 DS5 DS1 DS2 DS3 DS4 DS5 URM xm: 3.49 4.28 5.17 6.14 7.20 xm:136.87 177.26 222.60 256.70 285.18 β: 0.25 0.22 0.19 0.16 0.12 β: 0.16 0.15 0.15 0.14 0.13 LW-A xm: 4.63 5.45 6.34 7.17 7.96 xm:104.12 130.13 158.80 201.53 230.30 β: 0.19 0.16 0.16 0.14 0.12 β: 0.18 0.14 0.18 0.21 0.19 LW-B xm: 4.86 5.90 6.54 7.43 8.33 xm:110.18 137.59 165.86 207.47 236.83 β: 0.12 0.15 0.14 0.11 0.09 β: 0.18 0.14 0.20 0.20 0.18 SC-A xm: 4.87 5.60 6.52 7.40 8.32 xm:122.14 149.67 178.05 222.68 256.26 β: 0.17 0.12 0.12 0.11 0.09 β: 0.18 0.14 0.21 0.21 0.18 SC-B xm: 4.62 5.43 6.16 7.26 8.17 xm:125.02 157.52 190.12 243.92 270.10 β: 0.16 0.15 0.10 0.11 0.11 β: 0.18 0.18 0.17 0.17 0.16 RC-A xm: 5.11 5.89 6.82 7.59 8.43 xm:145.23 181.70 210.73 255.46 281.16 β: 0.16 0.13 0.12 0.10 0.08 β: 0.20 0.17 0.17 0.14 0.13 RC-B xm: 4.85 5.55 6.42 7.36 8.18 xm:230.27 266.00 298.31 338.73 366.65 β: 0.17 0.14 0.14 0.12 0.11 β: 0.08 0.12 0.12 0.10 0.11 Table 2. xm and β values of the fragility functions. 75% (LW-B) probabilities of meeting or exceeding DS4, and 52% (LW-A) and 33% (LW-B) likelihood for DS5. For semi-concrete typologies, still considering PEIS VIII, there is 76% (SC-A) and 81% (SC-B) probabilities of reaching or exceeding DS4, and 33% (SC-A) and 42% (SC-B) probabilities for DS5. For RC typologies, DS4 has 70% (RC-A) and 76% (RC-B) chances of being reached or exceeded, while 25% (RC-A) and 42% (RC-B) for DS5. Generally, URM tends to be the most vulnerable typology to seismic impacts while the other typologies perform better, either because of low structure weights (LW-A, LW-B), more robust lateral force resisting systems (RC-A, RC-B), or a combination of these features (SC-A, SC-B). ), ( , ) While URM might be vulnerable to seismic impacts, it generally tends to perform better against wind along- side RC typologies. At 100 km/h 3-s peak gust, URM has a 2% likelihood of reaching or exceeding DS1, RC-A has a 3% probability and RC-B has a negligible probability. At the same wind intensity, lightweight typologies show 41% (LW-A) and 30% (LW-B) probabilities of meeting or exceeding DS1, while semi-concrete typolo- gies show 13% (SC-A) and 11% (SC-B) probabilities of exceedance. Fragility functionsh Pacheco et al.52 derived their functions using a hybrid approach (computational and heuristic) while Naguit et al.53 generated their functions using empirical methods using data collected by communities. g g p g y Comparing seismic fragilities of lightweight wooden structures (see Fig. 6), our functions provide higher probabilities for complete damage or collapse. Whereas Naguit et al.’s53 functions estimate ~ 50% probabilities of exceedance for collapse and Pacheco et al.’s52 functions estimate ~ 85% for complete damage at the maximum seismic intensity possible (PEIS X / MMI XII), our functions assume complete damage at this intensity close to 100% probability of exceedance. Our functions also indicate that slight damage may start to manifest between Intensities II and III, close to Naguit et al.’s53 which suggest minor cracks starting to manifest around Intensity II. Meanwhile, Pacheco et al.’s52 functions indicate slight damage starting to become possible at Intensity IV. For wind comparisons (see Fig. 7), both our functions and Pacheco et al.’s52 suggest > 75% probabilities of exceedance for complete damage for wind speeds greater than 350 km/h. For both functions, slight/minor and moderate Scientific Reports | (2023) 13:22008 | https://doi.org/10.1038/s41598-023-49398-2 www.nature.com/scientificreports/ e.com/scientificreports/ damage start to arise around 100 km/h but ours have steeper curves suggesting a more rapid change in prob- abilities with the increase of wind speed. In comparing functions, caution should be taken since differences can Figure 6. Comparison of seismic fragility functions to other studies for lightweight, wooden-framed typology. (Note: PEIS stands for PHIVOLCS Earthquake Intensity Scale while MMI stands for Modified Mercalli Intensity). Figure 7. Comparison of wind fragility functions to other studies for lightweight, wooden-framed typology. p Figure 6. Comparison of seismic fragility functions to other studies for lightweight, wooden-framed typology. (Note: PEIS stands for PHIVOLCS Earthquake Intensity Scale while MMI stands for Modified Mercalli Intensity). Figure 6. Comparison of seismic fragility functions to other studies for lightweight, wooden-framed typology. (Note: PEIS stands for PHIVOLCS Earthquake Intensity Scale while MMI stands for Modified Mercalli Intensity). Figure 6. Comparison of seismic fragility functions to other studies for lightweight, wooden-framed typology. (Note: PEIS stands for PHIVOLCS Earthquake Intensity Scale while MMI stands for Modified Mercalli Intensity). Figure 7. Comparison of wind fragility functions to other studies for lightweight, wooden-framed typology. Figure 7. www.nature.com/scientificreports/ of 3 or greater (out of 5). As shown in Table 3, there was variation in experts’ confidence in their assessments. The median of confidence level for wind assessments for each typology is 3 across all typologies. Meanwhile, for seismic assessments, heavier typologies (URM, RC-A, and RC-B) have a median confidence rating of 4 while the rest, which are the lighter weight counterparts, have a median confidence level of 3. Considering experts’ unweighted (or raw) inputs, standard deviations across damage states for earthquake intensities range from PEIS 0.83–PEIS 1.54, while for typhoon wind speeds, they range from 43.29 to 105.65 km/h. The minimum and maximum values of the consolidated estimates from both local experts and specialists are presented in Table 3 and these values show the variation of inputs solicited for this assessment.i of 3 or greater (out of 5). As shown in Table 3, there was variation in experts’ confidence in their assessments. The median of confidence level for wind assessments for each typology is 3 across all typologies. Meanwhile, for seismic assessments, heavier typologies (URM, RC-A, and RC-B) have a median confidence rating of 4 while the rest, which are the lighter weight counterparts, have a median confidence level of 3. Considering experts’ unweighted (or raw) inputs, standard deviations across damage states for earthquake intensities range from PEIS 0.83–PEIS 1.54, while for typhoon wind speeds, they range from 43.29 to 105.65 km/h. The minimum and maximum values of the consolidated estimates from both local experts and specialists are presented in Table 3 and these values show the variation of inputs solicited for this assessment. p To summarise, respondents were more confident in their assessments of heavier typologies for both hazards. However, for typhoon hazards, variance of responses increased from light to heavy typologies, suggesting wider variation in expert assessments. In general, we argue that the variability of experts’ inputs should be consid- ered an advantage for the context of this assessment because such variability encompasses the broad scenario- based observations of housing performance. This consideration is beneficial most especially where construction resources are used less prescriptively against building codes and standards requiring less straightforward appraisal of housing performance. Table 3. Ranges of consolidated experts’ estimates shown through minimum and maximum values, including the median. *Confidence levels are ordinal ratings from 1 to 5. **IM stands for intensity measure. www.nature.com/scientificreports/ For earthquake, it is expressed in PHIVOLCS Earthquake Intensity Scale (PEIS). For typhoon, it is expressed in kilometres per hour (km/h). Table 3.   Ranges of consolidated experts’ estimates shown through minimum and maximum values, including the median. *Confidence levels are ordinal ratings from 1 to 5. **IM stands for intensity measure. For earthquake, it is expressed in PHIVOLCS Earthquake Intensity Scale (PEIS). For typhoon, it is expressed in kilometres per hour (km/h). Fragility functionsh Comparison of wind fragility functions to other studies for lightweight, wooden-framed typology damage start to arise around 100 km/h but ours have steeper curves suggesting a more rapid change in prob- abilities with the increase of wind speed. In comparing functions, caution should be taken since differences can emanate from the varied characterisations adopted by authors. For example, the use three-tier damage scale (e.g., Naguit et al.53) can result to a different set of functions when applying more granular observations to visualise or represent five damage states.fii damage start to arise around 100 km/h but ours have steeper curves suggesting a more rapid change in prob- abilities with the increase of wind speed. In comparing functions, caution should be taken since differences can emanate from the varied characterisations adopted by authors. For example, the use three-tier damage scale (e.g., Naguit et al.53) can result to a different set of functions when applying more granular observations to visualise or represent five damage states.fii i Benchmarking the accuracy of the functions derived in this study is difficult as these are the first to be derived for this geographical context. In the interim, these functions can be considered as medium quality having satisfied the criteria of Porter et al.27,28 to have at least three experts whose confidence ratings are ≥ 3. For the expert-driven approach in ATC-58, only low and medium-quality benchmarks are provided in reporting on the quality of the derived functions. At least 68% of the responses for every typology for each hazard received confidence ratings https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ i g y earthquake, it is expressed in PHIVOLCS Earthquake Intensity Scale (PEIS). For typhoon, it is expressed in kilometres per hour (km/h). Table 3.   Ranges of consolidated experts’ estimates shown through minimum and maximum values, including he median. *Confidence levels are ordinal ratings from 1 to 5. **IM stands for intensity measure. For www.nature.com/scientificreports/ Earthquake intensity (PEIS) Typhoon intensity (km/h) URM LW-A LW-B SC-A SC-B RC-A RC-B URM LW-A LW-B SC-A SC-B RC-A RC-B Confidence levels* Min 1 1 3 1 1 1 1 1 1 1 1 1 1 1 Max 4 4 4 5 5 5 4 5 5 5 5 5 5 5 Median 4 3 3 3 3 4 4 3 3 3 3 3 3 3 DS 1 Median IM** Min 2 1 3 2 2 4 3 50 30 30 60 60 45 70 Max 6 4 8 8 7 7 7 300 225 225 300 300 300 400 Median 3 3 5 4 4 5 4.5 100 100 100 100 100 120 150 Lower bound IM Min 1 1 2 1 1 1 2 30 20 25 50 55 30 60 Max 5 7 8 7 6 6 5 250 200 200 250 250 250 400 Median 2 3 4 3 3 4 4 80 60 70 80 80 100 130 DS 2 Median IM Min 3 3.5 4 3 2.5 4.5 3 70 40 40 75 80 55 90 Max 6 8 8 8 8 8 8 325 250 250 325 325 325 400 Median 4 5 6 5 5 5.75 5.5 150 120 126 135 140 150 200 Lower bound IM Min 2 2 3 2 1 2 2 40 25 30 60 70 45 70 Max 5 7 8 8 7 7 6 275 225 225 275 275 275 400 Median 3 4 5 4 4 5 5 120 100 100 100 100 125 155 DS 3 Median IM Min 3 4 4.5 3.5 3 5 4 75 60 60 90 90 75 160 Max 7 9 9 9 8 9 8 350 275 275 350 350 350 400 Median 5 6 6.75 6 6 7 6.75 180 155 155 160 180 200 300 Lower bound IM Min 2 3 4 3 2 4 2 50 40 45 60 60 50 100 Max 6 8 8 8 8 8 7 300 250 250 300 300 300 400 Median 4 5 5.5 5 5 6 5.5 160 115 120 125 145 150 200 DS 4 Median IM Min 4 5 6 4 4 6 5 80 90 90 140 140 90 220 Max 8 10 10 9 9 10 9 375 300 300 375 375 375 400 Median 6 7 7.25 7 7 7.5 7.5 200 200 200 200 205 240 350 Lower bound IM Min 3 3 4 3 2 4 3 70 80 90 100 100 75 160 Max 7 9 9 8 9 9 8 325 275 275 325 325 325 400 Median 5 6 6.25 6 6 7 6.5 175 150 150 150 175 200 300 DS 5 Median IM Min 5 6 6.5 5 5 7 6 90 110 110 150 150 100 250 Max 9 10 10 10 10 10 10 400 325 325 400 400 400 400 Median 7 8 8 8 8 8 8 250 245 250 250 240 260 400 Lower bound IM Min 4 5 6 4 3 5 5 60 90 100 100 100 85 180 Max 8 9 9 9 9 10 9 375 300 300 350 350 350 400 Median 6.5 7 7.25 7 7 7.5 7.25 200 180 185 200 200 222.5 325 Table 3. Discussion d However, in some instances, there is no definite historical upper bound of hazard intensities for wind events due to previ- ous data limitations. For example, recorded peak gusts of Typhoon Meranti (Ferdie) in 2016 are unavailable in Itbayat where it made ­landfall54. Likewise, peak gusts of Typhoon Haiyan (Yolanda) were not recorded across some weather stations in the Visayas region due to the damage sustained by the weather ­instruments48,55,56. To compensate for such limitations, intensity readings of neighbouring international weather agencies were used. Additionally, estimated intensities evident from impact signs to infrastructure as derived in some studies were ­referenced55–57. However, without officially recorded intensity readings of some of the largest typhoons in the Philippines, estimates will always be confined within the proxied or assumed values. For seismic impacts, a fac- tor to consider as raised by one specialist is the possibility of circular logic between PEIS intensities and damage states. That is, PEIS ground shaking is at least partly pegged to certain descriptors of building damage. h f h d h bl l h l l d l d h On the use of the expert-driven approach as a viable alternative where analytical and empirical data are currently impractical to acquire, we realise that expertise can also be a rare commodity. Local expertise might be limited at a municipal level especially in small, geographically remote areas. We have addressed this issue by broadening the jurisdiction to the provincial level where district engineers compensated for this limitation. Additionally, while there is a reasonable number of specialists who could be prospective respondents, their availability was not guaranteed, and response rates mainly dictated the sampling of the respondents. Therefore, robustly qualifying who gets involved was the priority more than reaching a certain quota of respondents with a focus on quality over quantity of participant selection.hih These three insights guided our derivation of the first-generation fragility functions in Batanes. The non- engineered nature of the typologies surveyed makes it a challenge to definitively assess the variability inherent to this building stock. This study, however, advanced this pursuit by acknowledging the nuanced characteristics of non-engineered typologies, which could have otherwise been categorised within existing generic taxonomies. In the Philippines, previous efforts to generate fragility or vulnerability functions for residential typologies have been conducted for Greater Metro Manila ­Area52, ­Bohol53, and ­Cebu58, with contributions in the GEM database. Discussion d In conducting the expert-driven approach of deriving fragility functions, we gleaned three insights to consider when using this heuristic alternative for damage analysis. These insights include how disaster sub-culture influ- ences experts’ estimates, some caveats to be aware of when relying on hazard intensities published by agencies, and the logistical challenges of soliciting experts’ opinions. In areas like Batanes where people have perennial encounters with hazards, disaster preparedness practices instinctively emerge to become part of their disaster sub-culture. For example, before a typhoon hits, houses are tied up with ropes to secure their envelopes (a practice called kap’yakuyakut in Itbayat and kapanpet in mainland Batanes). Meanwhile, windows are covered with an additional layer of improvised shutters (tapangko). During the solicitation of experts’ opinions, a local expert commented that his estimates were guided by how the houses perform in conjunction with these prevailing disaster preparedness practices in the area. These considerations provide a layered understanding of housing performance embedded in local settings—and why the develop- ment of localised fragility functions is important. Conventional approaches to damage analysis would suggest equal, unifying assumptions for assessments. However, understanding these local practices requires context and nuance not captured by decoupling building elements and preparedness activities. Commanding local experts to “disregard” such considerations is counterintuitive given that the core basis of their estimates is on actual obser- vations. Beyond the expert-driven approach, there is an opportunity to consider these types of non-traditional measures in computational fragility modelling done experimentally. These disaster preparedness practices will also have an impact on future empirical data collected in Batanes since housing damage will likely be reflective of the housing performance in conjunction with such practices. Damage estimates based on experts’ opinions are guided by actual observations of housing performance based on past disaster events. These observations are most likely referenced with impactful hazard intensities as broadcasted by agencies. Since damage estimates are relative or “framed” within agency-interpreted intensities, any errors, limitations, or discrepancies in how these intensities are interpreted affect the experts’ estimates. On the survey forms, we provided information sheets that contained ranges of hazard intensities of notable disaster events in the Philippines from different data sources to guide respondents in situating their estimates. The inten- tion was to confine their estimates within reasonable hazard intensities that were actually recorded. Discussion d This study branched out further north to consider the rural context of a small island geography which has been pressured to address multi-hazard housing safety due to the competing impacts of extreme events. The functions derived are fundamental tools for practitioners to understand the vulnerability of non-engineered structures and offer targeted structural mitigation and preparedness programmes contextualised in the area. It is suggested that when more empirical data becomes available, the possibility of combining new and existing functions should be ­explored50,59. www.nature.com/scientificreports/ Ranges of consolidated experts’ estimates shown through minimum and maximum values, including the median. *Confidence levels are ordinal ratings from 1 to 5. **IM stands for intensity measure. For earthquake, it is expressed in PHIVOLCS Earthquake Intensity Scale (PEIS). For typhoon, it is expressed in kilometres per hour (km/h). 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Porter, K. ‘A beginner’s guide to fragility, vulnerability, and risk’, in Encyclopedia of Earthquake Engineering, Beer, M., Kougioumt- zoglou, I. Conclusion Using fragility functions in risk assessments is fundamental to model anticipated structural housing damage against the impacts of natural hazards. We used an expert-driven approach to derive wind and seismic fragility functions for the Province of Batanes. Theoretically, this study provides new estimates of the performance of non- engineered housing in the Philippines, which would traditionally be discounted by conventional fragility assess- ments relying on generic building taxonomies. This region-specific evaluation is a step to advance more localised risk assessments. Practically, the set of fragility functions derived in this study is seen to assist practitioners in exploring risk preparedness and mitigation measures applicable in Batanes. On a national scale, we fill gaps on the lacking representation of building archetypes in rural and remote areas as most attention to understanding building-level risk reduction has, to date, focused in urban centres where data are more accessible. Our functions https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ lay a foundation for more holistic and contextualised approaches to risk modelling nationwide considering the inclusion of neglected geographic areas. As new damage data and analysis emerge in the future, our functions can aid hybrid approaches to generate the next generation of fragility estimates. lay a foundation for more holistic and contextualised approaches to risk modelling nationwide considering the inclusion of neglected geographic areas. 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Quantifying scientific uncertainty from expert judgement elicitation, in Risk and Uncertainty Assessment for Natural Hazards, 1st ed., Rougier, J., Sparks, S., and Hill, L. J. Eds., Cambridge University Press, 2013, pp. 64–99. https://​doi.​org/​10.​1017/​CBO97​81139​047562.​005. p g 0. Lallemant, D., Kiremidjian, A. & Burton, H. Statistical procedures for developing earthquake damage fragility curves. Earthq Engng. Struct. Dyn. 44(9), 1373–1389. https://​doi.​org/​10.​1002/​eqe.​2522 (2015). g g y p g q 51. Philippine Atmospheric, Geophysical, and Astronomical Services, ‘Regional Severe Wind Hazard Maps’. Accessed: Jul. 17, 2 [O l ] A l bl h // d h/ d d / d 51. Philippine Atmospheric, Geophysical, and Astronomical Services, ‘Regional Severe Wind Hazard Maps’. Accessed: Jul. 17, 2023. [Online]. Available: https://​www.​pagasa.​dost.​gov.​ph/​produ​cts-​and-​servi​ces/​severe-​wind-​maps [Online]. Available: https://​www.​pagasa.​dost.​gov.​ph/​produ​cts-​a p p g g p p p 52. Pacheco, B. et al. Development of Vulnerability Curves of Key Building Types in the Greater Metro Manila Area, Philippines Report (University of the Philippines Diliman, Philippines, Quezon City, Philippines, 2014). g g t al. Development of Vulnerability Curves of Key Building Types in 52. Pacheco, B. et al. Development of Vulnerability Curves of Key Building Types in the Greater Metro Manila Area, Philippines Report (University of the Philippines Diliman, Philippines, Quezon City, Philippines, 2014). p y y 53. Naguit, M. et al. From source to building fragility: Post-event assessment of the 2013 M7.1 Bohol, Philippines, earthquake. Earthq. Spectra 33(3), 999–1027. https://​doi.​org/​10.​1193/​01017​16eqs​173m (2017). p y y 53. Naguit, M. et al. From source to building fragility: Post-event assessment of the 201 Spectra 33(3), 999–1027. https://​doi.​org/​10.​1193/​01017​16eqs​173m (2017). p p g q 54. Paciente, R. Competing interests h p g The authors declare no competing interests. References Soil Dynam. Earthq. Eng. 28(10–11), 764–777. https://​doi.​org/​10.​1016/j.​soild​yn.​2007.​10.​011 (2008).l p g j y 6. Winter, M. G. et al. An expert judgement approach to determining the physical vulnerability of roads to debris flow. Bull. Eng Geol. Environ. 73(2), 291–305. https://​doi.​org/​10.​1007/​s10064-​014-​0570-3 (2014). p g 7. Porter, K., Kennedy, R. & Bachman, R. Creating fragility functions for performance-based earthquake engineering. Earthq. Spectra 23(2), 471–489. https://​doi.​org/​10.​1193/1.​27208​92 (2007). p g 28. Porter, P. K., Kennedy, R. and Bachman, R. Developing fragility functions for building components for ATC-58’, Applied Technol- ogy Council, Redwood City, CA, (2006). gy y 29. International Federation of Red Cross and Red Crescent Societies, ‘Philippines: Batanes Eart l ‘ f h l d ( ) d b gy y 29. International Federation of Red Cross and Red Crescent Societies, ‘Philippines: Batanes Earthquake’, (2020). 30 Perez J et al ‘Impacts of the 27 July 2019 Magnitudes (Mw) 5 4 5 9 and 5 8 Itbayat Batanes Earthquakes’ Dep 29. International Federation of Red Cross and Red Crescent Societies, ‘Philippines: Batanes Earthquake’, (2020). 30. Perez J. et al., ‘Impacts of the 27 July 2019 Magnitudes (Mw) 5.4, 5.9, and 5.8 Itbayat, Batanes Earthquakes’, Department of Scie and Technology Philippine Institute of Volcanology and Seismology (2019) pp q 30. Perez J. et al., ‘Impacts of the 27 July 2019 Magnitudes (Mw) 5.4, 5.9, and 5.8 Itbayat, Batanes Earthquakes’, Department of Science and Technology - Philippine Institute of Volcanology and Seismology, (2019). 30. Perez J. et al., ‘Impacts of the 27 July 2019 Magnitudes (Mw) 5.4, 5.9, and 5.8 Itbayat, Batanes E and Technology - Philippine Institute of Volcanology and Seismology, (2019).i 30. Perez J. et al., Impacts of the 27 July 2019 Magnitudes (Mw) 5.4, 5.9, and 5.8 Itbayat, Batanes Earthquakes, Department of Sc and Technology - Philippine Institute of Volcanology and Seismology, (2019).i gy pp gy gy ( ) 31. Silva, V. et al. A building classification system for multi-hazard risk assessment. Int. J. Disaster Risk Sci. 13(2), 161–177. https://​ doi.​org/​10.​1007/​s13753-​022-​00400-x (2022). 32. Venable, C., Javernick-Will, A., Liel, A. B. and Koschmann, M. A. Revealing (mis)alignments between household perceptions and engineering assessments of post-disaster housing safety in typhoons, Int. J. Disaster Risk Reduct., 53, (2021), https://​doi.​org/​10.​ 1016/j.​ijdrr.​2020.​101976. https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | Author contributions A.H. wrote the main manuscript text, conducted the field visits, data collection, and analysis. A.O. provided primary supervision while S.A.H. provided secondary supervision. A.H. and A.O. edited the manuscript. All authors conceptualised the project and reviewed the manuscript. Open Access  This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. Additional information Correspondence and requests for materials should be addressed to A.H. Correspondence and requests for materials should be addressed to A.H. Reprints and permissions information is available at www.nature.com/reprints. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and nstitutional affiliations. https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 | www.nature.com/scientificreports/ www.nature.com/scientificreports/ Open Access  This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. © The Author(s) 2023 https://doi.org/10.1038/s41598-023-49398-2 Scientific Reports | (2023) 13:22008 |
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Mitochondrial transport, partitioning, and quality control at the heart of cell proliferation and fate acquisition
American journal of physiology. Cell physiology
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To cite this version: Rakesh Kumar Sharma, Abderrahman Chafik, Giulia Bertolin. Mitochondrial transport, partitioning, and quality control at the heart of cell proliferation and fate acquisition. American Journal of Physi- ology - Cell Physiology, 2022, 322 (2), pp.C311-C325. ￿10.1152/ajpcell.00256.2021￿. ￿hal-03578475￿ Distributed under a Creative Commons Attribution 4.0 International License To cite this version: Rakesh Kumar Sharma, Abderrahman Chafik, Giulia Bertolin. Mitochondrial Transport, Partitioning and Quality Control at the Heart of Cell Proliferation and Fate Acquisition. 2021. ￿hal-03383673￿ Mitochondrial Transport, Partitioning and Quality Control at the Heart of Cell Proliferation and Fate Acquisition Rakesh Kumar Sharma, Abderrahman Chafik, Giulia Bertolin Rakesh Kumar Sharma, Abderrahman Chafik, Giulia Bertolin HAL Id: hal-03578475 https://hal.science/hal-03578475v1 Submitted on 17 Feb 2022 L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci- entific research documents, whether they are pub- lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. Distributed under a Creative Commons Attribution 4.0 International License Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Correspondence should be addressed to GB: giulia.bertolin@univ-rennes1.fr; Tel: +330223237516 Correspondence should be addressed to GB: giulia.bertolin@univ-rennes1.fr; Tel: +330223237516 Rakesh Kumar Sharma1,*, Abderrahman Chafik1,* and Giulia Bertolin1 akesh Kumar Sharma1,*, Abderrahman Chafik1,* and Giulia Bertolin1 1Univ Rennes, CNRS, IGDR (Genetics and Development Institute of Rennes), UMR 6290, F-35000 Rennes, France * * These authors equally contributed to this work. * These authors equally contributed to this work. HAL Id: hal-03383673 https://hal-univ-rennes1.archives-ouvertes.fr/hal-03383673 Preprint submitted on 18 Oct 2021 L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci- entific research documents, whether they are pub- lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. Distributed under a Creative Commons Attribution| 4.0 International License Introduction Mitochondria are found in most of the eukaryotic cells and they contribute to many functions such as ATP generation, β oxidation of fatty acids, and cellular metabolism (1). Mitochondria are also implicated, among other functions, in reactive oxygen species (ROS) generation and turnover, in apoptotic pathways, and in calcium signaling (1). Mitochondria are dynamic and motile organelles (2, 3) that constantly fragment (a mechanism also known as fission) and fuse (3, 4). Mitochondria also undergo turnover, which comprises selective clearance by mitophagy when organelles are damaged and biogenesis events to increase the mass of the mitochondrial network (4). Mitochondrial fission is driven by the binding of Dynamin-1-like protein (Drp1/DNM1L) to its receptor proteins MFF (mitochondrial fission factor), MID49/51, and/or FIS1 on the mitochondrial outer membrane (4, 5). Oligomerized DNM1L wraps around mitochondria by forming a ring that causes Outer Mitochondrial Membrane deformation and scission (6). Daughter mitochondria obtained after fission may undergo re-fusion with the rest of the network, or they can be subjected to mitophagy in case their activity is compromised, such as after the accumulation of deleterious mtDNA mutations, of ROS, or of misfolded proteins (7). In contrast to fission, mitochondrial fusion is a mechanism in which two mitochondria fuse together, and the two mitochondrial units share tRNAs, rRNAs, proteins and matrix metabolites (8). Fusion between Inner Mitochondrial Membranes is mediated by Optic Atrophy Protein 1 (OPA1), while on the Outer Mitochondrial Membranes (OMM) Mitofusin1 (MFN1), and Mitofusin2 (MFN2) are the key players (9). Mitochondrial fusion and fission processes are collectively known as mitochondrial dynamics and influence nearly all mitochondrial functions including respiration, calcium buffering, bioenergetic adaptation, and apoptosis (10, 11). Here, we will review our current state of the art on how mitochondrial dynamics is involved in and required for the transport of mitochondria within the cell, and for the effective clearance of mitochondria under physiological conditions. We will also recapitulate our current knowledge on the consequences of mitochondrial transport, dynamics and mitophagy failures for mitochondrial homeostasis, cell stemness and fate acquisition. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Abstract Mitochondria are essential to cell homeostasis, and alterations in mitochondrial distribution, segregation or turnover have been linked to complex pathologies such as neurodegenerative diseases or cancer. Understanding how these functions are coordinated in specific cell types is a major challenge to discover how mitochondria globally shape cell functionality. In this review, we will first describe how mitochondrial transport and dynamics are regulated throughout the cell cycle in yeast and in mammals. Second, we will explore the functional consequences of mitochondrial transport and partitioning on cell proliferation, fate acquisition, stemness, and on the way cells adapt their metabolism. Last, we will focus on how mitochondrial clearance programs represent a further layer of complexity for cell differentiation, or in the maintenance of stemness. Defining how mitochondrial transport, dynamics and clearance are mutually orchestrated in specific cell types may help our understanding of how cells can transition from a physiological to a pathological state. 1 Mitochondrial transport and inheritance during cell cycle progression As introduced above, mitochondria play multiple functions and their proper distribution during cell division is essential for cell survival. However, these organelles can only be generated by an increase in mitochondrial mass, followed by the separation of pre-existing mitochondria from the network (16). Therefore, the maintenance of the mitochondrial pool must be coordinated throughout the cell cycle to ensure the proper distribution of these organelles in the daughter cells. Mutations in genes encoded by the mitochondrial genome are lethal in higher vertebrates, thereby limiting our capacity to explore how these mutations might affect mitochondrial inheritance. To overcome this issue, early studies on mitochondrial inheritance were performed in baker's yeast (Saccharomyces cerevisiae), and showed that organelle inheritance is well coordinated with the cell cycle. Actin cables – bundles of F-actin acting as a track for the bidirectional movement of cargo – are responsible for the transfer of mitochondria from the mother to the bud. In addition, these cables also arise from the bud tips and undergo continuous movements toward the mother cell tip. This backwards movement is called retrograde cable flow (RCAF) and as described below, increased RCAF rates for mitochondria are linked with the fitness of the mitochondria that are transferred to the bud. In the early stage of the G1 phase, actin starts to polarize, and mitochondria align with the mother-bud axis. In the S phase and until the G2 phase, mitochondrial movement occurs towards the bud tip by anterograde linear excursions, and towards the mother tip by retrograde linear excursions (17, 18). This bidirectional movement leads to the accumulation of mitochondria into both bud and mother cell tips in an actin- dependent manner. During the M phase instead, mitochondria are shed from actin and distributed throughout the bud (17, 18). The mutant yeast strain tpm1∆ lacking a functional actin stabilizing tropomyosin 1 gene (TPM1) shows abnormal mitochondrial distribution and morphology (17). Mutations in the actin-encoding gene ACT1 (19), or in the chaperone- encoding genes CCT4 and CCT6 which are essential for actin folding, cause defects in mitochondrial morphology and unequal distribution of mitochondria to the daughter cell (19– 21). During cell division, mitochondrial inheritance mechanisms ensure the transfer of metabolically active mitochondria to the daughter cell, while mitochondria with a highly- oxidized redox potential are retained in the mother cell and maintain the mother-daughter age asymmetry in yeast (18, 22). Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 with the cytoskeletal protein Kinesin 5 on the other hand (13). MIRO proteins also interact with the mitochondrial fusion proteins MFN1 and MFN2, thereby linking mitochondrial dynamics and transport (12, 14). This link is further corroborated by the observation that the motor protein dynein is critical for DNM1L-mediated fission (15). The disruption of dynein functions in HeLa cells dramatically changes the organization of the mitochondrial network and inhibits organelle fission, causing extensive branching and tubular mitochondria (15). However, what are the consequences on cell physiology, metabolism and proliferation if mitochondrial transport and dynamics are impaired? The interplay of mitochondrial transport and dynamics ensures faithful organelle distribution. Mitochondria move along the cytoskeleton with the help of the motor proteins and this function is critical for organelles to orchestrate fission, fusion and quality control events. In specialized cells as neurons, mitochondrial movements towards the axonal ends are critical for fulfilling the energy required at synapses. In mammals, mitochondrial movements occur on the microtubules with the help of motor proteins such as kinesins and dyneins (12, 13). The recruitment of the motor proteins on the mitochondrial surface is essential for mitochondrial transport. Typically, these motor proteins are opposite in nature, and the kinesins transport the mitochondria to the plus end of the microtubule (anterograde), while dynein to the minus end (retrograde). The adaptor proteins Milton/TRAK help in the anchoring of mitochondria by motor proteins, as they interact directly with the OMM proteins MIRO 1/2 on one hand, and 2 2 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 essential for the normal RCAF and for mitochondrial inheritance during cell division. Any perturbation of its functions causes the transfer of mitochondria containing high reactive oxygen species to daughter cells and reduces yeast lifespan (18, 22, 23). essential for the normal RCAF and for mitochondrial inheritance during cell division. Any perturbation of its functions causes the transfer of mitochondria containing high reactive oxygen species to daughter cells and reduces yeast lifespan (18, 22, 23). Last, Altmann et al. showed that the class V myosin motor protein Myo2 is essential for actin- mediated mitochondrial transport (24). They showed that Myo2 facilitates the binding of mitochondria to actin, and it helps mitochondrial motility during cell division. Moreover, mutations in Myo2 that alter the binding of mitochondria to actin cables cause the abnormal accumulation of mitochondria in the mother cell (24). Although a significant body of evidence illustrated that mitochondrial delivery and quality control in yeast is mediated by actin throughout the cell cycle, the majority of the molecular motors involved beyond Myo2 still remains to be discovered. Last, Altmann et al. showed that the class V myosin motor protein Myo2 is essential for actin- mediated mitochondrial transport (24). They showed that Myo2 facilitates the binding of mitochondria to actin, and it helps mitochondrial motility during cell division. Moreover, mutations in Myo2 that alter the binding of mitochondria to actin cables cause the abnormal accumulation of mitochondria in the mother cell (24). Although a significant body of evidence illustrated that mitochondrial delivery and quality control in yeast is mediated by actin throughout the cell cycle, the majority of the molecular motors involved beyond Myo2 still remains to be discovered. In mammalian cells, mitochondrial segregation also occurs during mitosis. However, a cross- talk between the mitochondrial dynamics and the cell cycle machinery begins as early as a cell commits to cell cycle entry (G0-G1), and both cell cycle progression and mitochondrial division occur in parallel. During the G1 phase, the biosynthesis of the mitochondrial complexes occurs (25, 26). As the cell progresses towards the S phase, the levels of Cyclin E increase together with the Cyclin E-dependent inhibition of DNM1L (27, 28). Mitochondrial transport and inheritance during cell cycle progression Deleting the Mmr1p protein, a member of the DSL1 family that assists the tethering of mitochondria to the bud, was shown to compromise the quality of mitochondria delivered to the daughter cell (22). Yeast Sirtuin (SIRT2) was also found to be 3 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/prep Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 causes the aggregation of mitochondria and alter the mitochondrial positioning at this cell cycle phase (37). These discrepancies may be due to differential incubations with latrunculin A (10 min (34) or 1 h (37)), or they might be intrinsic to the resolution power of the microscopy setups used to image the samples (Airyscan high-resolution microscopy (37) or conventional confocal microscopy (34)). Overall, mitochondrial segregation at mitosis is a complex, but well-coordinated process in mammalian cells: after the release of mitochondria from motor proteins during the early stages of mitosis, actin cables ensure the uniform distribution of mitochondria prior to cell division. The requirements for mitochondrial transport in proliferating cells and in cells largely in quiescence share functional similarities, although in specific cell types as neurons the mechanisms of mitochondrial transport on cytoskeletal tracks have been better characterized. Neurons mostly rely on mitochondrial ATP for their survival, and they maintain a comparatively higher number of mitochondria than other cell types. Neurons typically have higher ATP demands at synapses, and this finding is supported by the high amount of mitochondria that can be found at these locations following their transport from the cell body. Similarly, the dependence of mitochondria on the nuclear genome for organelle-specific turnover programs necessitates the transport of damaged mitochondria back from the axon and dendrites to the cell body (38). As in other cell types, mitochondria in neurons travel long-distance along the microtubule cytoskeleton, and short-distance along the actin network (39). The long-distance transport of mitochondria along microtubules is facilitated by kinesins and dynein (40). There are three classes of kinesin motors: the major transporter class Kinesin-1 family (KIF5s – KIF5A, KIF5B and KIF5C–), the Kinesin-3 family (KIF1B-α) and Kinesin-Like Protein 6 (KLP6) (41, 42). As introduced above, the loading of kinesins on mitochondria is performed with the help of the adaptor protein Milton in Drosophila, or the TRAK proteins in mammals. Milton links the OMM protein dMiro in Drosophila /MIRO1 and MIRO2 in mammals (43) to the cargo binding domain of KIF5. This complex constituted by MIRO (receptor), KIF5 (motor), and Milton/TRAKs (adaptors) facilitates the anterograde mitochondrial movement of mitochondria (36, 42). Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 This tips the mitochondrial dynamics balance towards fusion, and mitochondria appear as a hyper-fused and compact tubular network (27, 28), together with high ATP synthesis capabilities needed for the cell cycle to progress (29). During the S phase, mitochondrial DNA content also increases, thereby reflecting a strong coordination between nuclear and mitochondrial DNA synthesis processes (30). As the cell progresses toward mitosis, the levels of Cyclin B increase and the CDK1 (Cyclin-dependent kinase 1)/Cyclin B complex phosphorylates DNM1L on Ser585 (31) and on Ser616 (32). The phosphorylation of DNM1L is critical to activate its GTPase activity, leading to the activation of mitochondrial fission programs during cell division (33) (Fig. 1). From the beginning of the G1 phase and until mitosis, mitochondria are associated with motor proteins for their transport. After fission at mitosis, mitochondria are released from microtubules upon the phosphorylation of dynein by CDK1, and of kinesin-1 (Kinesin Heavy Chain or KHC) by Aurora A/AURKA (31, 34, 35). Interestingly, motor proteins were shown to be required for mitochondrial fission events during early mitosis. After fission is achieved, motor shedding is necessary for the symmetric distribution of mitochondria in mammalian cells (34). The forced attachment of kinesin to mitotic mitochondria causes an asymmetric mitochondrial distribution in the daughter cells, while the attachment of dynein-bound mitochondria to the mitotic spindle arrests cell at mitosis (34). This strongly supports the notion that the release of motor proteins from the mitochondrial membrane is crucial for successful progression through mitosis (Fig. 2). However, the mechanism of mitochondrial distribution after the release of motor proteins remains controversial (12, 34, 36). Chung et al. showed that mitochondrial distribution occurs passively after the release of the motor proteins during mitosis, and treatment of cultured cells with the actin-depolymerizing agent latrunculin A did not alter mitochondrial partitioning into the two daughter cells (34). However, Moore et al showed that mitochondria were associated with a dynamic wave of actin filament during mitosis, and depolymerizing the actin meshwork with either latrunculin A or cytochalasin D 4 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints2021 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 TCTEX1 favors the binding of dynein with the OMM protein voltage-dependent anion- selective channel (VDAC) (50). Then, dynactin binds directly to dynein, and it also binds to microtubules through its p150Glued component (51). Dynein in complex with dynactin is then capable to interact with Milton/TRAK2 and MIRO to mediate retrograde mitochondrial transport (36, 52) (Fig. 3A and B). TCTEX1 favors the binding of dynein with the OMM protein voltage-dependent anion- selective channel (VDAC) (50). Then, dynactin binds directly to dynein, and it also binds to microtubules through its p150Glued component (51). Dynein in complex with dynactin is then capable to interact with Milton/TRAK2 and MIRO to mediate retrograde mitochondrial transport (36, 52) (Fig. 3A and B). Although most mitochondrial transport takes place on microtubule tracks with the help of kinesins and dynein, the short distance movements in dendritic spines are orchestrated by myosins on the actin network (53). As introduced above, myosins are ATP-dependent motor proteins and out of 18 classes of myosin proteins, Myo-19 (53, 54) and Myo-5 were associated with mitochondrial transport in mammalian cells, with Myo-5 acting through the SPIRE1 actin- nucleating protein (55, 56). Both Myo-19 and Myo-5 were shown to bind to MIRO proteins to facilitate the mitochondrial transport (36) (Fig. 3C). However, the involvement of these motors in specific cells as neurons remains to be fully elucidated. Mitochondrial transport is crucial for the survival of neurons and for the maintenance of synapses. Perturbations of mitochondrial transport have been linked to neurodegenerative diseases such as Alzheimer’s (57–61) and Parkinson's (62–66), amyotrophic lateral sclerosis (67–70), schizophrenia (71, 72) and Huntington's diseases (73–75). Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/prep Although the complete mechanism of mitochondrial transport by KIF1B-α and KLP6 motor proteins is not well understood yet, their loading on mitochondria appears to be facilitated by the adaptor protein KBP (kinesin binding protein) (44, 45). Impairing the function of KLP6 by RNAi in C. elegans was shown to cause an alteration of mitochondrial morphology (46). Similarly, HeLa and Neuro-2a cells expressing a mutant KLP6 construct lacking the motor domain showed altered mitochondrial morphology and an inhibited transport of mitochondria in neurites of differentiated Neuro-2a cells (46) (Fig. 3A). The retrograde mitochondrial motion in neurons is driven by the dynein motor complex and its partner dynactin (47). The dynein motor is a multimeric protein consisting of two heavy chains (DHC), several intermediate chains (DICs) and dynein light intermediate chains (DLICs), and dynein light chains (DLC) (47–49). The dynein heavy chains act as the motor, and the other subunits participate to the association of the dynein motor with the cargo and in regulating the mobility of dynein along the microtubule tracks. However, the large structure of dynein complexifies experimental analyses, and the dynein-mediated mitochondrial transport mechanism has not been fully elucidated yet. One study suggests that the DLC protein 5 The transport of mitochondria among cell populations as a potential route to adapt cell metabolism and contribute to chemoresistance in cancer The transport of mitochondria among cell populations as a potential route to adapt cell metabolism and contribute to chemoresistance in cancer Metabolic adaptation is an essential aspect for survival in the adverse tumor microenvironment, where every cell is undergoing multiple rounds of uncontrolled cell division. In such a competitive environment for nutrients availability, it is challenging to fulfill both substrate and energy requirements. Mitochondria play an essential role by fueling the energy requirements of the cancer cell by using various substrates, maintaining a pool of cancer stem cells, and helping in the development of metastasis (79–81). However, it is not clear whether the role(s) of mitochondria in these processes is played by the entire mitochondrial network within a particular cell population, or it is due to an exchange of mitochondria among the various cell populations constituting a tumor. It has been shown that mitochondria can be transferred from adult stem cells and/or somatic cells to defective cells with no mitochondrial DNA (r0 cells) (82, 83). This transfer restores aerobic respiration in r0 cells, and provided the first evidence of mitochondrial transfer between two cell populations (82). After this report, mitochondrial transfer was shown to occur under various paradigms: from the pluripotent mesenchymal stem cells to lung epithelial cells to protect from cigarette smoke-induced damage (84); from mesenchymal stem cells to epithelial cells to protect the injured cells in ischemia-reperfusion models (85, 86); from mesenchymal stem cells to rotenone-stressed mitochondrial myopathy, encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) fibroblasts to rescue their bioenergetics capabilities (87). Furthermore, the transfer of dysfunctional mitochondria from neurons to astrocytes and the consequent clearing of defective mitochondria within the astrocytes (88) was shown to provide neuroprotection in an animal model of stroke. In the context of cancer, the transfer of mitochondria was shown to occur from endothelial cells to cancer cells (89), and from bone marrow stromal cells to leukemic cells (90). This transfer protects the cancer cells from apoptosis and increases its chemoresistance. Last, the intracellular transfer of functional mitochondria from a highly invasive bladder cancer cells increases their metastatic and invasive properties, and results in an increased tumor size in a T24 xenograft mice model (91). The transport of mitochondria to active sites of inflammation or metastasis was also shown to be key to disease progression. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.06 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 different sets of “aged” mitochondria (78). Based on the relative content of aged mitochondria, lymphocytes will enter separate metabolic pathways. The cells that follow PI3K-dependent catabolic pathways were shown to contain “younger” mitochondria, to clear damaged organelles more efficiently and self-renew as naive stem cells. On the contrary, cells following AMPK-related anabolic pathways contain more “aged” mitochondria and undergo senescence (78). Although the respective molecular mechanisms and the player involved still remain to be fully understood, these studies show that the asymmetric partitioning of mitochondria is key to cell metabolism, together with the capacity of the cell to maintain stemness in specific cell types. Asymmetric mitochondrial inheritance during mitosis and its link to stemness In general, somatic cell division show a symmetric distribution of mitochondria into the two daughter cells, which receive comparable amounts of mitochondria with similar membrane potential levels. DNM1L-mediated mitochondrial fission is critical for the correct distribution of mitochondria in the daughter cells. AURKA and the Cyclin B/CDK1 complex, together with RALA (small Ras-like GTPase) and its adaptor and RALBP1 were shown to be key for mitochondrial fission at mitosis. AURKA phosphorylates RALA at Ser194 and upon phosphorylation, RALA localizes to mitochondria and favors the localization of its effector RALBP1 and of DNM1L itself to this compartment (32). Impairing this cascade of events alters DNM1L-dependent mitochondrial fission, resulting in the asymmetric segregation of mitochondria in the two daughter cells (32). Unlike in somatic cells, the uneven distribution of “aged” mitochondria often occurs during the asymmetric cell division of stem cells. One of the daughter cells receives the majority of newly- synthesized mitochondria and maintains the stem cell fate, while the daughter cell receiving a higher proportion of “aged” mitochondria will acquire a differentiated, non-stem fate (76). In addition, the inhibition of DNM1L-mediated mitochondrial fission events in the stem cell blocks the asymmetrical distribution of “old” mitochondria, leading to the loss of stem cell properties (76). Therefore, mitochondrial fission is also crucial for the maintenance of the stem cell phenotype. A similar study showed that the alteration of mitochondrial dynamics, or the presence of mitochondrial stress during the division of hematopoietic stem cells (HSCs) causes the asymmetric distribution of mitochondria in the daughter cells (77). The cells receiving dysfunctional mitochondria fail to manage the biosynthetic demands needed to progress throughout the cell cycle, and undergo replicative senescence (77). Another study illustrated that LPS-activated lymphocytes divide asymmetrically, and give rise to daughter cells having 6 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 However, the involvement of mitochondrial transport and its role in providing ATP for cell migration has been neglected. A study on epithelial breast cancer cell lines shows that the localization of mitochondria to the leading edge of the migrating cell increases the migration velocity and helps directional persistence (99). Similarly to the impact of mitochondrial fission for lymphocyte migration (94), promoting mitochondrial fusion by overexpressing OPA1, blocking fission by overexpressing a dominant-negative form of DNM1L (DNM1LK38A) or impairing mitochondrial transport using a MIRO1 shRNA slow down the migration of cancer cells (99). These data further corroborate the importance of mitochondrial dynamics and transport in cancer metastasis, although our current view of the importance of their interplay for cancer progression is still partial. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 process that requires high quantities of ATP for lymphocytes to adhere, contract and perform protrusions. In this light, mitochondria play a crucial role in lymphocyte migration (94): mitochondrial fission and redistribution were shown to be critical for migration, while an increase in mitochondrial fusion slows down this process (94). process that requires high quantities of ATP for lymphocytes to adhere, contract and perform protrusions. In this light, mitochondria play a crucial role in lymphocyte migration (94): mitochondrial fission and redistribution were shown to be critical for migration, while an increase in mitochondrial fusion slows down this process (94). process that requires high quantities of ATP for lymphocytes to adhere, contract and perform protrusions. In this light, mitochondria play a crucial role in lymphocyte migration (94): mitochondrial fission and redistribution were shown to be critical for migration, while an increase in mitochondrial fusion slows down this process (94). Similarly, cell migration is a characteristic feature of cancer cells that allows them to metastasize away from the primary site of the tumor (95). Cytoskeletal proteins are known to be crucial for cell migration and cancer metastasis, and many dugs developed to target cytoskeletal stability and functions are under investigation and show promising results (96– 98). However, the involvement of mitochondrial transport and its role in providing ATP for cell migration has been neglected. A study on epithelial breast cancer cell lines shows that the localization of mitochondria to the leading edge of the migrating cell increases the migration velocity and helps directional persistence (99). Similarly to the impact of mitochondrial fission for lymphocyte migration (94), promoting mitochondrial fusion by overexpressing OPA1, blocking fission by overexpressing a dominant-negative form of DNM1L (DNM1LK38A) or impairing mitochondrial transport using a MIRO1 shRNA slow down the migration of cancer cells (99). These data further corroborate the importance of mitochondrial dynamics and transport in cancer metastasis, although our current view of the importance of their interplay for cancer progression is still partial. Similarly, cell migration is a characteristic feature of cancer cells that allows them to metastasize away from the primary site of the tumor (95). Cytoskeletal proteins are known to be crucial for cell migration and cancer metastasis, and many dugs developed to target cytoskeletal stability and functions are under investigation and show promising results (96– 98). The transport of mitochondria among cell populations as a potential route to adapt cell metabolism and contribute to chemoresistance in cancer Lymphocyte migration is vital for adequate immunological response at the site of injury or inflammation, and it is guided by the cytokines or chemokines released at the site of the injury (92, 93). Lymphocyte migration is an energy-consuming 7 Mechanisms of mitophagy in red blood cells The maturation of erythroblasts into mature red blood cells is a process commonly known as terminal erythropoiesis. It starts in the bone marrow within erythroblastic islands, which consist of a central macrophage surrounded by erythroblasts, and it ends in the bloodstream, where reticulocytes complete their maturation in approximately two days (106, 107). The maturation of erythroblasts into red blood cells leads to profound changes in cell morphology, such as the loss of nearly 20% of the plasma membrane surface area, an overall reduced cell volume, the increased association of the cytoskeleton with the outer plasma membrane, enucleation and the loss of all residual cytoplasmic organelles, such as the Golgi apparatus, the endoplasmic reticulum (ER), mitochondria and ribosomes (106). The disappearance of mitochondria during terminal erythropoiesis gathered significant attention after the discovery that the main mechanism of mitochondrial clearance in erythroblast maturation is mitophagy (107). During the final step of erythroid differentiation LC3, an ubiquitin-like modifier required for the growth of autophagosomal membranes is converted from its unmodified form – known as LC3-I – to a lipidated form, LC3-II (108). The presence of autophagy during erythroid differentiation was confirmed by the work of Mortensen et al, where it was shown that the conditional knockout of the essential autophagy gene ATG7 in mouse erythrocytes induces the accumulation of damaged mitochondria with altered membrane potential (ΔΨm), increased susceptibility to cell death and anemia (109). During erythroblast maturation, it was shown that the outer mitochondrial membrane protein NIP3-like protein X (NIX), also named Bcl-2/adenovirus E1B 19 kDa interacting protein 3- like (BNIP3L) induces a loss of ΔΨm and the recruitment of LC3 to mitochondria (110). These events target mitochondria to autophagosomes for clearance during erythroid maturation. At the molecular level, NIX plays the role of a mitophagy receptor by recruiting LC3 and its cognate protein GABARAP, to damaged mitochondria through its amino-terminal LC3- interacting region (LIR) (111). Mice lacking the NIX:LC3/GABARAP interaction showed an altered mitochondrial clearance in maturing reticulocytes, a restored ΔΨm, altered erythroid maturation, and anemia. Other proteins were also shown to play a role in erythroid maturation, such as the serine- threonine kinase ULK1 (Uncoordinated 51-Like Autophagy Activating Kinase 1). ULK1 deficiency was shown to delay the clearance of mitochondria in mouse reticulocytes and embryonic fibroblasts (112). Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 In the sections below, we will review our current knowledge on the main mechanisms of basal mitophagy, and explore the consequences of impaired mitophagy for cell proliferation, stemness and fate acquisition. In the sections below, we will review our current knowledge on the main mechanisms of basal mitophagy, and explore the consequences of impaired mitophagy for cell proliferation, stemness and fate acquisition. Mitochondrial quality control as a requirement for cell differentiation, fate acquisition and stemness. As introduced above, the capacity of cells to activate and achieve the clearance of dysfunctional mitochondria is key to cell physiology, and organelle turnover heavily relies on mitochondrial dynamics and transport (100). Mitochondria are selectively cleared by mitophagy, an organelle-specific autophagy pathway (101, 102). In mitophagy, dysfunctional mitochondria are engulfed in a double-membrane vesicles known as autophagosomes and then degraded by lysosomes. Mitochondrial quality control begins before the entry into the cell cycle, as cells with defective mitochondria were shown to remain in G0 (103). Interestingly, an in vivo study in Drosophila showed that the disruption of mitochondrial complex I functions can compromise mitochondrial membrane potential, ATP synthesis, and it causes G1-S arrest (104). A recent report linked the PINK1/PARKIN mitophagy pathway and a successful cell cycle progression. Upon widespread mitochondrial dysfunction, induced by incubating cells with an oligomycin/antimycin cocktail, the PINK1/PARKIN pathway was shown to sequester the mitotic Tank Binding Kinase 1 (TBK1) to damaged mitochondria. Genetic ablation or pharmacological inhibition of TBK1 triggered cell cycle arrest at mitosis (105). These studies suggest that mitochondrial quality control is a prerequisite for cell cycle entry and progression. Whether these events are important also in physiological paradigms of mitophagy, and whether the mitochondrial transport machinery is involved in basal quality control events is currently a matter of intense investigation in the field. 8 8 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/prepr Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 as RB1CC1, the formation of BECN1-PtdIns3K complexes, and it ultimately inhibits mitophagy. Mitochondria not undergoing mitophagy display excessive mitochondrial ROS levels and overall oxidative stress, which was proposed to cause the destruction of erythrocytes by hemolysis. Although ATG7 and ULK1 were shown to play key roles in mitophagy during terminal erythropoiesis, their absence does not completely abolish mitochondrial turnover, and it suggests the existence of an alternative pathway that can be implicated in this process (112, 114, 115). In this optic, RAB9A, a member of the Rab GTPase family implicated in endosome trafficking (116), was shown to trigger mitophagy activation in erythroid leukemic cell lines and in vivo even when the canonical, ATG7-dependent autophagy pathway is blocked (115, 117) (Fig. 4). However, further studies are required to understand the spatiotemporal activation of these two pathways in physiological conditions. Mitochondrial elimination by mitophagy during the maturation of red blood cells is an important process, and its deficiency is associated with many diseases such as myelodysplastic syndromes anemia and sickle cell disease (118, 119). This is why investigating the mechanisms and actors implicated in the clearance of mitochondria from red blood cells is necessary to unravel how this process is compromised in patients, and may help developing new therapeutic strategies. Mechanisms of mitophagy in red blood cells The mitophagy-inducing function of ULK1 during erythroid maturation was shown to require AMPK activity, and more specifically the activity of the a1 isoform (PRKAA1) (113). The lack of PRKAA1 activity (by PRKAA1 inactivation or gene deletion in mice erythroid precursors) decreases ULK1 phosphorylation on Ser555, a key modification required for the nucleation of autophagic vesicles. The absence of this phosphorylation prevents the direct association of ULK1 with autophagy-related partners such 9 Basal mitophagy in Drosophila, C. elegans and mice: paternal mitophagy after fertilization Despite the fact that spermatozoan mitochondria are found in the oocyte upon fertilization, only maternal mitochondria are inherited in the majority of eukaryotic species (128). Several reports have shown that paternal mitochondria sperm-derived (PMS) are eliminated shortly after fertilization. In mice, PMS disappear from embryos during the 4-cell to 8-cell stage transition (129). In 2011, Sato and Sato demonstrated that the elimination of PMS in C. elegans requires autophagy, as PMS were maintained in zygotes with defective autophagy, and they were detectable even at the first larval stage (130). By following the expression of LGG-1 and LGG- 2, the C. elegans homologs of LC3, Rawi et al. showed that the entry of the spermatozoan organelles into the oocyte upon fertilization triggers an autophagy response (131). Under these conditions, structures positive for LGG-1 and LGG-2 were found to surround PMS. Similarly, several autophagosomal markers such as LC3, GABARAP, SQSTM1 and Lys63-positive ubiquitin chains were found in the vicinity of ubiquitinated PMS in the fertilized mouse oocyte and corroborating the role of autophagy for the clearance of paternal mitochondria (131). However, the molecular mechanisms of mitochondrial turnover seem to partially differ among species, as mammalian PMS are ubiquitinated while C. elegans sperm mitochondria are not (131, 132). The elimination of paternal mitochondria has been also shown to occur in Drosophila. Transgenic flies with fluorescently-tagged sperm mitochondria revealed that PMS disappear 90 minutes after egg laying (133). Eggs fertilized by DJ-GFP, a fluorescent sperm-specific mitochondrial protein, and maternally expressing the fluorescent autophagy reporter mCherry- Atg8, the Drosophila homolog of LC3, showed a localization of Atg8-positive vesicles in the vicinity of DJ-positive paternal mitochondria, which start to be degraded 30 minutes after egg laying. In contrast to C. elegans, ubiquitination seems to be required for paternal mitochondrial clearance in Drosophila. Directly after fertilization, PMS are ubiquitinated and SQSTM1, an autophagy receptor recognizing ubiquitylated proteins (134), is recruited to the PMS. While PARKIN does not appear to be involved in the paternal clearance of mitochondria in Drosophila, it seems to be required for the mammalian turnover of PMS (133, 135). Recently, Prohibitin 2 (PHB2) an inner mitochondrial membrane protein has been found to function as a key mitophagy receptor for PARKIN-mediated mitophagy in mammalian cells and to play a critical role in the elimination of paternal mitochondria in C. elegans (136). By following the fate of paternal mitochondria stained by MitoTracker Red in fertilized C. Mitophagy in Stem Cell Maintenance and Differentiation As described above, the correct maintenance of the blood system is critical to homeostasis. In addition to the mitophagy mechanisms regulating terminal erythropoiesis, HSCs continuously repress oxidative metabolism and eliminate active mitochondria via mitophagy to remain in a quiescent state (120). HSCs were shown to rely on anaerobic glycolysis for their energy needs, and this is a potential strategy used by the stem cell to prevent the accumulation of high levels of ROS that can lead to blood aging phenotypes (121, 122). It has been demonstrated that mitophagy in HSCs involves the autophagy factor ATG12 (120). The knockout of ATG12 in mice HSCs induces an increase in the total number of mitochondria, which were shown to adopt an elongated morphology. Under these conditions, HSCs also display an increased mitochondrial membrane potential compared to the controls, revealing an accumulation of active mitochondria which cannot undergo ATG12-mediated autophagic degradation. In a parallel study, Ito et al. have demonstrated that Tie2+ HSCs, a subpopulation of mouse HSCs, can maintain their stemness potential by upregulating a PINK1/PARKIN-dependent mitophagy program (123). Complementary data show that the absence of PINK1 in mouse embryonic fibroblasts (MEFs) lowers their capacity to be reprogrammed into induced pluripotent stem cells (iPSCs) and conversely, PINK1-deficient iPSCs tend to spontaneously differentiate and to lose their ability to maintain stemness proprieties (124). In addition, the overall reprogramming of MEFs into iPSCs was recently associated with a decrease in mitochondrial mass and an increase of BNIP3L/NIX-dependent mitophagy, and this independently of a ΔΨm loss (125). Mitophagy has also been shown to be implicated in the differentiation of mouse neuroblast stem cells into retinal ganglion cells (RGCs). This process has been found to involve NIX- 10 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprint Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 dependent mitophagy induced by hypoxia to eliminate mitochondria and shift their metabolism from mitochondrial respiration towards glycolysis (126). In muscle differentiation, mitophagy was also found to play a role in differentiating primitive myoblasts into mature myotubes (127). This was shown to require mitochondrial network remodeling and the induction of SQSTM1 (sequestosome1)-mediated mitophagy. Mitophagy in this model temporally occurs before the biogenesis of new mitochondria, and this transition parallels a metabolic shift: myoblasts were found to be mainly in a glycolytic state, while mature myotubes switch to oxidative phosphorylation. Basal mitophagy in Drosophila, C. elegans and mice: paternal mitophagy after fertilization Basal mitophagy in Drosophila, C. elegans and mice: paternal mitophagy after fertilization Conclusions and open questions. Our knowledge on how mitochondrial dynamics, transport and mitophagy are orchestrated in specific cell types and in physiological conditions is core to our understanding of how cell homeostasis is maintained. These functions are not only required to maintain proper mitochondrial functionality, but they also allow the correct partitioning of the mitochondrial pool to daughter cells during cell division. In addition, the molecular machineries involved in maintaining these mitochondrial functions were shown to directly participate to the acquisition of cell fate and stemness, and to regulate the overall metabolic capacity of the cell. Failure in regulating these functions by altering the abundance of the molecular players involved has been linked to pathological conditions, such as neurodegenerative disorders or cancer. Although the importance of mitochondrial dynamics, transport or clearance is increasingly clear, our knowledge of how these functions are mutually connected at the physiological level remains partial. Recent data shed light on paradigms and molecular actors of basal, piecemeal mitophagy in mammalian cells, which appears to be turned on when cells rely on oxidative phosphorylation for ATP production (138, 139). So far, the major players appear to be ATG8 proteins, SQSTM1 and the import protein SAMM50, while no involvement of PINK1 or of DNM1L has been found (138, 139). Therefore, piecemeal mitophagy seems to be different from the physiological clearance of paternal mitochondria, which utilizes the PINK1/PARKIN pathway and mitochondrial dynamics actors instead (135). However, differences in the abundance of proteins regulating mitochondrial dynamics can be observed in SAMM50- induced piecemeal mitophagy (139). Whether this is directly linked to a mitochondrial transport impairment or a chronic protein import deficiency still remains to be ruled out. Together, it appears that several paradigms of physiological mitophagy exist, each of them being activated in specific cell types or metabolic conditions, and each of them showing a unique set of molecular actors only partially shared with the other ones. Whether these paradigms all rely on an efficient transport machinery still remains to be determined. In conclusion, the link between physiological paradigms of mitophagy and their relationship to organelle transport still remains to be fully elucidated, together with the importance that these processes have for mitochondrial segregation at cell division in both symmetrically- and asymmetrically-dividing cells. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 oocytes, it has been shown, that the knockdown of PHB2 in spermatozoids impaired paternal mitochondrial clearance. In this study, it was shown that PHB2 has an LC3-interacting motif allowing it to bind to LC3 during mitophagy. However, PHB2 is an inner mitochondrial membrane protein and its interaction with LC3 requires its exposure to the cytosol. Indeed, it was demonstrated that a proteasome-dependent OMM rupture is necessary for the interaction between PHB2 and active, lipidated LC3 (LC3-II) (136). These findings were further corroborated in vivo, as paternal mitochondria were shown to undergo depolarization and a ruptured OMM upon the entry of the PMS into the oocyte in C. elegans (137). Basal mitophagy in Drosophila, C. elegans and mice: paternal mitophagy after fertilization elegans 11 Conclusions and open questions. Last, future studies are needed to explore how the adaptation of cellular and mitochondrial metabolism can shape mitochondrial transport and basal mitophagy pathways, and the consequences that this metabolic adaptation has for cell proliferation or 12 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 doi:10.20944/preprints202106.0657.v1 quiescence, differentiation or stemness, and fate acquisition in physiological and pathological conditions. quiescence, differentiation or stemness, and fate acquisition in physiological and pathological conditions. 13 reprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Figures and figure legends Fig. 1. Changes in mitochondrial dynamics during cell cycle. The levels of Cyclin E increase during S phase, and this inhibits DNM1L-mediated mitochondrial fission in favor of fusion. The resulting hyper-fused mitochondria have high ATP synthesis capabilities, that sustain cycle progression. At mitosis, Cyclin B/CDK1 activate DNM1L by phosphorylating it on Ser585 and Ser616 residue. These modifications cause mitochondrial fission, which is mandatory for cells to progress throughout mitosis. Figure assembled using templates freely available on https://bioicons.com/ and on https://smart.servier.com/) Fig. 1. Changes in mitochondrial dynamics during cell cycle. The levels of Cyclin E increase during S phase, and this inhibits DNM1L-mediated mitochondrial fission in favor of fusion. The resulting hyper-fused mitochondria have high ATP synthesis capabilities, that sustain cycle progression. At mitosis, Cyclin B/CDK1 activate DNM1L by phosphorylating it on Ser585 and Ser616 residue. These modifications cause mitochondrial fission, which is mandatory for cells to progress throughout mitosis. Figure assembled using templates freely available on https://bioicons.com/ and on https://smart.servier.com/) 14 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints2021 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Fig. 2. The release of motor proteins from mitochondria during mitosis is essential for successful cell cycle progression (A) CDK1 causes the phosphorylation of dynein, which causes release of mitochondria from this motor. (B) Inhibiting the release of mitochondria from dynein, or the forced attachment of dynein to mitochondria causes cell cycle arrest at mitosis. (C) Aurora A/AURKA causes phosphorylation of kinesins, which causes the release of mitochondria from the motor protein. (D) Inhibiting the release of mitochondria from kinesins, or the forced attachment of kinesins to mitochondria causes the asymmetric distribution of Fig. 2. The release of motor proteins from mitochondria during mitosis is essential for successful cell cycle progression (A) CDK1 causes the phosphorylation of dynein, which causes release of mitochondria from this motor. Conclusions and open questions. (B) Inhibiting the release of mitochondria from dynein, or the forced attachment of dynein to mitochondria causes cell cycle arrest at mitosis. (C) Aurora A/AURKA causes phosphorylation of kinesins, which causes the release of mitochondria from the motor protein. (D) Inhibiting the release of mitochondria from kinesins, or the forced attachment of kinesins to mitochondria causes the asymmetric distribution of 15 mitochondria at mitosis. Figure assembled using templates freely available on https://bioicons.com/ and on https://smart.servier.com/) Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 doi:10.20944/preprints202106.0657.v1 mitochondria at mitosis. Figure assembled using templates freely available on https://bioicons.com/ and on https://smart.servier.com/) mitochondria at mitosis. Figure assembled using templates freely available on https://bioicons.com/ and on https://smart.servier.com/) mitochondria at mitosis. Figure assembled using templates freely available on https://bioicons.com/ and on https://smart.servier.com/) 16 16 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Fig. 3. Mitochondrial transport in neurons. (A) Mitochondrial transport is carried by dynein and kinesins. Due to the difference in polarity of microtubules in axon, mitochondrial anterograde movement is carried by kinesins, and retrograde movement by dynein. (B) Microtubule in dendrite have mixed polarity and unlike in axons, both anterograde and retrograde movements are facilitated by dynein. (C) Short-distance mitochondrial transport in the actin-rich dendritic spines is performed by myosins. Mitochondria previously traveling on Fig. 3. Mitochondrial transport in neurons. (A) Mitochondrial transport is carried by dynein and kinesins. Due to the difference in polarity of microtubules in axon, mitochondrial anterograde movement is carried by kinesins, and retrograde movement by dynein. (B) Microtubule in dendrite have mixed polarity and unlike in axons, both anterograde and retrograde movements are facilitated by dynein. (C) Short-distance mitochondrial transport in the actin-rich dendritic spines is performed by myosins. Mitochondria previously traveling on 17 doi:10.20944/preprints202106.0657.v1 microtubule tracks can be transferred to myosin motors, which facilitate their anchoring on actin tracks. Figure assembled using templates freely available on https://bioicons.com/ and on https://smart.servier.com/) microtubule tracks can be transferred to myosin motors, which facilitate their anchoring on actin tracks. Figure assembled using templates freely available on https://bioicons.com/ and on https://smart.servier.com/) 18 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Fig. 4. Mitochondrial elimination by mitophagy during the maturation of red blood cells. Conflicts of Interest The authors declare no conflict of interest. Funding This work was supported by the Centre National de la Recherche Scientifique (CNRS), the Ligue Contre le Cancer Comités d’Ille et Vilaine, et du Finistère, and the Association pour la Recherche Contre le Cancer (ARC) to G.B. R.K.S. was supported by a fellowship from the Brittany region, France (Région Bretagne). Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657.v1 Author Contributions Author Contributions R.K.S. and A.C. wrote the manuscript; G.B. conceptualized, wrote and reviewed the manuscript and provided funding. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 doi:10.20944/preprints202106.0657 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 June 2021 Conclusions and open questions. When red blood cell maturation is not perturbed, mitochondrial elimination by mitophagy occurs following two pathways: a NIX/BNI3PL-dependent mitophagy, and a RAB9A- dependent clearance. NIX/BNI3PL induces mitochondrial depolarization and recruitment of LC3 on autophagosomal membranes, followed by degradation of the cargo. RAB9A-dependent mitophagy was also shown to occur in parallel. In case of ATG7 deficiency, altered and depolarized mitochondria accumulate in erythrocytes, while ULK1 deficiency results in delayed mitochondrial clearance. Mitochondria not undergoing mitophagy display excessive mitochondrial ROS levels and overall oxidative stress, which was proposed to be the leading cause for the destruction of erythrocytes by hemolysis and anemia. Figure assembled using templates freely available on https://bioicons.com/ and on https://smart.servier.com/) ndrial elimination by mitophagy during the maturation of red blood cells. Fig. 4. Mitochondrial elimination by mitophagy during the maturation of red blood cells. When red blood cell maturation is not perturbed, mitochondrial elimination by mitophagy occurs following two pathways: a NIX/BNI3PL-dependent mitophagy, and a RAB9A- dependent clearance. NIX/BNI3PL induces mitochondrial depolarization and recruitment of LC3 on autophagosomal membranes, followed by degradation of the cargo. RAB9A-dependent mitophagy was also shown to occur in parallel. In case of ATG7 deficiency, altered and depolarized mitochondria accumulate in erythrocytes, while ULK1 deficiency results in delayed mitochondrial clearance. Mitochondria not undergoing mitophagy display excessive mitochondrial ROS levels and overall oxidative stress, which was proposed to be the leading cause for the destruction of erythrocytes by hemolysis and anemia. Figure assembled using templates freely available on https://bioicons.com/ and on https://smart.servier.com/) 19 References 1. Osellame LD, Blacker TS, Duchen MR. Cellular and molecular mechanisms of mitochondrial function. 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An Analytical Comparison of the Opinions of Physicians Working in Emergency and Trauma Surgery Departments at Tabriz and Vienna Medical Universities Regarding Family Presence during Resuscitation
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OPEN ACCESS Citation: Soleimanpour H, Behringer W, Tabrizi JS, Sarahrudi K, Golzari SEJ, Hajdu S, et al. (2015) An Analytical Comparison of the Opinions of Physicians Working in Emergency and Trauma Surgery Departments at Tabriz and Vienna Medical Universities Regarding Family Presence during Resuscitation. PLoS ONE 10(4): e0123765. doi:10.1371/journal.pone.0123765 * soleimanpourh@tbzmed.ac.ir An Analytical Comparison of the Opinions of Physicians Working in Emergency and Trauma Surgery Departments at Tabriz and Vienna Medical Universities Regarding Family Presence during Resuscitation Hassan Soleimanpour1*, Wilhelm Behringer2, Jafar Sadegh Tabrizi1, Kambiz Sarahrudi3, Samad E J Golzari4, Stefan Hajdu3, Maryam Rasouli5, Mehdi Nikakhtar6, Robab Mehdizadeh Esfanjani7 Hassan Soleimanpour1*, Wilhelm Behringer2, Jafar Sadegh Tabrizi1, Kambiz Sarahrudi3, Samad E J Golzari4, Stefan Hajdu3, Maryam Rasouli5, Mehdi Nikakhtar6, Robab Mehdizadeh Esfanjani7 1 Tabriz Health Services Management Research Center, Tabriz University of Medical Sciences, Tabriz- 51664, I.R., Iran, 2 Department of Emergency Medicine, Medical University of Vienna, Vienna General Hospital, Waehringer Guertel 18–20, 1090 Vienna, Austria, 3 Department of Traumatology, Medical University of Vienna, Waehringer Guertel 18–20, A-1090 Vienna, Austria, 4 Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz-51664, I.R., Iran, 5 Students’ Research Committee, Tabriz University of Medical Sciences, Tabriz-51664, I.R., Iran, 6 Department of Emergency Medicine, Tabriz University of Medical Sciences, Tabriz-51664, I.R., Iran, 7 Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz-51664, I.R., Iran RESEARCH ARTICLE Abstract Most physicians at Vienna and Tabriz Medical universities were not open towards family members’ presence during resuscitation. Introduction Conventionally, throughout the resuscitation procedure, in case of in-hospital cardiac arrest, patients’ relatives are guided to a separate room in which an experienced nurse advises them of the patient’s status. Permitting patients’ relatives to witness the resuscitation has always been a controversial issue. In general, relatives are rarely asked to be present in the resuscitation room, unless they are eager to be [1–5]. Throughout the international meeting of the American College of Chest Physicians in 2000, experts from all over the world presented numerous perspectives on dealing with Family Pres- ence during Resuscitation (FPDR). At this conference, scholars emphasized that FPDR is an ethnic and cultural issue and that the results obtained from related research are country-specif- ic and not universally applicable [6]. Given the global challenge posed by FPDR in the field of cardiopulmonary resuscitation (CPR), we resolved to evaluate the opinions of physicians working in the emergency depart- ments of Austrian and Iranian medical universities regarding the presence of patients’ relatives during resuscitation. Our primary hypothesis was that the opinions of physicians working in the emergency and trauma surgery departments of Tabriz and Vienna medical universities (serving as models for developing and developed countries, respectively) and, therefore, within different cultures and societies, vary with regard to approval of FPDR relatives’ witnessing of patients’ resuscitation. Abstract The present study evaluated the opinions of physicians working in the emergency and trau- ma surgery departments of Vienna Medical University, in Austria, and Tabriz Medical Uni- versity, in Iran, regarding the presence of patients’ relatives during resuscitation. In a descriptive-analytical study, the data obtained from questionnaires that had been distribut- ed randomly to 40 specialists and residents at each of the participating universities were an- alyzed. The questionnaire consisted of two sections aimed at capturing the participants’ demographic data, the participants’ opinions regarding their support for the family’s pres- ence during resuscitation, and the multiple potential factors affecting the participants’ atti- tudes, including health beliefs, triggers that could facilitate the procedure, self-efficacy, intellectual norms, and perceived behavioral control. The questionnaire also included a di- rect question (Question 16) on whether the participants approved of family presence. Each question could be answered using a Likert-type scale. The results showed that the mean scores for Question 16 were 4.31 ± 0.64 and 3.57 ± 1.31 for participants at Vienna and Ta- briz universities, respectively. Moreover, physicians at Vienna University disapproved of the presence of patients’ families during resuscitation to a higher extent than did those at Tabriz University (P = 0.018). Of the studied prognostic factors affecting the perspectives of Vienna Medical University’s physicians, health beliefs (P = 0.000; B = 1.146), triggers (P = 0.000; B = 1.050), and norms (P = 0.000; B = 0.714) were found to be significant. Moreover, of the studied prognostic factors affecting the perspectives of Tabriz Medical University’s Academic Editor: Chang-Qing Gao, Central South University, CHINA Received: December 26, 2014 Accepted: February 20, 2015 Published: April 23, 2015 Copyright: © 2015 Soleimanpour et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Data are from the published FPDR study whose authors may be contacted at H_MOFID1357@YAHOO.COM. Competing Interests: The authors have declared that no competing interests exist. 1 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765 April 23, 2015 Family Presence during Resuscitation physicians, health beliefs (P = 0.000; B = 0.875), triggers (P = 0.000; B = 1.11), self-efficacy (P = 0.001; B = 0.5), and perceived behavioral control (P = 0.03; B = 0.713) were significant. PLOS ONE | DOI:10.1371/journal.pone.0123765 April 23, 2015 (1) (2) (3) (4) (5) Q6 Patients’ relatives have the right to be in the resuscitation room. (1) (2) (3) (4) (5) Q7 There are many people in our department who support FPDR. (1) (2) (3) (4) (5) Q8 My clinical practice is affected by the presence of a patient’s family. (5) (4) (3) (2) (1) Q9 My supervisor expects me to allow patients’ relatives to be present during resuscitation. (1) (2) (3) (4) (5) Q10 The resuscitation team’s stress levels will increase as a result of the presence of a patient’s family. (5) (4) (3) (2) (1) Q11 Ending the resuscitation process would be difficult in the presence of a patient’s family. (5) (4) (3) (2) (1) Q12 The patient’s relatives may believe that the resuscitation process was disorganized. (5) (4) (3) (2) (1) Q13 FPDR would increase the likelihood of litigation. (5) (4) (3) (2) (1) Q14 If absent, relatives would be angry at staff, due to the belief that they did not exhaust their efforts. (5) (4) (3) (2) (1) Q15 FPDR is a privacy breach, regardless of the patient’s prior consent. (5) (4) (3) (2) (1) Q16 I support the legalization of FPDR. (1) (2) (3) (4) (5) Q17 If I were a patient’s relative, I would like to be present during resuscitation. (1) (2) (3) (4) (5) Q18 If I were a patient undergoing resuscitation, I would like my relatives to be present during resuscitation. (1) (2) (3) (4) (5) doi:10.1371/journal.pone.0123765.t001 PLOS ONE | DOI:10.1371/journal.pone.0123765 April 23, 2015 3 doi:10.1371/journal.pone.0123765.t001 participants’ general opinions regarding their support for FPDR and multiple factors possibly affecting their attitudes (Table 1). g ( ) Valid behavioral theories and models that informed the questionnaire items included the Health Belief Model [7], Theory of Reasoned Action [8], programmed behavior [9], and the Theory of Self-Efficacy [10]. Since no solid theory or model has ever been used to predict be- havioral patterns, we combined several behavioral theories to design the questionnaire, which was based on questionnaires that had been validated in a previous study [11]. Questions 1, 2, 3, 4, 17, and 18 are related to health beliefs (i.e., if health experts believe that FDOR is useful to the patients’ health and/or the family’s psychological health). Questions 5, 6, and 7 evaluated the triggers that could facilitate FPDR initiation. Methods Using a descriptive-analytical approach, the data obtained from 40 questionnaires that had been distributed randomly among specialists and residents in emergency and trauma surgery departments of Imam Reza Hospital, Tabriz University of Medical Sciences, Iran and Vienna General Hospital, Vienna University of Medical Sciences, Austria were captured and analyzed. The questionnaire is shown in Table 1. Tabriz Imam Reza Hospital is a 300-bed tertiary general hospital and Vienna General Hospital is a 2500-bed tertiary hospital. Overall, 32 and 35 ques- tionnaires were returned and analyzed in Vienna General Hospital and Tabriz Imam Reza Hospital, respectively. The response rate was 80% (32/40) for Vienna General Hospital and 87.5% (35/40) for Tabriz Imam Reza Hospital. This study was approved by the Ethics Committee of Tabriz University of Medical Sciences and the Research Committee of the Vienna Emergency Medicine Department. Prior to the completion of the questionnaire, the participants received information on FPDR through a typed letter attached to the distributed questionnaires. Written informed consent was obtained by the first author of this manuscript (HS). FPDR was defined as the presence of a family member or relative in the CPR room environ- ment, providing them with the opportunity to witness the CPR procedure. The questionnaire consisted of the following two sections: Section 1, which was aimed at collecting the partici- pants’ demographic data, and Section 2, which consisted of 18 questions evaluating 2 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765 April 23, 2015 PLOS ONE | DOI:10.1371/journal.pone.0123765 April 23, 2015 Question 8 evaluated if clinical practice is af- fected by the presence of a patient’s family. Question 9 focuses on the intellectual norms of the participants (i.e., experiencing pressure from a superior to allow FPDR). Questions 10–15, which evaluate perceived behavioral control, reflect the participants’ conceptualization of ob- stacles and risks associated with their approval of FPDR. In Question 16, the participants were directly asked as to whether they approved of FPDR or not. Each of the 18 questions was rated on a Likert scale (1 = strongly support, 2 = support, 3 = indifferent, 4 = do not support, and 5 = do not support at all) [7]. To test for consistency in the participants’ responses, some of the questions were reverse-scored. Table 1 presents the real scores assigned to all the questions. The effect of each predictor (i.e., health beliefs, triggers, self-efficacy, and intellectual norms) on participants’ attitudes towards FPDR was presented as the mean of the Likert score for each corresponding question. Linear regression was used to determine the effect of the independent Valid behavioral theories and models that informed the questionnaire items included the Health Belief Model [7], Theory of Reasoned Action [8], programmed behavior [9], and the Theory of Self-Efficacy [10]. Since no solid theory or model has ever been used to predict be- havioral patterns, we combined several behavioral theories to design the questionnaire, which was based on questionnaires that had been validated in a previous study [11]. Questions 1, 2, 3, 4, 17, and 18 are related to health beliefs (i.e., if health experts believe that FDOR is useful to the patients’ health and/or the family’s psychological health). Questions 5, 6, and 7 evaluated the triggers that could facilitate FPDR initiation. Question 8 evaluated if clinical practice is af- fected by the presence of a patient’s family. Question 9 focuses on the intellectual norms of the participants (i.e., experiencing pressure from a superior to allow FPDR). Questions 10–15, which evaluate perceived behavioral control, reflect the participants’ conceptualization of ob- stacles and risks associated with their approval of FPDR. In Question 16, the participants were directly asked as to whether they approved of FPDR or not. Each of the 18 questions was rated on a Likert scale (1 = strongly support, 2 = support, 3 = indifferent, 4 = do not support, and 5 = do not support at all) [7]. Family Presence during Resuscitation Table 1. Likert scores (in parentheses) for answers to each questionnaire item. Table 1. Likert scores (in parentheses) for answers to each questionnaire item. Strongly agree Agree Indifferent Disagree Strongly disagree Q1 Patients’ relatives endure grief after experiencing FPDR. (1) (2) (3) (4) (5) Q2 Patients’ relatives will have a better understanding of the resuscitation process. (1) (2) (3) (4) (5) Q3 Patients’ relatives can talk to the dying patient. (1) (2) (3) (4) (5) Q4 Seeing the resuscitation process is a traumatic experience for family members. (5) (4) (3) (2) (1) Q5 The following question should be included in our departmental checklist: Does the patient’s family want to be present during CPR or not? (1) (2) (3) (4) (5) Q6 Patients’ relatives have the right to be in the resuscitation room. (1) (2) (3) (4) (5) Q7 There are many people in our department who support FPDR. (1) (2) (3) (4) (5) Q8 My clinical practice is affected by the presence of a patient’s family. (5) (4) (3) (2) (1) Q9 My supervisor expects me to allow patients’ relatives to be present during resuscitation. (1) (2) (3) (4) (5) Q10 The resuscitation team’s stress levels will increase as a result of the presence of a patient’s family. (5) (4) (3) (2) (1) Q11 Ending the resuscitation process would be difficult in the presence of a patient’s family. (5) (4) (3) (2) (1) Q12 The patient’s relatives may believe that the resuscitation process was disorganized. (5) (4) (3) (2) (1) Q13 FPDR would increase the likelihood of litigation. (5) (4) (3) (2) (1) Q14 If absent, relatives would be angry at staff, due to the belief that they did not exhaust their efforts. (5) (4) (3) (2) (1) Q15 FPDR is a privacy breach, regardless of the patient’s prior consent. (5) (4) (3) (2) (1) Q16 I support the legalization of FPDR. (1) (2) (3) (4) (5) Q17 If I were a patient’s relative, I would like to be present during resuscitation. (1) (2) (3) (4) (5) Q18 If I were a patient undergoing resuscitation, I would like my relatives to be present during resuscitation. (1) (2) (3) (4) (5) doi:10 1371/journal pone 0123765 t001 participants’ general opinions regarding their support for FPDR and multiple factors possibly affecting their attitudes (Table 1). Valid behavioral theories and models that informed the questionnaire items included the Health Belief Model [7], Theory of Reasoned Action [8], programmed behavior [9], and the Theory of Self-Efficacy [10]. Since no solid theory or model has ever been used to predict be- havioral patterns, we combined several behavioral theories to design the questionnaire, which was based on questionnaires that had been validated in a previous study [11]. Questions 1, 2, 4, 17, and 18 are related to health beliefs (i.e., if health experts believe that FDOR is useful to the patients’ health and/or the family’s psychological health). Questions 5, 6, and 7 evaluated the triggers that could facilitate FPDR initiation. Question 8 evaluated if clinical practice is af fected by the presence of a patient’s family. Question 9 focuses on the intellectual norms of th participants (i.e., experiencing pressure from a superior to allow FPDR). Questions 10–15, which evaluate perceived behavioral control, reflect the participants’ conceptualization of ob- stacles and risks associated with their approval of FPDR. In Question 16, the participants wer directly asked as to whether they approved of FPDR or not. Each of the 18 questions was rate on a Likert scale (1 = strongly support, 2 = support, 3 = indifferent, 4 = do not support, and 5 = do not support at all) [7]. To test for consistency in the participants’ responses, some of th questions were reverse-scored. Table 1 presents the real scores assigned to all the questions. The effect of each predictor (i.e., health beliefs, triggers, self-efficacy, and intellectual norms) on participants’ attitudes towards FPDR was presented as the mean of the Likert score for eac corresponding question. Linear regression was used to determine the effect of the independen Table 1. Likert scores (in parentheses) for answers to each questionnaire item. Strongly agree Agree Indifferent Disagree Strongly disagree Q1 Patients’ relatives endure grief after experiencing FPDR. (1) (2) (3) (4) (5) Q2 Patients’ relatives will have a better understanding of the resuscitation process. (1) (2) (3) (4) (5) Q3 Patients’ relatives can talk to the dying patient. (1) (2) (3) (4) (5) Q4 Seeing the resuscitation process is a traumatic experience for family members. (5) (4) (3) (2) (1) Q5 The following question should be included in our departmental checklist: Does the patient’s family want to be present during CPR or not? Results Of the 32 respondents at Vienna Medical University, 7 (21.9%) were emergency medicine spe- cialists, 21 (65.6%) were trauma surgeons, and 4 (12.5%) were emergency medical residents. Of the 35 respondents at Tabriz Medical University, 10 (28.6%) were emergency medicine special- ists and 25 (71.4%) were residents (Table 2). The responses to each of the 18 questions are presented in Table 3. No significant relationship was observed between Iranian and Austrian physicians’ (repre- sented by Tabriz and Vienna Medical universities, respectively) age and FPDR (P = 0.5 and P = 0.9, respectively). The mean Likert score obtained for Question 16 was 4.31 ± 0.64 and 3.57 ± 1.31 for the participants at Vienna and Tabriz Medical universities, respectively. Vienna physicians disapproved of FPDR more so than did Tabriz physicians; this result was significant (P = 0.018). Of the studied prognostic factors affecting the views of the Vienna physicians re- garding FPDR, health beliefs (P = 0.000; B = 1.146), triggers (P = 0.000; B = 1.050), and intellec- tual norms (P = 0.000; B = 0.714) were found to be significant. This means that these three factors significantly influenced Vienna physicians’ aversion towards FPDR. In contrast, of the studied prognostic factors affecting the views of the Tabriz physicians regarding FPDR, health beliefs (P = 0.000; B = 0.875), triggers (P = 0.000; B = 1.11), self-efficacy (P = 0.001; B = 0.5), and perceived behavioral control (P = 0.03; B = 0.713) proved significant. This means that these three factors significantly influenced Tabriz physicians’ aversion towards FPDR. The mean Likert scores obtained for each prognostic factor by the participants from the two groups are presented in Table 3. A comparison of the two groups revealed a statistically significant dif- ference for triggers (P = 0.0001), self-efficacy (P = 0.003), intellectual norms (P = 0.0001), and perceived behavioral control (P = 0.001). mean Likert scores obtained for each prognostic factor by the participants from the two groups are presented in Table 3. A comparison of the two groups revealed a statistically significant dif- ference for triggers (P = 0.0001), self-efficacy (P = 0.003), intellectual norms (P = 0.0001), and perceived behavioral control (P = 0.001). Family Presence during Resuscitation variables (i.e., health beliefs, triggers, self-efficacy, and intellectual norms) on the dependent variable (approval of FPDR). The Mann-Whitney U-test was used to compare the attitudes of participants from Tabriz Medical University and Vienna Medical University. A P-value of less than 0.05 was considered statistically significant. To test for consistency in the participants’ responses, some of the questions were reverse-scored. Table 1 presents the real scores assigned to all the questions. The effect of each predictor (i.e., health beliefs, triggers, self-efficacy, and intellectual norms) on participants’ attitudes towards FPDR was presented as the mean of the Likert score for each corresponding question. Linear regression was used to determine the effect of the independent 3 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765 April 23, 2015 Family Presence during Resuscitation Table 3. Number (%) of participants subscribing to each response category and means obtained for each question. City Strongly agree Agree Indifferent Disagree Strongly disagree Likert score P-value Health beliefs Tabriz 3.45 ± 1.10 0.374 Vienna 3.81 ± 0.44 Q1 Patients’ relatives endure the grief process after experiencing FPDR. Tabriz 2 (5.7) 1 (2.9) 6 (17.1) 16 (45.7) 10 (28.6) 3.88 ± 1.65 0.056 Vienna 0 (0) 1 (3.1) 0 (0) 18 (56.3) 13 (40.6) 4.34 ± 0.65 Q2 Patients’ relatives will have a better understanding of the resuscitation process. Tabriz 3 (8.6) 16 (17.1) 5 (14.3) 11 (31.4) 10 (28.6) 3.54 ± 1.31 0.153 Vienna 0 (0) 1 (3.1) 0 (0) 26 (81.3) 5 (15.6) 4.09 ± 0.53 Q3 Patients’ relatives can touch or talk to the dying patient. Tabriz 3 (8.6) 6 (17.1) 7 (20) 7 (20) 12 (34.3) 3.54 ± 1.35 0.022 Vienna 0 (0) 0 (0) 2 (6.3) 17 (53.1) 13 (40.6) 4.34 ± 0.60 Q4 Seeing the resuscitation process is a traumatic experience for family members. Tabriz 3 (8.6) 13 (37.1) 6 (17.1) 7 (20) 6 (17.1) 3 ± 1.28 0.001 Vienna 0 (0) 1 (3.1) 1 (3.1) 30 (93.8) 0 (0) 2.09 ± 0.39 Q17 If I were a patient’s relative, I would like to be present during resuscitation. Tabriz 5 (14.3) 7 (20) 1 (2.9) 7 (20) 15 (42.9) 3.57 ± 1.55 0.547 Vienna 1 (3.1) 1 (3.1) 0 (0) 21 (65.6) 9 (28.1) 4.12 ± 0.83 Q18 If I were a patient undergoing resuscitation, I would like my relatives to be present during resuscitation. Tabriz 7 (20) 8 (22.9) 2 (5.7) 7 (20) 11 (31.4) 3.200 ± 1.58 0.084 Vienna 2 (6.3) 2 (6.3) 6 (18.8) 9 (28.1) 13 (40.6) 3.90 ± 1.20 Triggers Tabriz 3.22 ± 0.78 0.0001 Vienna 4.21 ± 0.53 Q5 The following question should be included in our departmental checklist: Does the patient’s family want to be present during CPR or not? Tabriz 3 (8.6) 1 (2.9) 8 (22.9) 13 (37.1) 10 (28.6) 3.74 ± 1.17 0.017 Vienna 1 (3.1) 0 (0) 0 (0) 17 (53.1) 14 (43.8) 4.34 ± 0.78 Q6 Patients’ relatives have the right to be present in the resuscitation room. Discussion The results obtained from our study showed that most physicians at Vienna and Tabriz Medical universities disapprove of/strongly disapprove of FPDR; however, the proportion is much lower among physicians at Vienna Medical University (60% for Tabriz Medical University and 96.9% for Vienna Medical University; Table 3). Despite the fact that physicians at Tabriz Medical Uni- versity had a generally more positive attitude toward FPDR than did Vienna Medical Univer- sity’s physicians, most still did not approve of FPDR. Health beliefs and intellectual norms were identified as the most important factors influencing disagreement regarding FPDR, followed by self-efficacy and perceived behavioral control among physicians at Tabriz Medical University. Table 2. Participants’ demographic characteristics according to affiliation. Vienna Tabriz P-value Sex Male 25 (78.1%) 21 (60%) 0.11 Female 7 (21.9%) 14 (40%) Experience Percentile 25 3 2 0.005 Percentile 50 5 3 Percentile 75 14 6 Age 35.67 ± 7.76 33.88 ± 6.72 0.32 doi:10.1371/journal.pone.0123765.t002 PLOS ONE | DOI:10.1371/journal.pone.0123765 April 23, 2015 4 / 8 Table 2. Participants’ demographic characteristics according to affiliation. 4 / 8 Tabriz 2 (5.7) 7 (20) 4 (11.4) 12 (34.3) 10 (28.6) 3.600 ± 1.26 0.079 Vienna 0 (0) 0 (0) 1 (3.1) 23 (71.9) 8 (25) 4.21 ± 0.49 Q7 There are many people in our department who support FPDR. Tabriz 7 (20) 16 (45.9) 6 (17.1) 5 (14.3) 1 (2.9) 2.34 ± 1.05 0.0001 Vienna 0 (0) 1 (3.1) 1 (3.1) 24 (75) 6 (18.8) 4.09 ± 0.58 Self efficacy Tabriz 2.88 ± 1.36 0.003 Vienna 1.93 ± 0.50 Q8 My clinical practice is affected by the presence of a patient’s family. Tabriz 4 (11.4) 10 (28.6) 7 (20) 6 (17.1) 8 (22.9) 2.88 ± 1.36 0.003 Vienna 0 (0) 1 (3.1) 0 (0) 17 (53.1) 14 (43.8) 1.93 ± 0.50 Norms Tabriz 3.37 ± 0.91 0.0001 Vienna 4.40 ± 0.55 Q9 My supervisor expects me to allow patients’ relatives to be present during resuscitation. Tabriz 1 (2.9) 5 (14.3) 11 (31.4) 16 (45.7) 2 (5.7) 3.37 ± 0.9 0.0001 Vienna 0 (0) 0 (0) 1 (3.1) 17 (53.1) 14 (43.8) 4.40 ± 0.55 Perceived behavioral control Tabriz 2.91 ± 0.88 0.001 Vienna 2.34 ± 0.31 Q10 The emotional stress of the resuscitation team will increase as a result of the presence of a patient’s family. Tabriz 5 (14.3) 7 (20) 4 (11.4) 11 (31.4) 8 (22.9) 2.71 ± 1.40 0.081 Vienna 0 (0) 0 (0) 1 (3.1) 31 (96.9) 0 (0) 2.03 ± 0.17 Q11 Ending the resuscitation process would be difficult in the presence of a patient’s family. Tabriz 3 (8.6) 6 (17.1) 2 (5.7) 15 (42.9) 9 (25.7) 2.40 ± 1.28 0.649 Vienna 0 (0) 2 (6.3) 0 (0) 28 (87) 2 (6.3) 2.06 ± 0.56 (Continued) articipants subscribing to each response category and means obtained for each question. 5 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765 April 23, 2015 Family Presence during Resuscitation Table 3. (Continued) Table 3. (Continued) City Strongly agree Agree Indifferent Disagree Strongly disagree Likert score P-value Q12 The patient’s relatives may believe that the resuscitation process was disorganized. Tabriz 1 (2.9) 9 (25.7) 5 (14.3) 14 (40) 6 (17.1) 2.57 ± 1.14 0.01 Vienna 5 (15.6) 26 (81.3) 0 (0) 1 (3.1) 0 (0) 1.90 ± 0.53 Q13 FPDR would increase the likelihood of litigation. Tabriz 3 (8.6) 13 (37.1) 8 (22.9) 4 (11.4) 7 (20) 3.02 ± 1.29 0.001 Vienna 0 (0) 0 (0) 1 (3,1) 27 (84.4) 4 (12.5) 1.90 ± 0.39 Q14 If absent, relatives would be angry at staff, due to the belief that they did not exhaust their efforts. Tabriz 9 (25.7) 14 (40) 7 (20) 4 (11.4) 37 (13.4) 3.74 ± 1.06 0.0001 Vienna 13 (40.6) 13 (40.6) 3 (9.4) 3 (9.4) 0 (0) 4.12 ± 0.94 Q15 FPDR is a privacy breach, regardless of the patient’s prior consent. Tabriz 3 (8.6) 13 (37.1) 8 (22.9) 5 (14.3) 6 (17.1) 3.05 ± 1.25 0.0001 Vienna 0 (0) 0 (0) 1 (3.1) 29 (90.6) 1 (1.3) 2.00 ± 0.25 Support for FPDR Tabriz 3.57 ± 1.31 0.018 Vienna 4.31 ± 0.64 Q16 I support the legalization of FPDR. Tabriz 4 (11.4) 3 (8.6) 7 (20) 11 (31.4) 10 (28.6) 3.57 ± 1.31 0.018 Vienna 0 (0) 1 (3.1) 0 (0) 19 (59.4) 12 (37.5) 4.31 ± 0.64 Vienna 2 (6.3) 2 (6.3) 6 (18.8) 9 (28.1) 13 (40.6) 3.90 ± 1.20 doi:10 1371/journal pone 0123765 t003 doi:10.1371/journal.pone.0123765.t003 In other words, the most important factor determining their negative attitudes toward FPDR was their skepticism regarding the efficacy of FPDR, as well as their colleagues’ disagreement re- garding FPDR. No significant difference was found between the physicians at the two universi- ties regarding health beliefs; however, triggers, norms, self-efficacy, and perceived behavioral control were found to be more predictive of Vienna Medical University physicians’ negative at- titudes toward FPDR than Tabriz Medical University’s physicians attitudes. A previous study by Jabre et al. suggested that FPDR does not affect a medical team’s level of emotional stress and does not result in medico-legal claims [12]. Similar to many previous studies, the results ob- tained from our study revealed that FPDR is associated with increased fear of litigation, particu- larly among Tabriz Medical University’s physicians. This could explain these physicians’ aversion to FPDR [13]. PLOS ONE | DOI:10.1371/journal.pone.0123765 April 23, 2015 Conclusion In contrast to our hypothesis, emergency medicine and trauma surgery physicians in both Vi- enna and Tabriz medical universities disapproved of FPDR; however, this disapproval was more significant among Vienna than Tabriz physicians. FPDR should be assessed in every country, in consideration of country-specific traditions, culture, and religion. Therefore, knowledge of the different factors contributing towards physicians’ disapproval of FPDR in Iran and Austria would facilitate the removal of the obstacles hindering the execution of FPDR in those countries and enable health policymakers to implement related, required measures. Family Presence during Resuscitation similar results to ours, most physicians and nurses did not approve of FPDR in the cases of both pediatric and adult patients, believing that it would be of no benefit to the family during the grieving process [16, 17]. Although it is widely accepted that FPDR has a positive impact on the relatives witnessing CPR, in our study, the physicians in both countries tended not to accept this fact. Physicians at Tabriz Medical University seemed less reluctant to accept FPDR than those at Vienna Medical University. Based on the results obtained (Table 3), contributing factors for Austrian physi- cians were as follows: (1) significant disbelief in the argument, that relatives witnessing CPR would benefit from either talking to or touching the patient; (2) the assumption that the head of the department would disapprove of FPDR; and (3) the fear that most relatives would think of CPR as a disorganized procedure. Interestingly, the deterring factors were found to be differ- ent for Iranian physicians; these included fear of legislation, invasion of the patient’s privacy, reduced performance by the CPR team, traumatization of the witnessing relatives, and the as- sumption that the relatives would not doubt or question if the physicians did all they could. Limitations of the study: The number of the attending professors was more than the resi- dents in Vienna Medical University and also the number of the residents was more than the at- tending professors in Tabriz Medical University; this might have affected the significant differences observed between both studied groups. Our study was conducted in only two cen- ters and it was of a relatively small sample size. Hence, the conclusion derived from this study might be ungeneralizable to all populations. S2 Dataset. Demographic characteristics data for each participant according to affiliation. (SAV) S1 Questionnaire. Blank copy of the questionnaire. (DOC) S1 Questionnaire. Blank copy of the questionnaire. (DOC) Supporting Information S1 Dataset. Data for each participant according to answers to each questionnaire item and subscribing to each response category and means obtained for each question. (SAV) S2 Dataset. Demographic characteristics data for each participant according to affiliation. (SAV) S2 Dataset. Demographic characteristics data for each participant according to affiliation. (SAV) However, considering the results of Jabre et al.’s study, physicians should cast aside their fear of medico-legal claims when performing family-witnessed CPR in their daily practice. Furthermore, in Jabre et al.’s study, FPDR was had apparent positive impli- cations for the psychological aspects of the family members [12]. Most studies tend to focus on the experience of FPDR, with very few having focused on medical staff’s views in this regard. Most have stated that clear and precise policies are required regarding FPDR, so that sufficient psychological support can be provided to family members who choose to be present during CPR [14]. In a study by Duran et al., it was suggested that medical staff are mostly in favor of FPDR, which is in contrast with the results of our study [15]. This could have been due to the fact that, in addition to attending specialists, Duran et al.’s study involved other healthcare providers, such as nurses and non-attending specialists, who held more positive attitudes regarding FPDR. In our study, however, only the attitudes of the attending specialists and residents involved in FPDR were evaluated. According to the guidelines of the American Heart Association (AHA), medical staff should seriously consider the implementation of FPDR [14]. This is in sharp contrast with our study’s findings, in which the medical staff in both sub-groups did not seem open towards FPDR. In another study with 6 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765 April 23, 2015 References 1. Boehm J. Family presence during resuscitation. 2008; 3(5). Available: http://www.zoll.com/ CodeCommunicationsNewsletter/CCNL05_08/CodeCommunications05_08.pdf. 2. Meyers TA, Eichhorn DJ, Guzzetta CE. Do families want to be present during CPR? A retrospective survey. J Emerg Nurs. 1998; 24(5): 400–405. PMID: 9814254 3. Boyd R. Witnessed resuscitation by relatives. Resuscitation. 2000; 43(3): 171–176. PMID: 10711485 4. Offord RJ. Should relatives of patients with cardiac arrest be invited to be present during cardiopulmo- nary resuscitation? Intensive Crit Care Nurs. 1998; 14(6): 288–293. PMID: 10196912 5. Shaner K, Eckle N. Implementing a program to support the option of family presence during resuscita- tion. ACCH Advocate. 1997; 3(1): 3–7. 6. American Heart Association. American Heart Association guidelines for cardiopulmonary resuscitation and emergency cardiovascular care. Circulation. 2005; 112(Supp): IV-1–IV-211. 7. Rosenstock I. The health belief model: explaining health behavior through expectancies. In: Glanz K, Lewis FM, Rimer BK, editors. Health behavior and health education: theory research and practice. San Francisco: Jossey-Bass; 1990. pp. 39–61. 8. Fishbein M, Middlestadt S. Using the theory of reasoned action to develop educational intervention: ap- plications to illicit drug use. Health Educ Res. 1987; 2(4): 361–371. 9. Schifter DE, Ajzen I. Intention, perceived control, and weight loss: an application of the theory of planned behavior. J Pers Soc Psychol. 1985; 49(3): 843–851. PMID: 4045706 10. Schwarzer R. Self-efficacy in the adoption and maintenance of health behaviors: theoretical ap- proaches and a new model. In: Schwarzer R. editor. Self-efficacy: thought control of action. Washing- ton (DC): Hemisphere Publishing; 1992. pp. 217–243. 11. Lam DSY, Wong SN, Hui H, Lee W, So KT. Attitudes of doctors and nurses to family presence during paediatric cardiopulmonary resuscitation. HK J Paediatr (new series). 2007; 12: 253–259. 12. Jabre P, Belpomme V, Azoulay E, Jacob L, Bertrand L, Lapostolle F, et al. Family presence during car- diopulmonary resuscitation. N Engl J Med. 2013; 368(11): 1008–1018. doi: 10.1056/NEJMoa1203366 PMID: 23484827 13. Baird G, Sammy I, Nunes P, Paul J. Attitudes and practices regarding resuscitation in emergency de- partments in Trinidad and Tobago. Emerg Med J. 2014 Nov; 31(11):889–93. doi: 10.1136/emermed- 2012-201472 PMID: 23851033 14. The American Heart Association in collaboration with the International Liaison Committee on Resusci- tation. Guidelines 2000 for cardiopulmonary resuscitation and emergency cardiovascular care. Part 10: pediatric advanced life support. Circulation. 2000; 102(8 Suppl): I291–1342. PMID: 10966679 15. Duran CR, Oman KS, Abel JJ, Koziel VM, Szymanski D. Family Presence during Resuscitation forming part of Maryam Rasouli’s specialty thesis, entitled “An analytical comparison between the opinions of physicians working in Emergency Departments in Tabriz-Iran and Vienna- Austria regarding the Family Presence during Resuscitation." It is registered at Tabriz Universi- ty of Medical Sciences (No: 91.3–6.12) and was presented in June 2014. Author Contributions Conceived and designed the experiments: HS WB. Performed the experiments: JST KS SH. An- alyzed the data: RME ER. Contributed reagents/materials/analysis tools: MR MN. Wrote the paper: HS WB SG. Critical revisions of the manuscript: WB. PLOS ONE | DOI:10.1371/journal.pone.0123765 April 23, 2015 Acknowledgments The authors would like to express their gratitude towards participating physicians from Tabriz Medical University and Vienna Medical University. We would also like to thank Dr. Minou Gharehbaglou, at the Faculty of Architecture and urbanism, Tabriz Islamic Art University, Ta- briz, Iran, and Dr. Aida Maleki Gavgani, at the Department of Building Physics and Building Ecology, Vienna University of Technology, Karlsplatz 13, 1040 Vienna, Austria, for their assis- tance with the preparation of the electronic questionnaire. This article is based on a dataset 7 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765 April 23, 2015 References Attitudes toward and beliefs about family pres- ence: a survey of healthcare providers, patients’ families, and patients. Am J Crit Care. 2007; 16(3): 270–279. PMID: 17460319 16. Twibell RS, Siela D, Riwitis C, Wheatley J, Riegle T, Bousman D, et al. Nurses’ perceptions of their self- confidence and the benefits and risks of family presence during resuscitation. Am J Crit Care. 2008; 17 (2): 101–111. PMID: 18310646 17. Soleimanpour H, Tabrizi JS, Farnam A, Nikakhtar M, Mokhtarpour M, Golzari SE, et al. Attitudes of emergency medicine physicians towards family presence during resuscitation. Resuscitation. 2013; 84 (12): e149–150. doi: 10.1016/j.resuscitation.2013.07.031 PMID: 23973750 8 / 8 PLOS ONE | DOI:10.1371/journal.pone.0123765 April 23, 2015
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Characteristics and outcomes of patients with dyspnoea as the main symptom, assessed by prehospital emergency nurses- a retrospective observational study
BMC emergency medicine
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Kauppi et al. BMC Emergency Medicine (2020) 20:67 https://doi.org/10.1186/s12873-020-00363-6 Kauppi et al. BMC Emergency Medicine (2020) 20:67 https://doi.org/10.1186/s12873-020-00363-6 Open Access Characteristics and outcomes of patients with dyspnoea as the main symptom, assessed by prehospital emergency nurses- a retrospective observational study Wivica Kauppi1,2* , Johan Herlitz1,2, Carl Magnusson1,3, Lina Palmér2 and Christer Axelsson1,2 Abstract Background: Dyspnoea (breathing difficulty) is among the most commonly cited reasons for contacting emergency medical services (EMSs). Dyspnoea is caused by several serious underlying medical conditions and, based on patients individual needs and complex illnesses or injuries, ambulance staff are independently responsible for advanced care provision. Few large-scale prehospital studies have reviewed patients with dyspnoea. This study aimed to describe the characteristics and final outcomes of patients whose main symptom was classified as dyspnoea by the prehospital emergency nurse (PEN). Methods: This retrospective observational study included patients aged > 16 years whose main symptom was dyspnoea. All the enrolled patients were assessed in the south-western part of Sweden by PENs during January and December, 2017. Of 7260 assignments (9% of all primary missions), 6354 fulfilled the inclusion criteria. Analysis was performed using descriptive statistics, and the tests used were odds ratios and Kaplan-Meier analysis. Results: The patients mean age was 73 years, and approximately 56% were women. More than 400 different final diagnostic codes (International Statistical Classification of Diseases and Related Health Problems [ICD]-10th edition) were observed, and 11% of the ICD-10 codes denoted time-critical conditions. The three most commonly observed aetiologies were chronic obstructive pulmonary disease (20.4%), pulmonary infection (17.1%), and heart failure (15%). The comorbidity values were high, with 84.4% having previously experienced dyspnoea. The overall 30-day mortality was 11.1%. More than half called EMSs more than 50 h after symptom onset. Conclusions: Among patients assessed by PENs due to dyspnoea as the main symptom there were more than 400 different final diagnoses, of which 11% were regarded as time-critical. These patients had a severe comorbidity and 11% died within the first 30 days. Keywords: Dyspnoea, Epidemiology, Aetiology, Major incidents, Prevention, Emergency medical service, Prehospital emergency nurse, Ambulance * Correspondence: wivica.kauppi@hb.se Correspondence: wivica.kauppi@hb.se 1PreHospen- Centre for Prehospital Research, Faculty of Caring, Work Life and Social Welfare, University of Borås, SE- 501 90 Borås, Sweden 2Faculty of Caring Science, Work Life and Social Welfare, University of Borås, Borås, Sweden Full list of author information is available at the end of the article * Correspondence: wivica.kauppi@hb.se 1PreHospen- Centre for Prehospital Research, Faculty of Caring, Work Life and Social Welfare, University of Borås, SE- 501 90 Borås, Sweden 2Faculty of Caring Science, Work Life and Social Welfare, University of Borås, Borås, Sweden Full list of author information is available at the end of the article Competence of Swedish ambulances, and the associated guidelines and triage system Since 2005, all ambulances in Sweden have at least one registered nurse and one ambulance technician [13]. A majority of all such nurses have completed a three-year nursing course followed by a one-year Master’s course focusing on prehospital emergency care and have the professional title ‘PEN’. PENs provide assessment and treatment according to national and local guidelines. In Sweden, prehospital emergency nurses (PENs) have an important role in the assessment and triaging of dyspnoea patients at the scene. The treatment of dys- pnoea begins with the management of the underlying condition, due to which the diagnosis of acute dyspnoea is crucial in EMS settings to ensure the provision of ap- propriate treatment and care [7]. Patients with dyspnoea constitute a complex group, as the presence of additional health problems makes it difficult to identify the under- lying cause of the condition. In addition to the physio- logical perspective, severe anxiety and fear are observed commonly in connection with dyspnoea. This denotes that PENs have the responsibility of providing care aimed at increasing patients strength and focusing on their existential needs [8–10]. Previous studies have described the epidemiology and outcomes of patients with dyspnoea who are transported by EMSs to emergency departments (EDs) in Denmark, Australia/New Zealand and the United States [8, 11, 12]. However, few large-scale EMS studies have been conducted in such settings till date. In the present study, we aimed to describe the characteris- tics and final outcomes, overall and in relation to sex of patients receiving care from PENs and whose main symp- tom was dyspnoea. In order to assess and prioritise patients degree of pre- hospital care required, PENs perform triage classification according to the Rapid Emergency Triage and Treat- ment System for adults (RETTS- A) [14]. RETTS-A codes are divided into the following types: 1) vital signs (VS) and 2) 53 emergency signs and symptoms (ESS) codes [see Additional file 1: Red and orange VS and ESS code 04, dyspnoea]. Both types allow for the allocation of patients separately to a severity/triage level in which the highest level is used for the final assessment. The se- verity/triage level is assigned one of five different colours (red, orange, yellow, green, and blue) according to the time from assessment to the time a patient must be seen by a physician. Background inhabitants in urban, suburban, and rural areas. During 2017, the two EMS organisations had 123,614 ambulance missions with a priority level of 1 to 3. Of these, 87,611 missions involved an initial patient assessment defined as the primary mission (Fig. 1). Dyspnoea (breathing difficulty) is among the most com- monly cited reasons for contacting emergency medical services (EMSs) [1]. The American Thoracic Society defines dyspnoea as “a subjective experience of breathing discomfort that consists of qualitatively distinct sensa- tions that vary in intensity” [2]. It manifests itself in various ways such as shortness of breath, air hunger, and chest tightness [3]. Dyspnoea is caused by several medical conditions [4, 5], and respiratory failure is among the most severe time-critical conditions for which the provision of immediate prehospital care by EMSs can have a highly valuable impact [6]. © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Kauppi et al. BMC Emergency Medicine (2020) 20:67 Kauppi et al. BMC Emergency Medicine (2020) 20:67 Page 2 of 11 Competence of Swedish ambulances, and the associated guidelines and triage system Red and orange indicate the most urgent cases whereas yellow and green denote the absence of individual medical risk even if patients are made to wait to undergo physician assessment. The colour blue is not used in the prehospital triage. In ESS code 04 (dyspnoea as the main symptom), it is mandatory for the PENs to evaluate ECG in all patients. In addition of all prehospi- tal severe ill patients, it is also mandatory to evaluate the P-Glucose level. Inclusion and exclusion criteria The inclusion criteria were as follows: 1) a primary mission in which a patient (or e.g. a family member that represents the patient) calls the dispatch centre, an ambulance is dispatched and 2) the assignment of an ESS code of 04 (dyspnoea) is made by the PEN. The exclusion criteria were as follows: 1) lack of a personal identity number, 2) transportation to hospitals outside the research area, 3) age < 16 years, 4) duplicate EMS records, 5) missing record or lack of information, 6) incorrect triage (ESS), and 7) secondary transport use. A total of 7260 patients were initially identified from the sample (9% of all assignments). After a manual review, 908 patients were excluded due to various exclusion criteria, and a total of 6354 patients were finally included in the study (Fig. 1). Among the 6354 patients, a total of A quantitative, exploratory, descriptive design was employed based on a consecutive retrospective review of EMS and hospital records. The study included all patients over a one-year time-period who called the emergency number (112) in Sweden, had an ambulance dispatched and were assessed by the prehospital emergency nurses (PENs) with the main symptom of dyspnoea. Endpoints The primary endpoint was the aetiology according to the final diagnosis. Secondary endpoints were comorbidity according to patients previous history and the 30- day mortality. Tertiary endpoints were the patients delay time from symptom onset until calling for EMS and clinical findings on arrival of PENs. Time-critical conditions are defined as conditions where prompt management and medical interventions are crucial to avoid severe complications and early death [16, 17]. Population The study was conducted within two EMS organisations, which together include 16 ambulance stations in the south- western part of Sweden. The two EMS organisations cover a combined area of 7400 km2, with a population of 962,000 Page 3 of 11 Kauppi et al. BMC Emergency Medicine Kauppi et al. BMC Emergency Medicine (2020) 20:67 Fig. 1 Flow chart of the studied patients, assessed as the main symptom of dyspnoea the ICD-10 which comprises 22 chapters (I–XXII). In all the ambulances, only 12 lead ECG was used. In order to achieve the best possible data quality, data on ECG inter- pretations were collected first from prehospital records, second from ED notes, and third, in cases in which no interpretation was documented but an ECG was recorded, by the author (WK). ECG deviations comprise atrial fibrilla- tion/flutter, ST-elevation, ST-depression, T-wave inversion, and left bundle branch block. Other deviations include AV- block I, II, III, ectopic atrial rhythm/tachycardia, and ventricular tachycardia. P-glucose levels were measured through a capillary test performed by the PEN, and a value ≥9.5 mmol/l was defined as high [15]. 3665 patients had one EMS contact during the study period and 2689 patients had multiple contacts. A total of 4587 unique patients were included in the survival analysis of which 922 patients were randomly selected from the patients with multiple contacts. Statistics In the tables, results are presented as number (percent- age), median (25th, 75th percentiles), or mean (standard deviation). For two-group comparisons, crude odds ratios with their correspondent confidence intervals were calculated. A Kaplan-Meier survival curve stratified by sex was plotted (Fig. 2), while the lifelines survival func- tion was used to report differences by sex for 30-day mortality. All tests are two-sided, and due to the number of tests performed, p-values < 0.01 were considered significant. Confidence intervals computed at the 99% level were used. Data processing and statistical analyses were performed using SPSS version 24 (Armonk, NY, USA: IBM Corp.) and Python version 3.7 (Python software foundation) with lifelines package (Cameron Davidson-Pilon, Jonas Kalderstam, Paul Zivich, et al. CamDavidsonPilon/lifelines: v0.23.9. 2020). Results Totally, 7262 EMS missions fulfilled the inclusion cri- teria, and 908 cases (13%) were excluded due to reasons shown in Fig. 1. Overall, patients with the ESS code 04 (dyspnoea as the main symptom) conformed 9% of all primary EMS missions and more than 60% of those patients were hospitalised (Fig. 1). Symptoms and clinical findings In all, 23.1% of the patients had pain, 1.2% had syncope, and 1.6% showed alcohol/drug-related issues. Abnormal vital parameters were seen with the following rates (according to the RETTS-A): respiratory rate < 8/min or > 25/min (48.7%), oxygen saturation < 90% (35.2%), heart rate < 40/min or > 120/min (11.5%), systolic blood pres- sure < 90 mmHg (1.8%), body temperature < 35 or > 41 de- grees (0.5%), and degree of consciousness > RLS 2 (1.6%). An ECG was recorded in 74% of the cases; 70.8% of them showed a sinus rhythm, whereas 22.8% showed atrial fib- rillation/flutter. Signs of possible myocardial ischemia were revealed as ST-elevation (2.5%), ST-depression (13.9%), T-wave inversion (9.5%), and left bundle branch block (6%). P-glucose levels were measured in 31.3% of the cases, of whom 37.6% showed elevated values. Men had more often deviation of the systolic blood pressure and atrial fibrillation than women (Table 2). Data collection The patients in this study were consecutively included by assignment through an EMS record database (Ambu- link) and followed-up by hospital records (Melior) accord- ing to the directions for inclusion and exclusion. Ambulink contains the RETTS-A triage classification and Melior con- tains the International Classification of Diseases (ICD) code. Medical history and final diagnoses were categorised using These were defined by our research group consisting of a cardiologist and number of PENs based on the avail- able literature and clinical experience. This definition has been previously described [16]. However, a few further diagnoses (e.g. acute respiratory failure with Page 4 of 11 Page 4 of 11 Kauppi et al. BMC Emergency Medicine (2020) 20:67 hypercapnia or hypoxia, ketoacidosis and lactacidosis) fulfilling the above criteria appeared in the analyses of the present study cohort and have therefore been added. hypercapnia or hypoxia, ketoacidosis and lactacidosis) fulfilling the above criteria appeared in the analyses of the present study cohort and have therefore been added. dyspnoea. A large proportion had a history of cardiovascu- lar disease including hypertension (46.5%), heart failure (30%), atrial fibrillation (29%), ischemic heart disease (26%). Furthermore, 47.5% had a history of pulmonary disease, 18.8% had diabetes and 19.4% had cancer. Men had a higher prevalence of previous heart disease, diabetes and renal disease whereas women had a higher prevalence of previous pulmonary disease, system disease and psychiatric disease (Table 1). Discussion Discussion In this study, dyspnoea was classified as the main symptom in approximately 9% of all the EMS-assigned patients, similar to previous findings [1, 9, 12]. The most novel information was that among patients with dyspnoea there were more than 400 different final diag- noses. (ICD-10 codes) and 11% of them were assessed as time critical. Many of the patients had a severe comor- bidity and 11% were dead within 30 days. Despite this, only half of the patients dialled 112 within 50 h after onset of symptoms. Distribution of patients according to the final diagnosis (ICD-10 code) among groups more than 30 patients The patients showed 473 different ICD-10 codes pointing to the primary aetiology. The three most commonly ob- served aetiologies were Chronic Obstructive Pulmonary Disease (COPD) (20.4%), pulmonary infection (17.1%), and heart failure (15%). Totally, 11% of the ICD-10 codes showed time-critical conditions. After combining these ICD-10 codes, the three most common conditions were cardiovascular disease, followed by infection and pulmon- ary disease. Women more often had pulmonary disease (Table 4). The three most commonly observed disease groups were those of the respiratory system; those of the circulatory system; and symptoms, signs, and abnormal clinical findings not elsewhere classified. This finding is similar to that of a recent Danish study [8], with the exception for diseases of the circulatory system, which were more frequently noted in our study (23% versus 13%). Moreover, the three most commonly observed aetiologies were COPD (20%), pulmonary infection (17%), and heart failure (15%). In the United States, a lower frequency of COPD (13%) was observed [12], whereas a study from Australia/New Zealand showed higher rates of pulmonary infections (23%) and heart failure (20%) [11]. Age, sex, and previous history The three most commonly observed disease groups were: diseases of the respiratory system (49.1%); diseases The patients’ mean age was 73 years, and 56% of them were women. A majority (84.4%) had previously experienced Fig. 2 Kaplan-Meier survival plot of patients assessed by the PEN as the main symptom of dyspnoea and stratified by women and men er survival plot of patients assessed by the PEN as the main symptom of dyspnoea and stratified by women and men Kauppi et al. BMC Emergency Medicine (2020) 20:67 Page 5 of 11 Table 1 Age, sex and previous history All patients Women Men Missing n 6354 3538 2816 All Women Men Age - years Mean (±SD) 72.9 (17.5) 73.3 (18.1) 72.5 (16.6) Median (25th,75th percentile) 77 (66,86) 78 (67,86) 76 (66,85) Previous history - n(%) Dyspnoea 4971 (84.4) 2766 (84.0) 1.07 [0.89,1.29]a 467 247 220 Pulmonary diseaseb 2966 (47.5) 1762 (50.6) 0.76 [0.66,0.86] 116 59 57 Hypertension 2948 (46.5) 1718 (48.6) 0.82 [0.72,0.94] 8 5 3 Heart failure 1894 (30.0) 961 (27.4) 1.32 [1.15,1.52] 38 27 11 Atrial fibrillation 1838 (29.0) 945 (26.8) 1.27 [1.10,1.47] 14 8 6 Ischaemic heart disease 1642 (26.0) 785 (22.3) 1.54 [1.33,1.79] 40 16 24 Psychiatric disorderc 1337 (21.2) 862 (24.5) 0.63 [0.53,0.74] 34 20 14 Cancer 1226 (19.4) 669 (19.0) 1.06 [0.90,1.25] 23 15 8 Diabetes 1190 (18.8) 550 (15.6) 1.60 [1.35,1.89] 12 7 5 Renal disease 759 (12.0) 310 (8.8) 1.97 [1.61,2.42] 12 8 4 System disease 393 (6.2) 286 (8.1) 0.45 [0.33,0.61] 17 12 5 Other diseased 4412 (69.5) 2458 (69.6) 1.00 [0.87,1.15] 8 4 4 aOdds ratio and 99% - confidence interval bChronic obstructive pulmonary disease, asthma bronchiale, other pulmonary disease cPanic disorder, anxiety disorder, depression, bipolar disease, schizofrenia, other psychiatric disorder dOther disease: e.g. peripheral vascular diseases, other heart conditions, previous pulmonary embolism bChronic obstructive pulmonary disease, asthma bronchiale, other pulmonary disease cPanic disorder, anxiety disorder, depression, bipolar disease, schizofrenia, other psychiatric disorder dOther disease: e.g. peripheral vascular diseases, other heart conditions, previous pulmonary embolism of the circulatory system (23.1%); and symptoms, signs, and abnormal clinical findings not elsewhere classified (13.4%). Women had more often a respiratory disease (Table 3). Mortality The overall 30-day, and 1-year mortality values were 11.1, and 21.5%, respectively. Men had a higher 1-year mortality than women (p < 0.005)(Fig. 2). The three most common final diagnoses among all patients who died within 30 days were pneumonia, followed by heart failure and COPD with acute exacerbation. The three most common final diagnoses among patients with time- critical conditions who died within 30 days were stroke, sepsis followed by acute respiratory insufficiency. The patients in whom dyspnoea was the main symp- tom represent an older population (median age 77 years) with a high comorbidity. Such findings have also been Kauppi et al. Mortality BMC Emergency Medicine (2020) 20:67 Page 6 of 11 Table 2 Symptoms and clinical findings Table 2 Symptoms and clinical findings All patients Women Men Missing n 6354 3538 2816 All Women Men Time interval - median hh:mma Symptom onset - call for EMS 51:08 (3:57,145:02) 50:58 [47:49,55:18] 51:11 [47:47,55:59] 438 245 193 Symptoms - n(%) Pain 1402 (23.1) 806 (23.9) 0.91 [0.78,1.07]b 292 162 130 If yes, VAS mediana 4 (2,6) 3 [2,4] 4 [3,5] 1149 660 489 Syncope 77 (1.2) 47 (1.3) 0.80 [0.44,1.47] 24 14 10 Affected by alcohol, drugs 103 (1.6) 46 (1.3) 1.57 [0.94,2.63] 36 17 19 Vital signs; first recording – medianc Respiratory rate (breaths/min) 25 (20,32) 48.7 25 (20,32) 49.1 0.96 [0.84,1.01] 137 70 67 Oxygen saturation (%) 93 (86,97) 35.2 93 (85,97) 36.0 0.92 [0.81,1.06] 120 55 65 Heart rate (beats/min) 92 (80,110) 11.5 94 (80,110) 11.7 0.95 [0.77,1.17] 122 58 64 Systolic blood pressure (mmHg) 140 (120,160) 1.8 140 (120,160) 1.2 2.15 [1.30,3.57] 236 132 104 Diastolic blood pressure (mmHg) 80 (70,90) 0.3 80 (70,90) 0.3 1.26 [0.37,4.25] 870 482 388 Body temperature (°C) 37.0 (36.6,37.4) 0.5 37.0 (36.6,37.5) 0.5 1.34 [0.55,3.29] 234 128 106 Degree of consciousness (RLS) 1 (1,1) 1.6 1 (1,1) 1.7 0.91 [0.51,1.60] 1110 616 494 ECG recorded in ambulance - n(%) 4693 (74.0) 2540 (71.9) 1.28 [1.10,1.49] 8 4 4 ECG rhythm - n(%)d 873 512 361 Sinus rythm 3882 (70.8) 2257 (74.6) 0.67 [0.57,0.79] Atrial fibrillation/flutter 1249 (22.8) 648 (21.4) 1.19 [1.01,1.41] Other rythme 350 (6.4) 121 (4.0) 2.47 [1.83,3.33] ECG pattern - n(%)d 957 569 388 ST-elevation 137 (2.5) 67 (2.3) 1.29 [0.82,2.01] ST-depression 748 (13.9) 420 (14.1) 0.95 [0.77,1.16] T-wave inversion 511 (9.5) 270 (9.1) 1.10 [0.87,1.40] Left bundle branch block 325 (6.0) 181 (6.1) 0.97 [0.72,1.31] Blood Glucose measured - n(%) 1991 (31.3) 1034 (29.2) 1.25 [1.08,1.43] Blood glucose elevation ≥9.5 mmol/l 749 (37.6) 402 (38.9) 0.89 [0.70,1.14] aAll patients category denoted with 25th and 75th percentiles, women and men with 99% - confidence intervals;VAS: visual analogue scale bOdds ratio and 99% - confidence interval cAll patients and women category denoted with median (25th,75th percentiles) and percetage of deviating vital signs. Mortality Odds ratio and 99%-confidence intervals calculated on number of deviating vital signs Deviating vital signs: Respiratory rate < 8 or > 25 breaths/min; Oxygen saturation < 90%; Heart rate < 40/min or > 120/min; Systolic blood pressure < 90 mm/Hg; Diastolic blood pressure > 140 mm/hg; Body temperature (°C) < 35 or > 41; Reaction level scale (RLS) > 2 d almost three times as high as in the total EMS popula- tion in the same area [19]. Furthermore, our result also found that men with dyspnoea as the main symptom had a higher mortality rate than women. We have no clear explanation to this finding. There was no signifi- cant difference between women and men in terms of their final diagnosis with the exception of a lower rate of pulmonary disease among women. But men had a more severe comorbidity and more frequently suffered from a previous history of a cardiovascular disease and renal disease. This may have contributed the higher mortality among men. From an overall population perspective reported in previous studies [8, 11, 12]. This is not unexpected since the incidence of chronic conditions associated with dyspnoea (e.g. COPD, heart failure, and coronary artery disease) increase with age [18]. Surpris- ingly, the majority had previously experienced dyspnoea. In our result, more than 60% of all patients were hospi- talised. This is more than the entire EMS population in the same sampling area where the median age was 69 years and 50% of those taken to the ED were hospita- lised [19]. Overall, 11% of our study patients died within 30 days, similar to previous studies [8, 9]. The mortality risk was Kauppi et al. Mortality BMC Emergency Medicine (2020) 20:67 Page 7 of 11 Table 3 Distribution of patients across the 23 major ICD-10 code groups All patientsa Women Men Chapters - n(%) 6354 3538 2816 I Certain infections and parasites diseases A00 – B99 161 (3.0) 75 (2.6) 1.40 [0.92,2.10]b II Neoplasm C00 – D48 131 (2.5) 62 (2.1) 1.35 [0.85,2.12] III Diseases of the blood and blood forming organs and certain diseases involving the immuno-mechanisms D50 – D89 34 (0.6) 16 (0.6) 1.35 [0.56,3.29] IV Endocrine, nutritional and metabolic diseases E00 – E90 42 (0.8) 25 (0.9) 0.82 [0.36,1.84] V Mental and behavioural disorders F00 – F99 91 (1.7) 50 (1.7) 0.98 [0.57,1.70] VI Diseases of the nervous system G00 – G99 29 (0.5) 17 (0.6) 0.85 [0.32,2.24] VII Diseases of the eye and adnexa H00 – H59 0 (0.0) 0 (0.0) 0 [0,0] VIII Diseases of the eye and mastoid process H60 – H95 0 (0.0) 0 (0.0) 0 [0,0] IX Diseases of the circulatory system I00 – I99 1230 (23.1) 647 (22.3) 1.11 [0.94,1.31] X Diseases of the respiratory system J00 – J99 2615 (49.1) 1476 (50.8) 0.86 [0.75,0.99] XI Diseases of the digestive system K00 – K93 65 (1.2) 33 (1.1) 1.17 [0.61,2.22] XII Diseases of the skin and subcutaneous tissue L00 – L99 6 (0.1) 3 (0.1) 1.20 [0.15,9,85] XIII Diseases of the musculoskeletal tissue and connective tissue M00 – M99 51 (1.0) 37 (1.3) 0.45 [0.20,1.02] XIV Diseases of the genitourinery system N00 – N99 69 (1.3) 30 (1.0) 1.57 [0.84,2.95] XV Pregnancy, childbirth and puerperium O00 – O99 1 (< 0.1) 1 (< 0.1) 0 [0,0] XVI Certain conditions originating from the perinatal period P00 – P96 0 (0.0) 0 (0.0) 0 [0,0] XVII Congenital malformations, deformation and chromosomal malformations Q00 – Q99 1 (< 0.1) 0 (0.0) 0 [0,0] XVIII Symptoms, signs and abnormal clinical findings, not elsewhere classified R00 – R99 711 (13.4) 382 (13.2) 1.04 [0.84,1.28] XIX Injury, Poisoning and certain other consequences of external causes S00 – T98 33 (0.6) 23 (0.8) 0.52 [0.20,1.38] XX External causes of morbidity and mortality V00 – V99 1 (< 0.1) 1 (< 0.1) 0 [0,0] XXI External causes to disease and death Y01 – Y98 1 (< 0.1) 1 (< 0.1) 0 [0,0] XXII Factors influencing health status and contact with health services Z00 – Z99 48 (0.9) 23 (0.8) 1.31 [0.62,2.76] XXIII Codes for special purposes U00-U99 4 (0.1) 3 (0.1) 0.40 [0.20,7.84] aMissing diagnosis in 1030 patients (women 633, men 397) bOdds ratio and 99% - confidence interval Table 3 Distribution of patients across the 23 major ICD-10 code groups XIII Diseases of the musculoskeletal tissue and connective tissue M00 – M99 XIV Diseases of the genitourinery system N00 – N99 XV Pregnancy, childbirth and puerperium O00 – O99 XVI Certain conditions originating from the perinatal period P00 – P96 aMissing diagnosis in 1030 patients (women 633, men 397) bOdds ratio and 99% - confidence interval [20], it has been denoted that men have a greater vulner- ability to cardiovascular diseases which is a reason to their higher mortality rate in general. Mortality the five First Hour Quinted emergency time-related pathologies. This means that immediate prehospital treatment and early diagnosis may be crucial in reducing the morbidity and mortality risk [6]. Patients attending EMS due to dyspnoea appear to have a five times higher risk of death than those with chest pain [9, 21]. This is in agreement with other reports saying that regardless of the aetiology, patients who have dyspnoea in combination with other condi- tions have a poor prognoses [22]. Thus, dyspnoea should be perceived as a high-risk symptom and a strong predictor of an increased mortality risk [9, 11, 23, 24]. Further, respiratory failure has been defined as among This should be attributed to the fact that patients only call EMSs when they cannot manage the situation them- selves and indeed half of patients waited more than 2 days after symptom onset in our study. In one previ- ous study [25], patients tried to ignore their symptoms or manage them (working through), leading to delays in calling EMSs; some of these patients even took a “waiting approach”, while others were frustrated by their Kauppi et al. BMC Emergency Medicine (2020) 20:67 Kauppi et al. BMC Emergency Medicine Page 8 of 11 Table 4 Distribution of patients according to final diagnosis (ICD-10 code) among groups more than 30 patients All patientsa Women Men Final diagnosis - n(%) 6354 3538 2816 1. Cardiovascular disease 1316 (24.7) 694 (23.9) 1.10 [0.94,1.30]b a. Heart failure 801 (15.0) 402 (13.8) 399 (16.5) b. Ischemic heart disease 154 (2.9) 70 (2.4) 84 (3.5) c. Arrhythmia 142 (2.7) 87 (3.0) 55 (2.3) d. Pulmonary embolism 123 (2.3) 81 (2.8) 42 (1.7) 2. Pulmonary disease 1311 (24.6) 780 (26.9) 0.77 [0.65,0.91] a. Chronic obstructive pulmonary disease 1088 (20.4) 656 (22.6) 432 (17.9) b. Asthma bronchiale 127 (2.4) 87 (3.0) 40 (1.7) c. Other pulmonary diseases 94 (1.8) 37 (1.3) 57 (2.4) 3. Infection 1172 (22.0) 607 (20.9) 1.15 [0.97,1.37] a. Pulmonary 912 (17.1) 469 (16.1) 443 (18.3) b. Sepsis 97 (1.8) 43 (1.5) 54 (2.2) c. Ear, nose and throat and upper airways 81 (1.5) 52 (1.8) 29 (1.2) d. Other infection 74 (1.4) 40 (1.4) 34 (1.4) 4. Symptom diagnosis 662 (12.4) 353 (12.2) 1.06 [0.85,1.31] 5. Cancer 138 (2.6) 66 (2.3) 1.32 [0.85,2.01] a. Pulmonary 89 (1.7) 49 (1.7) 40 (1.7) b. Other localisation 31 (0.6) 13 (0.4) 18 (0.7) 6. Mortality Respiratory insufficiency 129 (2.4) 79 (2.7) 0.76 [0.47,1.21] 7. Psychiatric disorder 90 (1.7) 49 (1.7) 1.01 [0.58,1.74] 9. Urinary disease 69 (1.3) 30 (1.0) 1.57 [0.84,2.95] 10. Pleura Disease 54 (1.0) 32 (1.1) 0.82 [0.40,1.69] 11. Muscle skeletal pain 44 (0.8) 32 (1.1) 0.45 [0.19,1.07] 12. Organ failure 39 (0.7) 23 (0.8) 0.84 [0.36,1.95] 13. Gastrointestinal disease 33 (0.6) 18 (0.6) 1.00 [0.41,2.47] 14. Anaemia 33 (0.6) 15 (0.5) 1.44 [0.59,3.56] aMissing diagnosis in 1030 patients (women 633, men 397) bOdds ratio with 99% - confidence interval, subcategories with percentage Table 4 Distribution of patients according to final diagnosis (ICD-10 code) among groups more than 30 patients All patientsa Women Men Table 4 Distribution of patients according to final diagnosis (ICD-10 code) among groups more than 30 patients ents according to final diagnosis (ICD-10 code) among groups more than 30 patients aMissing diagnosis in 1030 patients (women 633, men 397) bOdds ratio with 99% - confidence interval, subcategories with percentage Almost one in four patients had atrial fibrillation and a few had signs of myocardial ischemia on ECG, indicat- ing that a cardiac pathology was not uncommon. This is most likely explained by the high degree of cardiovascu- lar comorbidity reported in such populations [26–29]. Atrial fibrillation and acute heart failure are often seen in combination, and since heart failure is one of the dominating aetiologies behind dyspnoea, this was an expected finding. Based on previous history, one may assume that when atrial fibrillation occurred, it was most often previously known. Dyspnoea due to acute heart failure and the presence of ECG-related abnormalities, such as ventricular or supraventricular arrhythmia, brady- cardia, or ongoing myocardial ischemia, may all be indica- tors of an increased risk of early hospital death [30]. symptoms. This information is vital for consideration in the meeting between the PEN and patient. The dyspnoea experience varies across people, and one can assume that some degree of tolerance to dyspnoea already existed in our patient group due to their comorbidities (e.g. COPD, heart failure, and hypertension). This is supported by earlier studies [10, 23] in which this patient group was characterised by poor health. Dyspnoea, to some extent, is a part of natural ageing and results in a decreasing degree of physical capacity; thus, it is not always explained by a specific illness or related to comorbidity presence. Mortality It may also be that elderly people are more tolerant and do not want to interfere or be perceived as disruptive. Thus, they may understate their symptom experience and severity when finally calling for help. This makes it even more difficult for both dispatchers and the PEN to determine disease severity [11]. One in four patients experienced pain, which may be important from a diagnostic as well as therapeutic perspective. The pain experience was mostly related to Page 9 of 11 Kauppi et al. BMC Emergency Medicine (2020) 20:67 Kauppi et al. BMC Emergency Medicine (2020) 20:67 Kauppi et al. BMC Emergency Medicine (2020) 20:67 Furthermore, due to the study design, the data had to be retrospectively collected from patient records, and important clinical parameters such as VS may have been measured but never recorded. In both EMS and hospital records, the documentation was sometimes insufficient. Likewise, it is possible that patients with other main symptoms who still have dyspnoea may have been classi- fied into other ESS codes (not only ESS 04) by the PEN, as dyspnoea is also present in other conditions such as chest pain. breathing-related chest discomfort, thoracic pain, chest wall pain, shoulder pain, or pain due to other unclear reasons. The presence of pain in dyspnoea patients has previously been reported [9, 21, 22, 31], mostly in the form of chest pain as a result of underlying causes including pulmonary embolism myocardial infarction, pneumonia and panic disorder. A large proportion had hyperglycaemia. This may be an alarming sign also among patients with dyspnoea. Hyperglycaemia is a marker of acute stress response which, especially in nondiabetic patients, is associated with higher rates of in-hospital complications and mortality [15, 32]. Information on the final diagnosis was missing in 1030 of all missions. Such cases were those left on- scene in whom there was no information on final diagnosis and patients who were brought to hospital and directly sent home from the Emergency Department, since some of them were never assessed by a physician. However, the present study was conducted in accordance with a paper by Kaji et al. [37], with the aim of reducing the bias associated with medical record reviews. Clinical implications Our results suggest that 11% of all patients seen by PENs due to dyspnoea have time critical diagnosis and 11% will die during the subsequent 30 days. Available infor- mation from age, sex, comorbidity and clinical findings including vital parameters, ECG recordings, blood glucose measurements and other symptoms may form the basis for the building of future decision support tools in order to differentiate patients with high and low risk for future adverse events. Supplementary information Supplementary information accompanies 1186/s12873-020-00363-6. Supplementary information Supplementary information accompanies this paper at https://doi.org/10. 1186/s12873-020-00363-6. Conclusions Dyspnoea, as the main symptom, constituted approxi- mately 9% of all the EMS missions in our study. A major- ity of the patients taken to hospital with dyspnoea as the main symptom were hospitalised and more than 400 different final diagnoses were observed, of which 11% were regarded as time-critical. A very high proportion (84%) had previously suffered from dyspnoea, which may explain why more than half showed delays greater than 2 days from symptom onset to EMS contact. High comorbidity values may contribute to this finding. Likewise, that pa- tients call for help only when the situation is truly unman- ageable makes them even more vulnerable. Dyspnoea, as the main symptom, is associated with a high risk of death, and 11% of all patients were dead within 30 days. However, more than half of these patients had abnormal vital parameters at the time of PEN assessment. This knowledge is important, not only for EMSs, but also for clinicians and those responsible for the provision of education in different emergency courses. Strengths and limitations Additional file 1. The supplementary file describes in more detail deviating vital signs Red/Orange level according to RETTS-A (2017 version) and RETTS ESS 04 (main symptom of dyspnoea). The major strength of our study is that data were collected from a relatively large representative sample. While the data were collected from a mix of urban and rural areas, the study itself is limited to a specific region of Sweden (southwest) which may impede the degree of generalisability of the findings to other settings. People living in the northern part of Sweden have greater diffi- culties in accessing EMSs and longer transport distances, which may lead to result variations. Mortality Although only 11% had time critical final diagnoses, a much larger proportion of these patients will be regarded as having a time-critical condition in the acute phase since the majority had abnormal VS, primarily an abnormal respiratory rate and oxygen saturation. This requires advanced knowledge from the PENs who is caring for patients with dyspnoea, as abnormal vital parameters may be a sign of a number of different serious conditions; both cardiogenic, pulmonary and other aetiologies of acute respiratory failure. This high- lights the importance of early recognition of the patients condition and directed treatment already at an early stage by EMS, as it might be crucial for the final out- come [33–35]. It has previously been reported that acute ill patients (including those with dyspnoea) admitted thorough ED [36] with abnormal vital parameters, have an increased risk of death. The most powerful predictors were abnormal respiratory rate, oxygen saturation and Glasgow Coma scale (GCS). Ethics approval and consent to participate The design of the study was approved by the Regional Ethics Committee in Gothenburg, Sweden (Dnr 989-17). All the procedures performed in this study were in accordance with the ethical standards of the Declaration of Helsinki [38]. Consent were obtained from chief executive officers in the participating EMS organisations for reviewing patient records and to use the data for analysis. Informed consent for participation was not required. This is mostly not recommended by Ethical Review Boards in Sweden for the following reasons: 13. Suserud BO. A new profession in the pre-hospital care field--the ambulance nurse. Nurs Crit Care. 2005;10:269–71. 13. Suserud BO. A new profession in the pre-hospital care field--the ambulance nurse. Nurs Crit Care. 2005;10:269–71. 14. Widgren BR, Jourak M. Medical emergency triage and treatment system (METTS): a new protocol in primary triage and secondary priority decision in emergency medicine. J Emerg Med. 2011;40:623–8. 14. Widgren BR, Jourak M. Medical emergency triage and treatment system (METTS): a new protocol in primary triage and secondary priority decision in emergency medicine. J Emerg Med. 2011;40:623–8. 15. Sud M, Wang X, Austin PC, Lipscombe LL, Newton GE, Tu JV, et al. Presentation blood glucose and death, hospitalization, and future diabetes risk in patients with acute heart failure syndromes. Eur Heart J. 2015;36:924–31. 15. Sud M, Wang X, Austin PC, Lipscombe LL, Newton GE, Tu JV, et al. Presentation blood glucose and death, hospitalization, and future diabetes risk in patients with acute heart failure syndromes. Eur Heart J. 2015;36:924–31. 1) Individual patients could never be identified since their identification number was translated to a code. Their integrity, therefore, remained intact. 1) Individual patients could never be identified since their identification number was translated to a code. Their integrity, therefore, remained intact. 16. Wibring K, Magnusson C, Axelsson C, Lundgren P, Herlitz J, Andersson HM. Towards definitions of time-sensitive conditions in prehospital care. Scand J Trauma Resusc Emerg Med. 2020;28:7. 16. Wibring K, Magnusson C, Axelsson C, Lundgren P, Herlitz J, Andersson HM. Towards definitions of time-sensitive conditions in prehospital care. Scand J Trauma Resusc Emerg Med. 2020;28:7. 2) Some of the most seriously ill patients could never be contacted retrospectively, since they had either died or were in a very poor clinical condition. This would increase the risk of selection bias, thereby, hampering the reliability of the data. 17. Sovso MB, Christensen MB, Bech BH, Christensen HC, Christensen EF, Huibers L. Abbreviations COPD: Chronic obstructive pulmonary disease; ECG: Electrocardiogram; ED: Emergency department; EMS: Emergency medical service; ESS: Emergency signs and symptoms; ICD-10: International Statistical Classification of Diseases and Related Health Problems – 10th revision; PEN: Prehospital emergency nurse; RETTS-A: Rapid emergency triage and treatment system for adults; VS: Vital signs Page 10 of 11 Page 10 of 11 Kauppi et al. BMC Emergency Medicine (2020) 20:67 Kauppi et al. BMC Emergency Medicine (2020) 20:67 3. Pooler C. Living with chronic lower pulmonary disease: disruptions of the embodied phenomenological self. Glob Qual Nurs Res. 2014;1: 2333393614548762. Funding WK i WK received funding from the University of Borås, Sweden. The funder did not have any role in the study design, aim, or process. Open access funding provided by University of Boras. 10. Hayen A, Herigstad M, Pattinson KT. Understanding dyspnea as a complex individual experience. Maturitas. 2013;76:45–50. 11. Kelly AM, Holdgate A, Keijzers G, Klim S, Graham CA, Craig S, et al. Epidemiology, prehospital care and outcomes of patients arriving by ambulance with dyspnoea: an observational study. Scand J Trauma Resusc Emerg Med. 2016;24:113. Consent for publication Not applicable. Not applicable. 19. Magnusson C, Herlitz J, Axelsson C. Patient characteristics, triage utilisation, level of care, and outcomes in an unselected adult patient population seen by the emergency medical services: a prospective observational study. BMC Emerg Med. 2020;20:7. Acknowledgements The authors wish to acknowledge the Ambulance and Prehospital Emergency Care, Sahlgrenska University Hospital in Gothenburg, Sweden and Ambulance and Prehospital Emergency Care, Södra Älvsborg hospital in Borås, Sweden for providing data on EMS assignments. We also acknowledge the help extended by Jonny Lindqvist, Region Västra Götaland, Gothenburg, Sweden in creating the data protocol. 4. Berliner D, Schneider N, Welte T, Bauersachs J. The differential diagnosis of dyspnea. Dtsch Arztebl Int. 2016;113:834–45. and Ambulance and Prehospital Emergency Care, Södra Älvsborg hospital in Borås, Sweden for providing data on EMS assignments. We also acknowledge the help extended by Jonny Lindqvist, Region Västra Götaland, Gothenburg, Sweden in creating the data protocol. 5. Gori CS, Magrini L, Travaglino F, Di Somma S. Role of biomarkers in patient with dyspnea. Eur Rev Med Pharmacol Sci. 2011;15:229–40. 5. Gori CS, Magrini L, Travaglino F, Di Somma S. Role of biomarkers in patients with dyspnea. Eur Rev Med Pharmacol Sci. 2011;15:229–40. 6. Krafft T, Garcia Castrillo-Riesgo L, Edwards S, Fischer M, Overton J, Robertson-Steel I, et al. European emergency data project (EED project): EMS data-based health surveillance system. Eur J Pub Health. 2003;13:85–90. Availability of data and materials The datasets analysed during the current study are available from the corresponding author on reasonable request. 12. Prekker ME, Feemster LC, Hough CL, Carlbom D, Crothers K, Au DH, et al. The epidemiology and outcome of prehospital respiratory distress. Acad Emerg Med. 2014;21:543–50. Received: 24 March 2020 Accepted: 21 August 2020 Received: 24 March 2020 Accepted: 21 August 2020 22. McConaghy JR, Oza RS. Outpatient diagnosis of acute chest pain in adults. Am Fam Physician. 2013;87:177–82. 23. Huijnen B, van der Horst F, van Amelsvoort L, Wesseling G, Lansbergen M, Aarts P, et al. Dyspnea in elderly family practice patients. Occurrence, severity, quality of life and mortality over an 8-year period. Fam Pract. 2006; 23:34–9. Authors’ contributions WK, CA, JH, and LP developed the design and the research protocol. WK, CA, and JH created the data forms. WK collected the data. CM supervised the statistical analyses and was discussed with WK, CA and JH. WK and JH wrote the first draft of the manuscript. WK, CA, JH, LP, and CM supervised and analysed the data and their interpretation. All the authors participated in the final drafting of the manuscript and have read and approved the final manuscript. 7. Christie A, Costa-Scorse B, Nicholls M, Jones P, Howie G. Accuracy of working diagnosis by paramedics for patients presenting with dyspnoea. Emerg Med Australas. 2016;28:525–30. 8. Lindskou TA, Pilgaard L, Sovso MB, Klojgard TA, Larsen TM, Jensen FB, et al. Symptom, diagnosis and mortality among respiratory emergency medical service patients. PLoS One. 2019;14:e0213145. analysed the data and their interpretation. All the authors participated in the final drafting of the manuscript and have read and approved the final manuscript. 9. Botker MT, Stengaard C, Andersen MS, Sondergaard HM, Dodt KK, Niemann T, et al. Dyspnea, a high-risk symptom in patients suspected of myocardial infarction in the ambulance? A population-based follow-up study. Scand J Trauma Resusc Emerg Med. 2016;24:15. Author details 1 20. Crimmins EM, Shim H, Zhang YS, Kim JK. Differences between men and women in mortality and the health dimensions of the morbidity process. Clin Chem. 2019;65:135–45. 1PreHospen- Centre for Prehospital Research, Faculty of Caring, Work Life and Social Welfare, University of Borås, SE- 501 90 Borås, Sweden. 2Faculty of Caring Science, Work Life and Social Welfare, University of Borås, Borås, Sweden. 3Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. 21. Pedersen CK, Stengaard C, Friesgaard K, Dodt KK, Sondergaard HM, Terkelsen CJ, et al. Chest pain in the ambulance; prevalence, causes and outcome - a retrospective cohort study. Scand J Trauma Resusc Emerg Med. 2019;27:84. Competing interests The authors declare that they have no competing interests. Ethics approval and consent to participate Contacting out-of-hours primary care or emergency medical services for time-critical conditions - impact on patient outcomes. BMC Health Serv Res. 2019;19:813. 3) Approaching patients with these issues may create more anxiety than satisfaction and may, therefore, be regarded as unethical. 18. Kelly AM, Keijzers G, Klim S, Graham CA, Craig S, Kuan WS, et al. An observational study of dyspnea in emergency departments: the Asia, Australia, and New Zealand dyspnea in emergency departments study (AANZDEM). Acad Emerg Med. 2017;24:328–36. 18. Kelly AM, Keijzers G, Klim S, Graham CA, Craig S, Kuan WS, et al. An observational study of dyspnea in emergency departments: the Asia, Australia, and New Zealand dyspnea in emergency departments study (AANZDEM). Acad Emerg Med. 2017;24:328–36. References 1. Pittet V, Burnand B, Yersin B, Carron PN. Trends of pre-hospital emergency medical services activity over 10 years: a population-based registry analysis. BMC Health Serv Res. 2014;14:380. 1. Pittet V, Burnand B, Yersin B, Carron PN. Trends of pre-hospital emergency medical services activity over 10 years: a population-based registry analysis. BMC Health Serv Res. 2014;14:380. 24. Berraho M, Nejjari C, El Rhazi K, Tessier JF, Dartigues JF, Barberger-Gateau P, et al. Dyspnea: a strong independent factor for long-term mortality in the elderly. J Nutr Health Aging. 2013;17:908–12. 2. Parshall MB, Schwartzstein RM, Adams L, Banzett RB, Manning HL, Bourbeau J, et al. An official American Thoracic Society statement: update on the mechanisms, assessment, and management of dyspnea. Am J Respir Crit Care Med. 2012;185:435–52. 25. McCabe PJ, Rhudy LM, Chamberlain AM, DeVon HA. Fatigue, dyspnea, and intermittent symptoms are associated with treatment-seeking delay for Page 11 of 11 Kauppi et al. BMC Emergency Medicine (2020) 20:67 Kauppi et al. BMC Emergency Medicine (2020) 20:67 symptoms of atrial fibrillation before diagnosis. Eur J Cardiovasc Nurs. 2016; 15:459–68. symptoms of atrial fibrillation before diagnosis. Eur J Cardiovasc Nurs. 2016; 15:459–68. 26. Odigie-Okon E, Jordan B, Dijeh S, Wolff A, Dadu R, Lall P, et al. Cardiac injury in patients with COPD presenting with dyspnea: a pilot study. Int J Chron Obstruct Pulmon Dis. 2010;5:395–9. 27. Wilhelmsen L, Rosengren A, Lappas G. Hospitalizations for atrial fibrillation in the general male population: morbidity and risk factors. J Intern Med. 2001; 250:382–9. 28. Ariansen I, Edvardsen E, Borchsenius F, Abdelnoor M, Tveit A, Gjesdal K. Lung function and dyspnea in patients with permanent atrial fibrillation. Eur J Intern Med. 2011;22:466–70. 29. Vanfleteren LE, Franssen FM, Uszko-Lencer NH, Spruit MA, Celis M, Gorgels AP, et al. Frequency and relevance of ischemic electrocardiographic findings in patients with chronic obstructive pulmonary disease. Am J Cardiol. 2011; 108:1669–74. 30. Beygui F, Castren M, Brunetti ND, Rosell-Ortiz F, Christ M, Zeymer U, et al. Pre-hospital management of patients with chest pain and/or dyspnoea of cardiac origin. A position paper of the Acute Cardiovascular Care Association (ACCA) of the ESC. Eur Heart J Acute Cardiovasc Care. 2015;9: 59–81. 31. Johansson EL, Ternesten-Hasseus E, Olsen MF, Millqvist E. Respiratory movement and pain thresholds in airway environmental sensitivity, asthma and COPD. Respir Med. 2012;106:1006–13. 32. Schuetz P, Kennedy M, Lucas JM, Howell MD, Aird WC, Yealy DM, et al. References Initial management of septic patients with hyperglycemia in the noncritical care inpatient setting. Am J Med. 2012;125:670–8. 33. Mebazaa A, Tolppanen H, Mueller C, Lassus J, DiSomma S, Baksyte G, et al. Acute heart failure and cardiogenic shock: a multidisciplinary practical guidance. Intensive Care Med. 2016;42:147–63. 34. Hensel M, Strunden MS, Tank S, Gagelmann N, Wirtz S, Kerner T. Prehospital non-invasive ventilation in acute respiratory failure is justified even if the distance to hospital is short. Am J Emerg Med. 2019;37:651–6. 35. Nielsen VM, Madsen J, Aasen A, Toft-Petersen AP, Lubcke K, Rasmussen BS, et al. Prehospital treatment with continuous positive airway pressure in patients with acute respiratory failure: a regional observational study. Scand J Trauma Resusc Emerg Med. 2016;24:121. 36. Barfod C, Lauritzen MM, Danker JK, Soletormos G, Forberg JL, Berlac PA, et al. Abnormal vital signs are strong predictors for intensive care unit admission and in-hospital mortality in adults triaged in the emergency department - a prospective cohort study. Scand J Trauma Resusc Emerg Med. 2012;20:28. 37. Kaji AH, Schriger D, Green S. Looking through the retrospectoscope: reducing bias in emergency medicine chart review studies. Ann Emerg Med. 2014;64:292–8. 37. Kaji AH, Schriger D, Green S. Looking through the retrospectoscope: reducing bias in emergency medicine chart review studies. Ann Emerg Med. 2014;64:292–8. 38. World Medical A. World medical association declaration of Helsinki: ethical principles for medical research involving human subjects. JAMA. 2013;310: 2191–4. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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Primary intestinal lymphangiectasia presenting as limb hemihyperplasia: a case report and literature review
BMC gastroenterology
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Khayat BMC Gastroenterol (2021) 21:225 https://doi.org/10.1186/s12876-021-01813-6 Khayat BMC Gastroenterol (2021) 21:225 https://doi.org/10.1186/s12876-021-01813-6 Abstract Background:  Primary intestinal lymphangiectasia is an exceedingly rare disorder. Epidemiology is unknown. It usu- ally presents with lower extremity swelling, diarrhea, ascites, and protein-losing enteropathy. Since the pathogenesis of edema is usually due to hypoalbuminemia; both extremities are typically involved. The edema can rarely be due to abnormal lymphatic circulation, causing lymphedema, which usually involves both extremities as well. Diagnosis is made by the constellation of clinical, biochemical, endoscopic, and histological findings. Treatment involves dietary modification, to reduce lymphatic dilation in response to dietary fat. Other pharmacologic (e.g., octreotide) and replacement measures may be indicated as well. The most serious long-term complication is intestinal lymphoma. Herein is a case of Primary intestinal lymphangiectasia presenting with unilateral lower limb swelling. Case presentation:  A 4-year-old boy presents with left foot swelling since the age of 4 months, in addition to inter- mittent diarrhea, and abdominal swelling. The foot swelling had been evaluated by different health care professionals in the past, and was mislabeled as either cellulitis, or congenital hemihyperplasia. Physical examination revealed mild ascites, and a non-pitting foot edema with a positive Stemmer’s sign (lymphedema). Blood work revealed hypoalbu- minemia (albumin 2 g/dl), and hypogammaglobulinemia. Endoscopy showed dilated lacteals throughout the duo- denum. Histopathologic examination revealed massively dilated lamina propria lymphatics in the duodenal biopsies. The patient was diagnosed with primary intestinal lymphangiectasia. He was treated with high-protein and low-fat diet, and supplemental formula high in medium chain triglycerides. On follow-up, the patient’s diarrhea completely resolved, and his ascites and edema improved significantly. Conclusions:  The presence of unilateral lower limb edema should not preclude the diagnosis of systemic disor- ders, and a high index of suspicion is required in atypical presentations. A good knowledge about Primary intestinal lymphangiectasia manifestations, and physical examination skills to differentiate edema or lymphedema from tissue overgrowth can significantly aid in the diagnosis. Keywords:  Lymphedema, Intestinal lymphangiectasis, Primary intestinal lymphangiectasia, Saudi Arabia, Hemihyperplasia, Case report Primary intestinal lymphangiectasia presenting as limb hemihyperplasia: a case report and literature review Ammar A. Khayat* © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. The Creative Commons Public Domain Dedication waiver (http://​creat​iveco​ mmons.​org/​publi​cdoma​in/​zero/1.​0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Background Primary intestinal lymphangiectasia (PIL) was first described by Waldman et al. in 1961, when they noticed an association between hypoproteinemia and gut protein loss [1]. Since then, sporadic cases from around the world have been reported on this rare disease [2, 3]. Prevalence is unknown, with most studies being limited to case *Correspondence: aakhayat@uqu.edu.sa Department of Pediatrics, Gastroenterology Unit, Department of Pediatrics, Faculty of Medicine, Umm AL Qura University, King Abdulaziz University, 24381 Al‑Abdiyyah, Makkah, Saudi Arabia © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. The Creative Commons Public Domain Dedication waiver (http://​creat​iveco​ mmons.​org/​publi​cdoma​in/​zero/1.​0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Khayat BMC Gastroenterol (2021) 21:225 Page 2 of 5 Page 2 of 5 Left foot examination revealed a significantly swollen dorsal aspect of the foot and toes confirming presence of edema up to the level of his ankle. The edema was minimally pitting, with a positive Stemmer’s sign (Fig. 1). Ankle joint examination was otherwise unremarkable. reports and series [4]. The majority of patients present in the first 3 years of life [4, 5]. The most common reported presentation is bilateral lower limb edema, with or with- out ascites, and often with diarrhea [4, 5]. PIL typically responds well to dietary modification [4, 5]. Herein is a case of PIL presenting with unilateral edema, initially mislabeled as limb hemihyperplasia (hemihypertrophy), and ascites. Laboratory workup showed a low albumin at 2  g/ dl (normal range 3.5–5.5  g/dl), total protein at 2.9  g/ dl (normal range 6–8 g/dl), total IgG at 147 mg/dl (nor- mal range 565–1765  mg/dl), IgM at 16  mg/dl (normal range 55–375 mg/dl), and IgA at 30 mg/dl (normal range 85–385 mg/dl). Other tests were essentially within nor- mal limits including a negative urine protein, normal liver enzyme levels, and a negative tissue transglutaminase IgA antibody. Upper and lower gastrointestinal endos- copies were performed and showed the classic appear- ance of white spots or dilated “lacteals” in the duodenum (Fig. 2). The colon showed lymphoid nodular hyperplasia. Otherwise, endoscopy was unremarkable. Histopatho- logic examination showed a remarkably dilated lamina propria lymphatic vessels in the duodenum (Fig. 3). Oth- erwise, no other significant abnormalities were observed. Lymphoscintigraphy of his left foot showed failure of progression to the proximal lymph nodes confirming the presence of massively dilated lymphatics.h Case presentation 2  Endoscopic image of the duodenum at the level of the second part, showing the mucosa completely covered with white spots or dilated “lacteals” Fig. 2  Endoscopic image of the duodenum at the level of the second part, showing the mucosa completely covered with white spots or dilated “lacteals” age of the duodenum at the level of the second part, showing the mucosa completely covered with white spots or dilated Fig. 2  Endoscopic image of the duodenum at the level of the second part, showing the mucosa completely covered with “lacteals” Fig. 2  Endoscopic image of the duodenum at the level of the second part, showing the mucosa completely covered with white spots or dilated “lacteals” Fig. 4   A and B: Photographic images of the patient’s left foot showing the edema prior to dietary modification (a) and the significant improvement after dietary modification (b) Fig. 3  Hematoxylin and Eosin stain of duodenal mucosal biopsy at 10X magnification, showing massively dilated lymphatic vessels in lamina propria, glandular and surface epithelium are unremarkable otherwise. Podoplanin stain highlighting the lymphatic vascular endothelium of duodenal mucosal biopsy at 10X magnification is shown in inset, again redemonstrating the massive dilation Fig. 4   A and B: Photographic images of the patient’s left foot showing the edema prior to dietary modification (a) and the significant improvement after dietary modification (b) Fig. 3  Hematoxylin and Eosin stain of duodenal mucosal biopsy at 10X magnification, showing massively dilated lymphatic vessels in lamina propria, glandular and surface epithelium are unremarkable otherwise. Podoplanin stain highlighting the lymphatic vascular endothelium of duodenal mucosal biopsy at 10X magnification is shown in inset, again redemonstrating the massive dilation Case presentation A 4-year-old boy with no known medical condition presents to an outpatient clinic with history of left foot swelling and diarrhea. The swelling was noted by par- ents at the age of 4 months, which had been evaluated by medical professionals and attributed to a local infec- tion according to parents. It had never disappeared com- pletely, despite a waxing and waning course, which led parents to believe it was a congenital condition. During the course, a physician mislabeled the swelling as hemi- hyperplasia (hemihypertrophy), due to the stark differ- ence in the size of the feet. More recently, the patient started complaining of intermittent watery to semi- formed stools, 3–6 times per day, that were aggravated by fatty diet, and were occasionally difficult to flush. He was noted to have poor subcutaneous fat in his face and arms but did not lose weight. Family history was negative for lymphedema, or any other genetic disorder. The diagnosis of primary intestinal lymphangiectasia was made based on the constellation of clinical, biochem- ical, endoscopic, and histological findings.h On examination, he was vitally stable. He looked undernourished even though his weight was on the 90th centile, likely due to ascites. Abdominal examination revealed mild ascites, normal bowel sounds, and no orga- nomegaly. Cardiac and respiratory examinations were unremarkable. His right foot showed almost no edema. i The patient was started on high protein, minimal fat diet, along with supplemental high medium chain triglyc- eride (MCT) formula. On follow up, his weight remained on the 90th cen- tile, however, his mid-arm circumference was on the 75th centile. His bowel movement frequency, Fig. 1  a and b Photographic images of the patient’s left foot (a), showing a positive Stemmer’s sign: the skin on the dorsum of the second toe cannot be easily pinched, compared to the right foot (b) Fig. 1  a and b Photographic images of the patient’s left foot (a), showing a positive Stemmer’s sign: the skin on the dorsum of the second toe cannot be easily pinched, compared to the right foot (b) Fig. 1  a and b Photographic images of the patient’s left foot (a), showing a positive Stemmer’s sign: the skin on the dorsum of the second toe cannot be easily pinched, compared to the right foot (b) Khayat BMC Gastroenterol (2021) 21:225 Page 3 of 5 Fig. Discussion and conclusion Unilateral limb swelling has a wide array of differential diagnoses, such as different types of lymphedema (pri- mary and secondary) [6, 7]. True Hemihyperplasia is seen in syndromes such as Beckwith-Weidemann syn- drome, or could be an isolated disorder [8]. Hemihy- perplasia differs from lymphedema where there is a true tissue overgrowth in the former, whereas only accumula- tion of excess interstitial fluid in the latter [7–9]. and consistency improved immediately, and so did his subcutaneous fat eventually. His ascites resolved completely, and his left leg swelling was significantly improving as well (Fig. 4), with persistence of Stem- mer’s sign however. His Albumin and total protein lev- els improved as well. l primary lymphedema without systemic manifes- tations or visceral involvement (i.e., PIL, or chylous Khayat BMC Gastroenterol (2021) 21:225 Khayat BMC Gastroenterol (2021) 21:225 Page 4 of 5 Treatment focuses mainly on dietary modification [4, 5, 11]. dietary fat induces dilation of lymphatics even in the normal intestines. Therefore, avoidance of fat decreases excessive dilation and risk of rupture in lymphangiectasia [5, 13]. High MCT containing formulas, and fat restric- tion along with high protein diet are the cornerstones of treatment for infants, and older children respectively [4, 5, 11]. MCTs are absorbed directly into the portal venous circulation and do not require lymphatic flow for absorp- tion [21]. Octreotide use for the treatment of chylous effusions has been described in the literature [22]. Its effect on the intestines is unclear, but it is hypothesized that it decreases triglycerides absorption, and induces splanchnic vasoconstriction [5]. Albumin and intrave- nous immunoglobulin (IVIG) infusions are frequently indicated as replacement therapies, depending on the levels and clinical scenarios [5]. Other treatment meas- ures include managing any nutritional deficiencies, spe- cifically fat-soluble vitamins [5, 23]. effusions) also occurs in a familial pattern and is often due to a genetic disorder [7]. The onset can be con- genital, or present later in life, and can be localized to the lower extremities or other body parts, including upper extremities and face [7]. The edema can be uni- lateral, but more commonly bilateral, as seen in Meige, and Melroy syndromes [7, 10]. PIL in comparison, com- monly presents as an isolated, or non-familial disorder [5, 11]. Rarely, it may occur in a familial or a syndro- mic pattern, where there is a widespread lymphatic malformations or dysplasia [5, 11]. Authors’ contributions AK has worked on drafting the manuscript, gathering data, obtaining consent, and critically revising the final manuscript. All authors read and approved the final manuscript. Acknowledgements I would like to thank Dr Layla Abdullah, and Dr Dania Saleh from the depart- ment of Pathology for providing me with high quality histopathology images, and Dr. Abdulhameed Ibrahim, as well as the patient’s father for providing clinical photographs. PIL diagnosis is usually made by endoscopic, and his- topathologic findings of the small intestines, showing the typical dilated lymphatic vessels in the lamina pro- pria and submucosa [4, 5]. Limb lymphatic vessels can be examined by various radiographic techniques, which can aid in the diagnosis, and to rule out secondary causes of limb lymphedema or chylous effusions [5, 20]. Examples include lymphoscintigraphy, lymphangiogra- phy, and magnetic resonance lymphangiography [5, 20]. Abbreviations IVIG I IVIG: Intravenous immunoglobulin.; MCT: Medium chain triglycerides.; PIL: Primary intestinal lymphangiectasia.. Discussion and conclusion Examples include Turner, Noonan, and Hennekam syndromes [5, 12]. The lymphedema associated with PIL (whether syndromic or isolated) is typically bilateral [4, 5]. Hypoalbuminemia is another mechanism of edema in PIL, which in fact, is more common than lymphedema [1, 5]. The underlying pathophysiology is lymph loss in bowel lumen, from excessive dilation and eventually rupture of the already ectatic lymphatic vessels of small bowels [1, 5]. Intestinal lymph is rich in long chain tri- glycerides, lymphocytes, and proteins [13]. The result of excessive lymph loss is the characteristic steatorrhea, lymphopenia, edema, and hypoproteinemia including hypogammaglobulinemia [1, 4, 5, 13]. Interestingly, the case herein predominantly had a combined pitting and non-pitting unilateral edema, despite presenting with- systemic manifestations and visceral involvement (PIL and ascites). i The most serious but rare long-term complication reported in PIL is intestinal B cell lymphoma [4, 24]. Other complications include nutritional deficiencies, lower extremity cellulitis, and the effects of chronic foot swelling on quality of life [5, 23]. In conclusion, PIL is a rare disorder that typically pre- sents with protein-losing enteropathy, diarrhea, and bilateral lower limb edema. Nonetheless, unilateral lower limb edema (non-pitting more so than pitting) should not preclude the diagnosis of a systemic disorder, and a high index of suspicion is required in atypical presentations. A good knowledge about PIL, and physical examination skills to differentiate edema or lymphedema from tissue overgrowth can significantly aid in the diagnosis. PIL responds well to dietary modification, but needs long- term monitoring into adulthood, for potentially serious complications. The most common clinical presentation in PIL includes bilateral lower extremity edema and intermit- tent or chronic diarrhea [4, 5, 14]. As discussed earlier, The edema is mainly pitting; due to hypoalbuminemia, but could rarely be non-pitting as well, when it is due to lymphedema [5, 11, 15, 16]. It is oftentimes difficult to distinguish them, especially when both are present [5]. Stemmer’s sign can be helpful in such cases, where a positive sign (the inability to pinch the skin at the dor- sum of the second toe) indicates lymphedema, rather than pitting edema [5, 17]. Other clinical manifesta- tions of PIL including abdominal mass, chylous effusion (ascitic, pleural, or pericardial), generalized anasarca, and intestinal mechanical obstruction have been rarely reported [5, 18, 19]. Declarations and pharmacological perspective. Open Access Macedonian J Med Sci. 2018;6:1682–4. and pharmacological perspective. Open Access Macedonian J Med Sci. 2018;6:1682–4. Ethics approval and consent to participate Not applicable. 11. Vardy PA, Lebenthal E, Shwachman H. Intestinal lymphagiectasia: a reap- praisal. Pediatrics. 1975;55:842–51. 12. Hennekam RC, Geerdink RA, Hamel BC, et al. Autosomal recessive intestinal lymphangiectasia and lymphedema, with facial anomalies and mental retardation. Am J Med Genet. 1989;34:593–600. intestinal lymphangiectasia and lymphedema, with facial References Very late onset small intestinal B cell lymphoma associated with primary intestinal lymphangiectasia and diffuse cutaneous warts. Gut. 2000;47:296–300. 8. Hoyme HE, Seaver LH, Jones KL, Procopio F, Crooks W, Feingold M. Isolated hemihyperplasia (hemihypertrophy): report of a prospective multicenter study of the incidence of neoplasia and review. Am J Med Genet. 1998;79:274–8. 9. Clericuzio CL, Martin RA. Diagnostic criteria and tumor screening for individuals with isolated hemihyperplasia. Genetics Med 2009;11:220–2. Consent for publication mental retardation. Am J Med Genet. 1989;34:593–600. I have obtained a written consent from the patient’s legal guardian to publish the case. 13. Alexander JS, Ganta VC, Jordan PA, Witte MH. Gastrointestinal lymphatics in health and disease. Pathophysiology. 2010;17:315–35. 13. Alexander JS, Ganta VC, Jordan PA, Witte MH. Gastrointe in health and disease. Pathophysiology. 2010;17:315–35. 14. Mushtaq I, Cheema HA, Malik HS, Waheed N, Hashmi MA, Malik HS. Causes of chronic non-infectious diarrhoea in infants less than 6 months of age: rarely recognized entities. JAMC. 2017;29:78–82. Funding No funding received for this work. Khayat BMC Gastroenterol (2021) 21:225 Page 5 of 5 Khayat BMC Gastroenterol Received: 28 October 2020 Accepted: 11 May 2021 Received: 28 October 2020 Accepted: 11 May 2021 festations. J Am Acad Dermatol. 2017;77:1009–20. 16. Boursier V, Vignes S. [Limb lymphedema as a first manifestation of primary intestinal lymphangiectasia (Waldmann’s disease)]. J Maladies Vascul. 2004;29:103–6. 17. Goss JA, Greene AK. Sensitivity and specificity of the stemmer sign for lymphedema: a clinical lymphoscintigraphic study. Plast Reconst Surg Global Open. 2019;7:e2295. References 1. Waldmann TA, Steinfeld JL, Dutcher TF, Davidson JD, Gordon RS. Jr. The role of the gastrointestinal system in “idiopathic hypoproteinemia”. Gas- troenterology. 1961;41:197–207. 1. Waldmann TA, Steinfeld JL, Dutcher TF, Davidson JD, Gordon RS. Jr. The role of the gastrointestinal system in “idiopathic hypoproteinemia”. Gas- troenterology. 1961;41:197–207. 18. Lenzhofer R, Lindner M, Moser A, Berger J, Schuschnigg C, Thurner J. Acute jejunal ileus in intestinal lymphangiectasia. Clin Investigator. 1993;71:568–71. 2. Isa HM, Al-Arayedh GG, Mohamed AM. Intestinal lymphangiectasia in children. A favorable response to dietary modifications. Saudi Med J. 2016;37:199–204. 19. Rao R, Shashidhar H. Intestinal lymphangiectasia presenting as abdomi nal mass. Gastrointest Endosc. 2007;65:522–3 (discussion 3) 19. Rao R, Shashidhar H. Intestinal lymphangiectasia presenting as abdomi- nal mass. Gastrointest Endosc. 2007;65:522–3 (discussion 3) 3. Valdovinos-Oregón D, Ramírez-Mayans J, Cervantes-Bustamante R, et al. [Primary intestinal lymphangiectasia: twenty years of experience at a Mexican tertiary care hospital]. Rev Gastroenterol Mexico. 2014;79:7–12. 20. Kamble RB, Shetty R, Diwakar N, Madhusudan G. Technical note: MRI lymphangiography of the lower limb in secondary lymphedema. Indian J Radiol Imaging. 2011;21:15–7. 4. Wen J, Tang Q, Wu J, Wang Y, Cai W. Primary intestinal lymphangi- ectasia: four case reports and a review of the literature. Dig Dis Sci. 2010;55:3466–72. 21. Łoś-Rycharska E, Kieraszewicz Z, Czerwionka-Szaflarska M. Medium chain triglycerides (MCT) formulas in paediatric and allergological practice. Przeglad gastroenterologiczny. 2016;11:226–31. 5. Vignes S, Bellanger J. Primary intestinal lymphangiectasia (Waldmann’s disease). Orphanet J Rare Dis. 2008;3:5. 22. Bui A, Long CJ, Breitzka RL, Wolovits JS. Evaluating the use of octreotide for acquired chylothorax in pediatric critically Ill patients following cardiac surgery. JPPT. 2019;24:406–15. 6. Tiwari A, Cheng K-S, Button M, Myint F, Hamilton G. Differential diagnosis, investigation, and current treatment of lower limb lymphedema. Arch Surg. 2003;138:152–61. g y 23. Braamskamp MJ, Dolman KM, Tabbers MM. Clinical practice. Protein- losing enteropathy in children. Eur J Pediatrics. 2010;169:1179–85. 23. Braamskamp MJ, Dolman KM, Tabbers MM. Clinical practice. Protein- losing enteropathy in children. Eur J Pediatrics. 2010;169:1179–85. 7. Jones GE, Mansour S. An approach to familial lymphoedema. Clin Med. 2017;17:552–7. 24. Bouhnik Y, Etienney I, Nemeth J, Thevenot T, Lavergne-Slove A, Matuchan- sky C. Very late onset small intestinal B cell lymphoma associated with primary intestinal lymphangiectasia and diffuse cutaneous warts. Gut. 2000;47:296–300. 24. Bouhnik Y, Etienney I, Nemeth J, Thevenot T, Lavergne-Slove A, Matuchan- sky C. Conflict of interest None to declare. g y g 15. Grada AA, Phillips TJ. Lymphedema. Pathophysiology and clinical man festations. J Am Acad Dermatol. 2017;77:1009–20. 15. Grada AA, Phillips TJ. Lymphedema. Pathophysiology a Publisher’s Note S N Springer Nature remains neutral with regard to jurisdictional claims in pub- lished maps and institutional affiliations. 10. Meshram GG, Kaur N, Hura KS. Unilateral primary congenital lymphedema of the upper limb in an 11-month-old infant: a clinical • fast, convenient online submission • thorough peer review by experienced researchers in your field • rapid publication on acceptance • support for research data, including large and complex data types • gold Open Access which fosters wider collaboration and increased citations maximum visibility for your research: over 100M website views per year • At BMC, research is always in progress. Learn more biomedcentral.com/submissions Ready to submit your research Ready to submit your research ? 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Analisis Pengetahuan, Sikap dan Perilaku Berisiko Tertular Human Immunodeficiency Virus/Acquired Immuno Deficiency Syndrome (Hiv/Aids)
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ABSTRAK , Latar Belakang : Human immunodeficiency virus (HIV) menargetkan sistem kekebalan tubuh dan melemahkan sistem pertahanan manusia terhadap infeksi dan beberapa jenis kanker. Ketika virus merusak fungsi sel-sel kekebalan, individu yang terinfeksi secara bertahap menjadi imunodefisiensi. Tujuan : Meningkatkan kerentanan terhadap berbagai infeksi, kanker, dan penyakit lain yang dapat dilawan oleh orang dengan sistem kekebalan tubuh yang sehat. Metode : Metode penelitian yang digunakan yaitu desain penelitian deskriptif. Penentuan responden menggunakan purposive sampling dan diperoleh sebanyak 89 responden. Pengumpulan data berupa pengisian kuesioner dan studi dokumentasi. Dalam penelitian ini telah dilakukan uji etik oleh Lembaga Etik STIKes Budi Luhur Cimahi. Hasil : Hasil penelitian menunjukkan bahwa dalam rumah tahanan negara kelas I Bandung Hampir setengahnya memiliki tingkat pengetahuan yang cukup dengan jumlah responden sebanyak 36 responden, Sebagian besar memiliki sikap mendukung untuk mencegah penularan HIV/AIDS dengan jumlah responden 54 responden, Sebagian besar memiliki berisiko tertular HIV/AIDS dengan jumlah responden 48 responden. Kesimpulan : Analisis tingkat Pengetahuan terhadap warga binaan hampir setengahnya memiliki tingkat pengetahuan yang cukup dengan jumlah responden sebanyak 36 responden. Keywords: Pengetahuan, Sikap dan Perilaku Berisiko, HIV/AIDS, Warga binaan Info Artikel : Diterima : 29 Januari 2022 Info Artikel : Diterima : 29 Januari 2022 Keywords: Knowledge, Attitudes and risk behavior, HIV/AIDS, Assisted residents JURNAL 1,2,3Program Studi D3 Kebidanan, STIKes Budi Luhur Cimahi, Indonesia Corresponding Author : Sri Wahyuni¹ Email : uni.budiluhur@gmail.com1, g widya.p.astuti@gmail.com2 dan imamsamadji@gmail.com3 Keywords: Pengetahuan, Sikap dan Perilaku Berisiko, HIV/AIDS, Warga binaan PENDAHULUAN Secara global hingga pertengahan tahun 2015 terdapat 15,8 juta orang yang hidup dengan HIV dan 2,0 juta orang baru terinfeksi HIV serta terdapat 1,2 juta orang meninggal karena penyebab terkait HIV (Ardhiyanti, Lusiana, & Megasari, 2015). Diperkirakan 0,8% dari orang dewasa berusia 15-49 tahun di seluruh dunia hidup dengan HIV. Berdasarkan Laporan Perkembangan HIV/AIDS dan Infeksi Seksual Menular tahun 2017 oleh Kementerian Kesehatan Republik Indonesia, jumlah kumulatif infeksi HIV sampai dengan Desember 2017 di Indonesia adalah sebanyak 280.263 kasus, dengan jumlah kumulatif AIDS sebanyak 102.667 kasus terhitung dari tahun 1987 hingga Desember 2017 (Yusran & Rezal, n.d.). Dalam laporan yang sama juga ditemukan bahwa jumlah penemuan kasus infeksi baru HIV dan AIDS mengalami peningkatan setiap tahunnya. Data ini mengindikasikan peningkatan jumlah penularan infeksi HIV di Indonesia. HIV AIDS dapat menyerang setiap orang, dengan komunitas Lesbian, Gay, Bisexual, and Transgender (LGBT), pekerja seksual, pengguna jarum suntik bersama, dan penghuni lapas sebagai populasi kunci yang memiliki risiko penularan tinggi (Sembiring & Yeni, 2021). Berdasarkan data yang diterima dari Dinas Kesehatan Jawa Barat kumulatif kasus HIV/AIDS di Jawa Barat dari tahun 2006-2017 mengalami kenaikan signifikan. Dan jika dibagi menjadi per Kabupaten/Kota ternyata Kota Bandung menduduki peringkat pertama dengan 945 kasus sepanjang 2018. Berdasarkan data dari Dinas Kesehatan Kota Bandung periode 2017-2019 yang ditemukan dalam kondisi HIV ialah 935 kasus dan yang ditemukan dalam keadaan AIDS adalah 380 kasus, yang meninggal sebanyak 22 orang sisanya sedang dalam perawatan. Menurut data dari Sistem Database Permasyarakatan (SDP) diambil dari seluruh Kantor Wilayah Seluruh Indonesia di awal bulan Februari 2020 terdapat 894 warga binaan yang terkena HIV/AIDS dan 9.601 yang berisiko terkena HIV/AIDS. Sedangkan di tingkat kantor wilayah Jawa Barat terdapat 117 warga binaan yang terkena HIV/AIDS dan 300 yang berisiko terkena HIV/AIDS. Lebih mendalam lagi terhadap RUTAN yang berada di Jawa Barat yaitu RUTAN Kelas I Bandung terdapat 7 warga binaan yang terkena HIV/AIDS dan 10 yang berisiko terkena HIV/AIDS akibat penggunaan narkoba suntik. Pengetahuan merupakan hasil dari tahu, dan ini terjadi setelah orang melakukan pengindraan terhadap suatu objek tertentu. Pengindraan terhadap obyek terjadi melalui panca indra manusia yakni penglihatan, pendengaran, penciuman, rasa dan raba dengan sendiri (Indah, Aswitami, & Diantari, 2020). Sikap merupakan reaksi atau respon seseorang yang masih tertutup terhadap stimulus atau objek (Ayu & Kurniawati, 2017). ABSTRACT Background : Human immunodeficiency virus (HIV) targets the immune system and weakens the human defense system against infections and some types of cancer. When the virus impairs the function of immune cells, the infected individual gradually becomes immunodeficient. Purpose : Increases susceptibility to various infections, cancers, and other diseases that people with healthy immune systems can fight off. Method : The research method used is descriptive research design. Determination of respondents using purposive sampling and obtained as many as 89 respondents. Data collection is in the form of filling out questionnaires and studying documentation. In this study, an ethical test was carried out by the Budi Luhur Cimahi Institute of Ethics for STIKes. Results : The results showed that in class I state detention centers in Bandung, almost half of them had a sufficient level of knowledge with 36 respondents, most had a supportive attitude to prevent HIV/AIDS transmission with 54 respondents, most were 244 http://sosains.greenvest.co.id 2022 Analisis Pengetahuan, Sikap dan Perilaku Beresiko Tertular Human Immunodeficiency Virus/Acquired Immuno Deficiency Syndrome (HIV/AIDS) at risk of contracting HIV/AIDS. with the number of respondents 48 respondents. Conclusion : Knowledge level analysis of the inmates Almost half of them have a sufficient level of knowledge with a total of 36 respondents. at risk of contracting HIV/AIDS. with the number of respondents 48 respondents. Conclusion : Knowledge level analysis of the inmates Almost half of them have a sufficient level of knowledge with a total of 36 respondents. Sri Wahyuni, Widya Putriastuti dan Imam Samiadji PENDAHULUAN Sikap adalah predisposisi untuk melakukan atau tidak melakukan suatu perilaku tertentu, sehingga sikap bukan hanya kondisi internal psikologis yang murni dari individu, sikap merupakan kesadaran yang sifatnya individual (Fadlilah & Rahil, 2019). Artinya proses ini terjadi secara subjektif dan unik pada diri setiap individu. Perilaku adalah respon individu terhadap suatu stimulus atau suatu tindakan yang dapat diamati dan mempunyai frekuensi spesifik, durasi dan tujuan baik disadari maupun tidak (Kurniawati & Wardani, 2020). Perilaku merupakan kumpulan berbagai faktor yang saling berinteraksi. Sehubungan dengan hal tersebut penulis tertarik untuk melakukan penelitian dengan judul “Analisis Pengetahuan, Sikap dan Perilaku Berisiko tertular Human Immunodeficiency Virus / Acquired Immuno Deficiency Syndrome (HIV/AIDS) Di Rumah Tahanan Negara Kelas I Bandung Tahun 2020”. Penelitian ini dimaksudkan untuk mengetahui analisis Sri Wahyuni, Widya Putriastuti dan Imam Samiadji 245 Volume 2, Nomor 2, Februari 2022 p-ISSN 2774-7018 ; e-ISSN 2774-700X Volume 2, Nomor 2, Februari 2022 p-ISSN 2774-7018 ; e-ISSN 2774-700X pengetahuan, sikap dan perilaku berisiko tertular Hu man Immunodeficiency Virus / Acquired Immuno Deficiency Syndrome (HIV/AIDS) di Rumah Tahanan Negara Kelas I Bandung. Tujuan penelitian ini adalah Meningkatkan kerentanan terhadap berbagai infeksi, kanker, dan penyakit lain yang dapat dilawan oleh orang dengan sistem kekebalan tubuh yang sehat. pengetahuan, sikap dan perilaku berisiko tertular Hu man Immunodeficiency Virus / Acquired Immuno Deficiency Syndrome (HIV/AIDS) di Rumah Tahanan Negara Kelas I Bandung. Tujuan penelitian ini adalah Meningkatkan kerentanan terhadap berbagai infeksi, kanker, dan penyakit lain yang dapat dilawan oleh orang dengan sistem kekebalan tubuh yang sehat. Analisis Pengetahuan, Sikap dan Perilaku Beresiko Tertular Human Immunodeficiency Virus/Acquired Immuno Deficiency Syndrome (HIV/AIDS) Analisis Pengetahuan, Sikap dan Perilaku Beresiko Tertular Human Immunodeficiency Virus/Acquired Immuno Deficiency Syndrome (HIV/AIDS) 2022 1. Pengetahuan Berdasarkan hasil penelitian yang tercantum tentang tingkat pengetahuan pada warga binaan didapatkan bahwa dari analisa tentang tingkat pengetahuan pada warga binaan didapatkan bahwa dari 89 responden, sebagian responden memiliki tingkat pengetahuan baik sebanyak 27 responden (30,3%) sedangkan responden memiliki tingkat pengetahuan cukup sebanyak 36 responden (40,4%) dan responden yang memiliki tingkat pengetahuan kurang sebanyak 26 responden (29,2%). Hasil penelitian tersebut menjelaskan bahwa sebagian besar responden memiliki tingkat pengetahuan yang cukup. Adapun kejadian tingkat pengetahuan yang baik sebanyak 27 responden dan tingkat pengetahuan yang kurang sebanyak 26 responden. Pengetahuan tentang HIV/AIDS ditemukan cukup, namun masih ada kesalahpahaman tentang HIV/AIDS pada warga binaan sehingga masih diperlukan edukasi untuk memperbaiki hal tersebut (Ristianadewi, Septimar, & Wibisono, 2021). Individu mampu mengingatkan kesehatan dengan cara meningkatkan pengetahuan. Teori tersebut menekankan pada kemampuan warga binaan untuk beradaptasi dalam meningkatkan pengetahuan tentang HIV/AIDS dengan cara menanyakan kepada teman seruangan maupun kepada petugas. Seseorang yang terpaksa tinggal di lembaga permasyarakatan karena menjalani hukuman akan mempengaruhi kondisinya. Mereka akan mengalami kesulitan untuk menyesuaikan kehidupan nya di lembaga permasyarakatan, tetapi mereka harus tetap mengikuti aturan-aturan yang berlaku di lembaga permasyarakatan. Selain itu, mereka juga harus terpisah dari keluarganya, teman sebayanya, kehilangan kebebasan untuk tinggal diluar. Hal tersebut akan menyebabkan seseorang mendapat tekanan karena hidup di lembaga permasyarakatan, untuk meningkatkan pengetahuan warga binaan tentang bahayanya tertular HIV/AIDS maka disini harus dilakukan edukasi dan penyuluhan kesehatan oleh petugas untuk menambah wawasan mengenai bahayanya tertular HIV/AIDS (Irawan, 2018). METODE PENELITIAN Penelitian ini menggunakan rancangan desain penelitian deskriptif. Metode penelitian deskriptif ini dilakukan untuk mengetahui keberadaan variabel mandiri, baik hanya pada satu variabel atau lebih (variabel yang berdiri sendiri atau variabel bebas) tanpa membuat perbandingan variabel itu sendiri dan mencari hubungan dengan variabel lain (Sugiyono, 2013). Populasi dalam penelitian ini adalah warga binaan sebanyak 828 responden. Teknik pengambilan sampel yang digunakan yaitu purposive sampling dengan jumlah sampel sebanyak 89 responden. Penelitian dilakukan di Rumah Tahanan Negara Kelas I Bandung. Analisis data pada penelitian ini menggunakan analisa univariat, analisa univariat adalah analisis yang bertujuan untuk mendeskripsikan atau menjelaskan karakteristik setiap variabel penelitian. Untuk mencegah timbulnya masalah etik, maka peneliti telah melakukan izin etik dan penelitian ini telah terdaftar di komisi Etik Penelitian dan Pengembangan Kesehatan Nasional (KEPPKN) Kementrian Kesehatan Republik Indonesia, dalam surat keterangan nomor :31/D/KEPK-STIKes/VIII/2020 dengan nomor kodefikasi : 3277042S, melakukan informed concent, menjaga kerahasiaan responden, memberikan manfaat terhadap penelitian yang sudah dilakukan dan menjaga keadilan antara responden yang satu dengan responden yang lainnya. HASIL DAN PEMBAHASAN Tabel 1. Hasil frekuensi tingkat Pengetahuan Tingkat Pengetahuan Frekuensi Persentase (%) Baik 27 30,3 % Cukup 36 40,4 % Kurang 26 29,2% Total 89 100 % Sumber : Data Primer 2020 Tabel 2. Hasil frekuensi Sikap Sikap Frekuensi Persentase (%) Mendukung 54 60,7 % Kurang Mendukung 35 39,3 % Total 89 100 % Sumber : Data Primer 2020 Tabel 3. Hasil frekuensi Perilaku Berisiko Sikap Frekuensi Persentase (%) Tidak Berisiko 41 46,1 % Berisiko 48 53,9 % Total 89 100 % Sumber : Data Primer 202 HASIL DAN PEMBAHASAN Tabel 1. http://sosains.greenvest.co.id 246 Analisis Pengetahuan, Sikap dan Perilaku Beresiko Tertular Human Immunodeficiency Virus/Acquired Immuno Deficiency Syndrome (HIV/AIDS) Sri Wahyuni, Widya Putriastuti dan Imam Samiadji 2. Sikap Berdasarkan hasil penelitian yang tercantum tentang sikap pada warga binaan didapatkan bahwa dari analisa tentang sikap pada warga binaan didapatan bahwa dari 89 responden, sebagian besar responden memiliki sikap mendukung sebanyak 54 responden (60,7%) dan sebagian responden sebanyak 35 (39,3 %) memiliki sikap kurang mendukung. Hasil penelitian tersebut menjelaskan bahwa sebagian besar responden memiliki sikap yang mendukung sebanyak 54 responden adapun 35 responden yang lainnya memiliki sikap kurang mendukung. Hasil ini sesuai dengan yang di paparkan oleh Nur Arifatun dan Dyah mahendrasari yang menyatakan bahwa warga binaan memiliki sikap yang mendukung. Berdasarkan hasil jawaban yang diperoleh sebagian besar responden memiliki sikap yang mendukung yaitu sebanyak 36 responden (55,4%) warga binaan setuju berperilaku sehat agar terhindar dari penularan HIV/AIDS dan responden yang memiliki sikap kurang mendukung sebanyak 29 responden (44,6) (Fachmi, Miharja, & Harianto, 2016). Teori Sister Callista Roy menjelaskan tentang bagaimana individu mampu mengingkatkan kesehatan dengan cara mempertahankan sikap yang mendukung. Teori tersebut menekankan pada kemampuan warga binaan untuk beradaptasi dalam meningkatkan sikap yang mendukung tentang HIV/AIDS. Seseorang yang terpaksa tinggal di lembaga permasyarakatan karena menjalani hukuman akan mempengaruhi kondisinya (Fajarani, 2017). Mereka akan mengalami kesulitan untuk menyesuaikan kehidupan nya di lembaga permasyarakatan, tetapi mereka harus tetap mengikuti aturan-aturan yang berlaku di lembaga permasyarakatan. Selain itu, mereka juga harus terpisah dari keluarganya, teman sebayanya, kehilangan kebebasan untuk tinggal diluar. Hal tersebut akan Sri Wahyuni, Widya Putriastuti dan Imam Samiadji Sri Wahyuni, Widya Putriastuti dan Imam Samiadji 247 Volume 2, Nomor 2, Februari 2022 p-ISSN 2774-7018 ; e-ISSN 2774-700X Volume 2, Nomor 2, Februari 2022 p-ISSN 2774-7018 ; e-ISSN 2774-700X menyebabkan seseorang mendapat tekanan karena hidup di lembaga permasyarakatan, untuk meningkatkan sikap yang mendukung untuk tidak tertular HIV/AIDS. Proses komunkasi yang terjalin antar warga binaan yang satu dengan yang lainnya ataupun dengan petugas rumah tahanan serta kerabat yang datang untuk menjenguk berindikasi terhadap segala bentuk proses perubahan komunikasi seorang warga binaan di rumah tahanan. Komunikasi tidak terlepas dari peran komunikator, dalam hal ini komunikasi seorang warga binaan di rumah tahanan melalui komunkasi yang saling mengungkapkan perasaan emosi, pendapat dan tujuan. Sehingga terjalin komunkasi yang efektik didalamnya untuk bersikap mendukung supaya tidak terkena HIV/AIDS selama di dalam rumah tahanan, sedangkan jika seorang warga binaan kurang komunkasi antar teman sesama warga binaan,petugas maupun kerabat akan dipastikan warga binaan mempunyai sikap yang kurang mendukung terhadap penularan HIV/AIDS di rumah tahanan. KESIMPULAN Berdasarkan pembahasan dari hasil penelitian yang berjudul “Analisis Pengetahuan, Sikap dan Perilaku Berisiko tertular Human Immunodeficiency Virus/Acquired Immuno Deficiency Syndrome (HIV/AIDS) di Rumah Tahanan Negara Kelas I Bandung” yang dilakukan pada tanggal 22-29 Juni 2020 terhadap 89 responden dengan tujuan umum untuk mengetahui Analisis Pengetahuan, Sikap dan Perilaku Berisiko tertular Human Immunodeficiency Virus/ Acquired Immuno Deficiency Syndrome (HIV/AIDS) di Rumah Tahanan Negara Kelas I Bandung dan untuk menafsirkan persepsi jawab dibuat pedoman tafsiran yang diambil dari sughiyono, maka dapat disimpulkan bahwa: Analisis tingkat Pengetahuan terhadap warga binaan Hampir setengahnya memiliki tingkat pengetahuan yang cukup dengan jumlah responden sebanyak 36 responden. Analisis Sikap pada warga binaan Sebagian besar memiliki sikap mendukung untuk mencegah penularan HIV/AIDS dengan jumlah responden 54 responden. Analisis Perilaku Berisiko pada warga binaan sebagian besar memiliki berisiko tertular HIV/AIDS dengan jumlah responden 48 responden. Sri Wahyuni, Widya Putriastuti dan Imam Samiadji 3. Perilaku Berisiko Berdasarkan hasil penelitian yang tercantum tentang perilaku berisiko pada warga binaan didapatkan bahwa dari analisa tentang perilaku berisiko pada warga binaan didapatkan bahwa dari 89 responden, sebagian besar responden berisiko tertular HIV/AIDS dengan perilaku menggunakan jarum suntik secara bergantian dan membuat tindik secara bergantian sebanyak 48 responden (53,9%) dan sebagian responden sebanyak 41(46,1%) tidak berisiko tertular HIV/AIDS. Hasil penelitian tersebut menjelaskan bahwa sebagian besar responden berjumlah 89 orang yang berisiko tertular HIV/AIDS (tindakan penggunaan jarum suntik NAPZA, tindakan terkait hubungan seksual berisiko, dan tindakan lainnya) sebanyak 48 responden (53,9%) berisiko terkena HIV/AIDS sedangkan sebagian kecil responden sebanyak 41 orang (46,1%) tidak berisiko terkena HIV/AIDS. Hasil ini sesuai dengan yang di paparkan oleh Mondesari,dkk (2016) yang menyatakan bahwa warga binaan yang berisiko tertular HIV/AIDS masih banyak. Berdasarkan hasil penelitian dapat diketahui bahwa responden yang berisiko tertular HIV/AIDS yaitu sebanyak 50 orang (93%), sedangkan yang tidak melakukan berisiko tertular HIV/AIDS sebanyak 4 orang (7%). Model adaptasinya dalam tatanan pelayanan keperawatan terdiri dari tujuan keperawatan dan aktivitas keperawatan. Kebutuhan akan pelayanan keperawatan timbul saat klien tidak dapat beradaptasi dengan tekanan lingkungan internal maupun eksternal. Warga binaan yang baru ataupun lama juga melakuan proses adaptasi, dimana warga binaan tersebut harus melakukan tindakan pencegahan mengenai perilaku berisiko agar tidak terkena penyakit HIV/AIDS. Hal ini sesuai dengan yang diungkapkan Nur Arifatun dan Dyah mahendrasari (2017) yang menyatakan bahwa 21 orang berperilaku berisiko dan 44 orang tidak berisiko, ini disebabkan sering diadakan nya penyuluhan tentang HIV/AIDS dan NAPZA secara rutin dan merata kepada semua warga binaan, meningkatkan kegiatan penanggulangan HIV/AIDS oleh petugas terutama pada awal napadina pertama kali masuk menjadi warga binaan rumah tahanan. Populasi warga binaan (narapidana) di lapas adalah juga merupakan salah satu populasi kunci yang penting dalam penyebaran HIV di Indonesia. Perilaku menggunakan narkotika suntik, pengaruhnya sangat kuat dan bermakna secara statistik terhadap risiko terkena infeksi HIV. Secara keseluruhan, faktor-faktor (determinan) yang dapat meningkatkan risiko terinfeksi HIV secara bermakna di kalangan para warga binaan dilapas/rutan di Indonesia adalah: berbagi jarum suntik tidak steril, kontak seksual dengan sesama warga binaan, terinfeksi PMS (khususnya sifilis) dan memakai tato dan tindik. 248 http://sosains.greenvest.co.id 2022 Analisis Pengetahuan, Sikap dan Perilaku Beresiko Tertular Human Immunodeficiency Virus/Acquired Immuno Deficiency Syndrome (HIV/AIDS) REFERENCES Ardhiyanti, Yulrina, Lusiana, Novita, & Megasari, Kiki. (2015). Bahan ajar AIDS pada asuhan kebidanan. Yogyakarta: Deepublish. Ayu, Suci Musvita, & Kurniawati, Tri. (2017). Hubungan Tingkat Pengetahuan Remaja Putri Tentang Aborsi Dengan Sikap Remaja Terhadap Aborsi Di Man 2 Kediri Jawa Timur. Unnes Journal of Public Health, 6(2), 97–100. Fachmi, Sintha Noor, Miharja, Ediyar, & Harianto, Joanggi. (2016). Hubungan antara Tingkat Kecemasan dengan Sikap Perawat dalam Penanganan Kekambuhan Pasien Perilaku Kekerasan di RSJD Atma Husada Mahakam Samarinda Tahun 2016. Fadlilah, Siti, & Rahil, Nazwar Hamdani. (2019). Faktor-Faktor Yang Berhubungan Dengan Perilaku Pencegahan Cidera Muskuloskeletal Pada Pemain Futsal. Jurnal Keperawatan BSI, 7(1). Fajarani, Anggit Saktika. (2017). Tingkat stres dan harga diri narapidana wanita di lembaga pemasyarakatan kelas II A Kota Bogor. Jurnal Riset Kesehatan Poltekkes Depkes Bandung, 9(2), 26–33. Indah, Pande Putu Indah Purnamayanthi, Aswitami, Ni Gusti Ayu Pramita, & Diantari, Ni Putu Ayu Mita. (2020). Gambaran Tingkat Pengetahuan Ibu Hamil Trimester III Tentang Tanda Bahaya Persalinan. Journal Center of Research Publication in Midwifery and Nursing, 4(2), 28–32. Irawan, Doni. (2018). Pengaruh Pendidikan Kesehatan Dengan Metode Pembelajaran Didaktif (Ceramah) Dan Sokratik (Buzz Group) Terhadap Tingkat Pengetahuan Mengenai Bahaya Perilaku Merokok Pada Peserta Didik Madrasah Tsanawiyah Al- Hidayah Sukawening. Kurniawati, Novi, & Wardani, Riska Aprilia. (2020). Hubungan Persepsi Remaja Tentang Perilaku Seksual Pranikah Dan Perilaku Seksual Pranikah Pada Remaja. Jurnal Keperawatan, 13(2), 11. Ristianadewi, Hannny Putri, Septimar, Zahrah Maulidia, & Wibisono, Ahmad Yusuf Gunawan. (2021). Perilaku Berisiko Dan Perilaku Pencegahan Tertular Penyakit Hiv/Aids Di Lembaga Pemasyarakatan Pada Tahun 2020. Nusantara Hasana Sri Wahyuni, Widya Putriastuti dan Imam Samiadji 249 Volume 2, Nomor 2, Februari 2022 p-ISSN 2774-7018 ; e-ISSN 2774-700X Volume 2, Nomor 2, Februari 2022 p-ISSN 2774-7018 ; e-ISSN 2774-700X Volume 2, Nomor 2, Februari 2022 p-ISSN 2774-7018 ; e-ISSN 2774-700X Volume 2, Nomor 2, Februari 2022 p-ISSN 2774-7018 ; e-ISSN 2774-700X Journal, 1(2), 130–137. Sembiring, Rony Pramana, & Yeni, Yeni. (2021). Analisis Faktor Yang Berhubungan Dengan Pencegahan Penularan Hiv/Aids Pada Warga Binaan Pemasyarakatan (Wbp) Di Lembaga Pemasyarakatan Kelas I Palembang Sumatera Selatan. Palembang: Sriwijaya University. Sugiyono, Dr. (2013). Metode penelitian pendidikan pendekatan kuantitatif, kualitatif dan R&D. Yusran, Sartiah, & Rezal, Farit. (n.d.). Kajian Empiris Stigma terhadap ODHA pada Masyarakat di Kota Kendari. Jurnal Wawasan Promosi Kesehatan, 1(1). This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License. 250 http://sosains.greenvest.co.id
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https://repozytorium.biblos.pk.edu.pl/redo/resources/30699/file/suwFiles/KozlowskiT_ArchitecturalSculpture.pdf
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Architectural sculpture
Brill’s New Pauly
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*  Ph.D. Arch. Tomasz Kozłowski, Department of Housing Architecture and Architectural Composition, Faculty of Architecture, Cracow University of Technology. ARCHITECTURAL SCULPTURE ARCHITEKTONICZNA RZEŹBA A b s t r a c t The paper presents the links between the different fields of art: painting, music, sculpture and architecture. The great influence of expressionist sculpture on architecture is emphasized. Modern buildings often look like built monuments. Architects like Zaha Hadid and Frank Ghery can distance themselves from their predecessors, but it seems to be evident that they unintentionally continue what was ‘born’ in the early twentieth century. A b s t r a c t The paper presents the links between the different fields of art: painting, music, sculpture and architecture. The great influence of expressionist sculpture on architecture is emphasized. Modern buildings often look like built monuments. Architects like Zaha Hadid and Frank Ghery can distance themselves from their predecessors, but it seems to be evident that they unintentionally continue what was ‘born’ in the early twentieth century. Keywords:  architecture, expressionism, new forms S t r e s z c z e n i e Tekst stara się pokazać powiązanie różnych dziedzin sztuki: malarstwa, muzyki, rzeźby i ar- chitektury. Wpływ, jaki rzeźba ekspresjonistyczna miała na architekturę, jest wielki. Współ- czesne budynki wyglądają niekiedy jak zbudowane pomniki. Architekci, tacy jak Zahy Hadid czy Franka Ghery, mogą odżegnywać się od poprzedników, ale może mimowolnie kontynuują to, co narodziło się na początku XX wieku. S t r e s z c z e n i e Tekst stara się pokazać powiązanie różnych dziedzin sztuki: malarstwa, muzyki, rzeźby i ar- chitektury. Wpływ, jaki rzeźba ekspresjonistyczna miała na architekturę, jest wielki. Współ- czesne budynki wyglądają niekiedy jak zbudowane pomniki. Architekci, tacy jak Zahy Hadid czy Franka Ghery, mogą odżegnywać się od poprzedników, ale może mimowolnie kontynuują to, co narodziło się na początku XX wieku. Słowa  kluczowe:  ekspresjonizm, architektura, rzeźba, dekompozycja *  Ph.D. Arch. Tomasz Kozłowski, Department of Housing Architecture and Architectural Composition, Faculty of Architecture, Cracow University of Technology. 48 It is difficult to define expressionist sculpture as a uniform style. The authors of The Encyclopedia of Expressionism tried to find two artistic trends making it easier to state its definition precisely. “One outlook prevailed among the German critics: sculpture revealed a considerable dose of openness to expressionism or rejected the existing conventions. According to the other outlook, expressionism means intensive expressiveness of forms going to such extremes as deformation and abstraction which results from an artist’s inner need”1. Expressionist sculpture created by artists belonging to the Die Brücke group, remained under the influence of primitive art. These authors explained their interest with the “primeval” expression of such works. Their creations often imitated African statuettes in a literal manner. Here again, artists talked about abandoning the past, meaning the immediate past, as usual. “The entire art of the late nineteenth century called art pompier, characterized by shameless odalisques, the nudity of classical deities as well as exaggerated historical references, can be easily identified as kitsch”2. Twentieth-century creation was expected to be different, free from passeism, more ideological, unorthodox and original. We can assume that an artist’s desire for the internal dynamics of a given work became a shared feature. That kind of  art combined various creative tendencies and included the achievements of such authors as Picasso, Barlach or Archipenko. Such a “primitive” style, which rejected the existing conventions of picturing destruction, ruins and absence in a metaphorical but also literal manner, can be exemplified by Ossip Zadkine’s sculpture entitled The Torn City also known as The Destroyed City (1951‒1953). The artist, defined as a post-cubist, created it by drilling the volumes deeply and producing a profoundly bombastic form3. Zadkine’s monument shows a human figure decomposed in the cubistic manner. In this case, we can say that the dramatic monument to the ruined city is a ruin or perhaps an expression itself. 1 L. Richard, Encyklopedia ekspresjonizmu, Warsaw 1996, 136. 2 U. Eco, Historia brzydoty, Poznan 2007, 400. 3 A. Borzeskowska, Całkiem nowe ruiny. Między romantyzmem a postmodernizmem, „Arteon” 2002, No. 5, 44-45. 4 A. Kotula, P. Krakowski, Rzeźba współczesna, Warsaw 1980, 117. S t r e s z c z e n i e Certainly, this work is expressive and full of curves – it bears the artist’s humane message concerning World War II and the bombings of the centre of Rotterdam in 1940. “Today’s young sculptor will borrow the daring concept of spontaneity and genuine freedom from Negro art in order to reach EXPRESSION”4. In  1994, Philip Johnson designed the visitor pavilion Glass House in  New Canaan, Connecticut. The author called this building, or maybe sculpture, Da Monsta which means a monster in hip-hop slang. It was constructed from plastered concrete laid upon a steel net. Provides an introduction to Johnson’s work. The entire estate together with some pavilion houses, a guesthouse, a painting gallery, a sculpture gallery and a library act as a museum these days. The entrance building itself consists of two intermingling irregular volumes with sharp edges. The middle is just the waiting room and the projection room. The author admits that he was inspired by Hermann Finsterlin’s art. However, it may be his authorial interpretation of the expressionism of the early twentieth century. The bodies forming a  part of this composition as well as  the  colours of the “elevations” become aggressive. Their redness and greyness help a visitor to find the shapes which formed this 49 pavilion. The work proves that a new monument need not be large – it can have a “regular” human scale. In the other outlook, one can search out some inspirations for the minimalist sculpture The Broken Obelisk (1967) created in Houston by an artist from the circle of abstract expressionism – Barnett Newman. It shows an elegant composition of “post-elementary” volumes against the background of an equally smart modernist architecture without causing discomfort through its instability. The artist moves towards abstraction but the onlooker’s attention is temporarily occupied by the “chipped” top of the slender quadratic prism which crowns the composition with its unreliable spot support. The following questions arise: Is this the beginning of an interrupted composition or the closing of a ruined one? Was the whole the basis for something bigger or can this thing be continued like The Endless Column by Constantine Brancusi? The present time has given architects some tools for creating new structures that could not be built by the expressionists of the early twentieth century. 5 M. Misiągiewicz, O prezentacji idei architektonicznej, Krakow 1999, 114. 6 D. Sharp, Modern Architecture and Expressionism, New York 1966, 98. S t r e s z c z e n i e Coop Himmelb(l)au’s Pavilion 21 MINI Opera 50 Space (2008‒2010) was built for the needs of the Munich Opera Festival 2010. Władysław Tatarkiewicz’s comments explaining various meanings of the word “beauty” could be its motto. The philosopher presented it as five definitions which best match the theory of beauty. “Namely: 1) Beauty is a simple quality characteristic of some things; 2) it is a particular shape characteristic of some things; 3) it is what arouses certain special emotions in people; 4)  it  is  the manifestation of a commonplace (typical, ideal) factor in  a  thing; 5) it is expression”7. The building is small and lacks decorations in the ordinary sense of the word. However, it becomes the essence of ornamentation itself. Its form is to correspond with the assignments it received. It is to be a place for a quest for new ways of perceiving art. The area is not big (560 m²) and has seats for 300 people only. The volume was shaped – as the authors claim – with a computer simulation of Jimi Hendrix’s song Purple Haze and the passages from Mozart’s Don Giovanni. Ideologically, this work resembles the Philips expositional pavilion designed by Le Corbusier in 1958. The building is an eyesore just like Finsterlin’s sculptures. On one hand, it encourages the passers-by to come closer and look at themselves in the polished metal; on the other hand, it scares them away like a fortress. However, the authors do not distance themselves from the functional explanation of the form of their work which is supposed to  absorb the noise from the  neighbouring streets. The  musical connotations are also important here considering the fleetingness of this work which, despite its considerable size, was disassembled and moved to another location to create a new category: “mobile architecture”. Referring to Wolf D. Prix’s words “Architecture should embrace, be passionate, smooth, hard, with sharp corners. It must be brutal, rounded, gentle, colourful, obscene, tempting, dreaming, alluring, surpassing, wet, dry, with a heartbeat. It has to be vital or lifeless. If it is cold, it must be stone-cold; if it is hot, it has to be as hot as fire. Architecture must burn”8, we could add that it should be an eyesore, too. In 1921, Walter Gropius designed Denkmal der Märzgefallenen (The Monument to the Casualties of the Kapp Putsch) whose form resembles an overturned obelisk with a  pyramid on top. S t r e s z c z e n i e Philip Johnson and John Burgee raised twin towers Puerta de Europa I and Puerta de Europa II – two leaning prisms, 114 metres tall, 15 degrees off the vertical – on one of Madrid’s boulevards. The chequered elevation of dark glass is decorated with a glittering frame in the corners of the building and in its centre. The slanting elevations are reinforced with some intersecting elements. Both towers are supported by enormous counterweights which facilitated construction. The structures were conceived as one spatial layout jointly creating a gateway to Europe and a new street perspective. A struggle against the gravitational forces forms the first leaning skyscrapers. Similarly to The Broken Obelisk, they fight with nature and win. Maria Misiągiewicz describes Hermann Finsterlin’s achievements: “…He treated a structure as a pointless and unequaled game of sublime forces included in rough matter frozen at the moment of the most profound reflection”5. As a young architect, Finsterlin created a number of utopian house designs. He was not an architect by profession. He decided to take up art after he had climbed Mount Watzmann at night and discovered the beauty of nature. In 1919, Walter Gropius invited him to take part in an exhibition of the Unknown Architects organized in Berlin. Similarly to Scharoun, Finsterlin created utopian designs but – contrary to Scharoun – he never managed to realize his visions. His designs were presented as clay sculptures, sharp, pointed, without right angles, sometimes resembling crystals. As Dennis Sharp writes, Finsterlin treated a building as a work of all the arts, a gigantic empty sculpture with unlimited possibilities of shaping the outside and the inside as well as only one requirement of esthetical balance.6 Such gesamtkunstwerk is  expressed in  a  combination  of  various domains of art: literature, painting, music, architecture. Finsterlin was also a poet, an essayist and a composer after all. The new approach to design was caused by his prophetic dream where he saw a completely new type of architecture with colourful bent walls, so different from the primitive cuboidal dwelling structure. The impact of such an outlook on architecture is still noticeable. While admiring the designs of The Mausoleum (1919) or The Little Guesthouse (1921), an association with some implemented designs by Coop Himmelb(l)au, Zaha Hadid or Frank Gehry comes to mind. 7 W. Tatarkiewicz, Dzieje sześciu pojęć, Warsaw 1975, 138. 8 Coop Himmelb(l)au, Architektur muß brennen, Graz 1980, V.M. Lampugnani, op. cit., 116. 9 P. Francastel, Sztuka a technika, Warsaw 1966, 275. S t r e s z c z e n i e However, it was built of concrete instead of stone. It was conceived to present a thunderbolt as a symbol of life. It was raised in 1922 and then destroyed by the fascists; its replica still stands on the grounds of the cemetery in Weimar. This work can make the prototype for Pavilion 21. Its form is uncompromising – with no ornaments, sharp, indicating the direction toward the sky. It could be explained with Pierre Francastel’s words: “Thus, a work of art is essentially an object of special nature, an imaginary object, i.e. a kind of sign transmitter which is not a pattern, an image which appeared in an artist’s mind, a picture he formed at the end of his work or an original image that emerges in every onlooker’s head. Since it includes this margin of indefiniteness, it can show specific yet fragmentary starting points. Moreover, it can express communicative reactions making us aware of one of the crucial features of a work of art and one of the possible tangent points between such apparently distant forms as an image and a building”9. In this case, a sculpture appears somewhere between an image and a building. The work looks as if it was moving – it is dynamic like in a motion picture. We do not know if this form goes up or down; 51 it becomes an expression of movement. The recipient feels like coming nearer and sustaining the  monument to save it from inescapable destruction. Perhaps it is a reminiscence of the strictly expressionist painting The Sea of Ice (1823‒1824) by the Romantic German artist Caspar David Friedrich. Looking at it, we are also uncertain if the ship was destroyed by the ice banks or absorbed by the concrete car park at the supermarket. “The assignment of art is not to facilitate general harmony but to come as a shock”10. These words uttered by the writer and poet Walter Husenclaver could act as the motto of contemporary art. Expressionist sculpture had a strong impact on architecture. Hans Poelzig’s design of Grosses Schauspielhaus (1919) in Berlin is one huge monument. Hermann Finsterlin’s buildings assumed the form of sculptural models only. Mendelsohn’s design of Einsteinturm includes independent sculptures instead of an architectural model. Both Zaha Hadid and Frank Gehry’s contemporary buildings are already constructed expressionist sculptures distinguished by their monumental scale, not by their form. W. Husenclaver, Zadania teatru, in Ekspresjonizm w teatrze europejskim, Warsaw 1993, 250.i 10 W. Husenclaver, Zadania teatru, in Ekspresjonizm w teatrze europejskim, Warsaw 1993, 250. 11 E.H. Gombrich, Pisma o sztuce i kulturze, selected and edited by R. Woodfield, Krakow 2011, 84. 12 E. Viollet-le-Duc, Dictionnaire raisonné de l’architecture française du XIe au XVIe siècle E. Porębska, M. Poprzęcka, Teoretycy, artyści i krytycy o sztuce 1700‒1870, Warsaw 1989, 470-471 H. Gombrich, Pisma o sztuce i kulturze, selected and edited by R. Woodfield, Krakow 2011, 84. , , yi , , 12 E. Viollet-le-Duc, Dictionnaire raisonné de l’architecture française du XIe au XVIe siècle, E. Porębska, M. Poprzęcka, Teoretycy, artyści i krytycy o sztuce 1700‒1870, Warsaw 1989, 470-471. S t r e s z c z e n i e The present day always pretends that it is not looking for the origins, but this is nothing but an artistic delusion. Creators try to avoid being accused of copying things which is understandable but we are always left with some aftersights, with a fugitive inspiration drawn from what used to be. Obviously, it is a blurred image – we are not always capable of seeing the original because we can remember the shape yet in different colours. If we treat the present state of architecture as evolution, we must not forget that evolution has no purpose. What we are observing right now was unpredictable to those who lived and worked in the early twentieth century. Let us quote Heinrich Wölfflin’s words cited by Ernst Gombrich in his ruminations on the psychology and mystery of styles which may become the motto of the return to expressionist art: “Not everything is possible at every time”11, or Viollet-le-Duc’s statement: “If the Gothic constructors had been able to use cast iron in large bars, they would have willingly mastered this technique necessary for making buttresses as slender and durable as possible. Perhaps they would have applied them more appropriately than we do”12. These days, owing to new building technologies and computers, we can fulfill our predecessors’ dreams. Contemporary architects have joined the artistic community, whereas the models of their houses or stadiums can be exhibited at museums beside sculptures created by the futurists and expressionists of the early twentieth century with no shame at all. We might venture a thesis on the appearance of a new tendency in contemporary art – architectural sculpture as an esthetical category unrelated to the function or scale of a work but related to its form. 52 Ill. 1. Ossip Zadkine, The Torn City of Rotterdam, The Netherlands 1953 (Rotterdam Der neubau einer Stadt, edited by C. Van Traa) Ill. 1. Ossip Zadkine, The Torn City of Rotterdam, The Netherlands 1953 (Rotterdam Der neubau einer Stadt, edited by C. Van Traa) Ill. 2. Philip Johnson, Visitor’s pavilion, New Canaan, Connecticut, 1994 (“Domus”, February 1996) . Philip Johnson, Visitor’s pavilion, New Canaan, Connecticut, 1994 (“Domus”, February 1996 53 Ill. 3. Barnett Newman, The Broken Obelisk, Houston, 1967 (Wojciech Włodarczyk, W poszukiwaniu istoty. Minimal-art i konceptualizm, [In:] Sztuka świata, tom 10, Warszawa 1996) Ill. 3. Barnett Newman, The Broken Obelisk, Houston, 1967 (Wojciech Włodarczyk, W poszukiwaniu istoty. S t r e s z c z e n i e Minimal-art i konceptualizm, [In:] Sztuka świata, tom 10, Warszawa 1996) Ill. 4. Hermann Finsterlin, Mausoleum, 1919 (Dennis Sharp, Modern Architecture and Expressionism, New York 1966) Ill. 4. Hermann Finsterlin, Mausoleum, 1919 (Dennis Sharp, Modern Architecture and Expressionism, New York 1966) 54 Ill. 5. Coop Himmelb(l)au, Pavilion 21 MINI Opera Space (Munich Opera Festival 2010, Munich, Germany, 2008‒2010) Ill. 5. Coop Himmelb(l)au, Pavilion 21 MINI Opera Space (Munich Opera Festival 2010, Munich, Germany, 2008‒2010) Ill. 6. Walter Gropius, The Monument to the Casualties of the Kapp Putsch, 1921 (Werlag Gerd Hatje, Bauhaus Weimar 1919‒1925 Dessau 1925‒28, Stuttgart 1955) Ill. 6. Walter Gropius, The Monument to the Casualties of the Kapp Putsch, 1921 (Werlag Gerd Hatje, Bauhaus Weimar 1919‒1925 Dessau 1925‒28, Stuttgart 1955) 55 Ill. 7. Caspar David Friedrich, The Sea of Ice, 1823‒1824, oil paint Ill. 7. Caspar David Friedrich, The Sea of Ice, 1823‒1824, oil paint
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https://researchonline.lshtm.ac.uk/id/eprint/4669681/1/Tapsoba-etal-2023-Do-Out-of-Pocket-Payments-for-Care-for-Children-under-5-Persist-Even-in-a-Context-of-Free-Healthcare-in-BurkinaFaso.pdf
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Do Out-of-Pocket Payments for Care for Children under 5 Persist Even in a Context of Free Healthcare in Burkina Faso? Evidence from a Cross-Sectional Population-Based Survey
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Citation: Tapsoba, L.D.G.; Yara, M.; Nakovics, M.I.; Somda, S.M.A.; Lohmann, J.; Robyn, P.J.; Hamadou, S.; Hien, H.; De Allegri, M. Do Out-of-Pocket Payments for Care for Children under 5 Persist Even in a Context of Free Healthcare in Burkina Faso? Evidence from a Cross-Sectional Population-Based Survey. Healthcare 2023, 11, 1379. https://doi.org/10.3390/ healthcare11101379 Keywords: free healthcare; out-of-pocket payments; children under 5; Burkina Faso healthcare healthcare healthcare healthcare Article Do Out-of-Pocket Payments for Care for Children under 5 Persist Even in a Context of Free Healthcare in Burkina Faso? Evidence from a Cross-Sectional Population-Based Survey Ludovic D. G. Tapsoba 1,* , Mimbouré Yara 1, Meike I. Nakovics 2, Serge M. A. Somda 1,3 , Julia Lohmann 2,4, Paul J. Robyn 5, Saidou Hamadou 5, Hervé Hien 1 and Manuela De Allegri 2 1 Centre MURAZ, National Institute of Public Health, Bobo-Dioulasso 390, Burkina Faso 2 H id lb I i f Gl b l H l h M di l F l d U i i H i l U i i f H id lb 1 Centre MURAZ, National Institute of Public Health, Bobo-Dioulasso 390, Burkina Faso 2 Heidelberg Institute of Global Health, Medical Faculty and University Hospital, University of Heidelberg, 69120 Heidelberg, Germany 1 Centre MURAZ, National Institute of Public Health, Bobo-Dioulasso 390, Burkina Faso 2 Heidelberg Institute of Global Health, Medical Faculty and University Hospital, University of Heidelberg, 69120 Heidelberg, Germany 3 UFR Exact and Applied Sciences, Nazi Boni University, Bobo-Dioulasso BP 1091, Burkina Faso 4 Department of Global Health and Development, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK pp , , 5 The World Bank Group, 1818 H St. NW, Washington, DC 20433, USA pp 5 The World Bank Group, 1818 H St. NW, Washington, DC 20433, USA * Correspondence: ludo_deo@yahoo.fr * Correspondence: ludo_deo@yahoo.fr * Correspondence: ludo_deo@yahoo.fr Abstract: Background: In April 2016, Burkina Faso began free healthcare for children aged from 0 to 5 years. However, its implementation faces challenges, and the goal of this study is to estimate the fees paid for this child care and to determine the causes of these direct payments. Methods: Data gathering involved 807 children aged from 0 to 5 years who had contact with the public healthcare system. The estimation of the determinants of out-of-pocket health payments involved the application of a two-part regression model. Results: About 31% of the children made out-of-pocket payments for healthcare (an average of 3407.77 CFA francs per case of illness). Of these, 96% paid for medicines and 24% paid for consultations. The first model showed that out-of-pocket payments were positively associated with hospitalization, urban area of residence, and severity of illness, were made in the East-Central and North-Central regions, and were negatively associated with the 7 to 23 month age range. The second model showed that hospitalization and severity of illness increased the amount of direct health payments. Conclusion: Children targeted by free healthcare still make out-of-pocket payments. The dysfunction of this policy needs to be studied to ensure adequate financial protection for children in Burkina Faso. 1. Background Academic Editor: Mustafa Z. Younis An increasing number of countries in Sub-Saharan Africa have recently implemented policies to waive/reduce the cost of healthcare for the poorest members of their populations or for specific sections of the populations such as pregnant women and children under five [1]. These policies vary from country to country in terms of the services covered and the social groups benefiting. For example, in 2006, Senegal introduced a policy of eliminating user fees for childbirth care at the national level; in 2005 Mali introduced a policy of eliminating fees for cesarean sections. Several studies have shown that out-of- pocket payments can be a barrier to the use of health services [2,3]. Fee removal/reduction policies aim to increase access to healthcare facilities, thereby contributing to the reduction of maternal and neonatal mortality and helping to achieve the Sustainable Development Goals [4]. The adoption of these policies is not an easy task, as public policy development and implementation in most African countries are fraught with difficulties [5]. Received: 2 March 2023 Revised: 24 April 2023 Accepted: 5 May 2023 Published: 10 May 2023 Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). p g The studies of fee removal/reduction policies have mostly focused on the impact on healthcare service utilization rather than on financial protection. They show that these https://www.mdpi.com/journal/healthcare Healthcare 2023, 11, 1379. https://doi.org/10.3390/healthcare11101379 Healthcare 2023, 11, 1379 2 of 12 policies increase the use of healthcare services [6]. However, studies have shown that out-of-pocket health payments still remain in free care settings, but the studies are not sufficiently representative of the country’s population [7–12]. y p y p p In Burkina-Faso, a series of measures to waive user fees have been taken since the 2000s. In 2005, the management of severe malaria cases was fully subsidized [13]. Impregnated mosquito nets have also been subsidized and distributed throughout the country since 2010. In the area of maternal health, a subsidy of 60 to 80%, depending on the services offered, is provided for complicated and elective deliveries. The Government of Burkina Faso has initiated the total exemption of healthcare fees for women and children aged from 0 to 5 years as of 1 June 2016 after successful pilot experiences. This free care strategy aims to significantly reduce preventable deaths among children aged from 0 to 5 years and women [14]. As part of this policy, many sub-Saharan countries are reimbursing health facilities [15]. However, Burkina Faso has started the financial management of this policy by pre-positioning funds for the covered services in accounts opened specifically for the free healthcare policy. This strategy was adopted to avoid delays in reimbursement, which encouraged out-of-pocket payments. Few studies have examined the drivers of out-of-pocket expenditure (OOPE) in a context of free care delivery [16,17]. This study aims at filling an existing gap in the literature as one of the first to exam- ine the effects of the national free healthcare policy on out-of-pocket spending for child healthcare services. Prior impact evaluations have either referred to pilot experiences [18] or examined the impact on payments for maternal care services [16]. This study builds on household data from 24 districts to measure out-of-pocket expenditure for children aged 0 to 5 years more than one year after the launch of the free healthcare policy. 2.1. Framework of the Study Burkina Faso is a low-income country with an agricultural vocation. Its economy is subject to climatic hazards, fluctuations in world trade conditions, and the exchange rate (INSD, Demographic and Health Survey and Multiple Indicators “EDSBF-MICS IV”, 2010). The 2014 Continuous Multisectoral Survey (CMS) reveals that 40.1% of the Burkinabe population is poor [19]. As one of the poorest countries in the world, the country has been making economic progress in recent years thanks to relatively high annual economic growth (+6.51% in 2018). However, Burkina Faso has a long way to go on the road to development. The GDP per capita is only XOF444,817.96 (US$740.75 (1 XOF = 0.0017 US$ (April 2023)) (2018). This makes it difficult for people to access basic social services and increases unemployment. In addition, the country suffers from high morbidity and mortality, mainly due to acute infectious diseases (acute malaria, acute respiratory infections, diarrhea, etc.) and high infant and maternal mortality rates (World Health Organization, 2015; African Health Observatory, 2016). As a result, the country ranks 185 out of 188 countries on the 2016 Human Development Index (HDI) (United Nations Development Program, 2016) [20]. Burkina Faso is a low-income country with an agricultural vocation. Its economy is subject to climatic hazards, fluctuations in world trade conditions, and the exchange rate (INSD, Demographic and Health Survey and Multiple Indicators “EDSBF-MICS IV”, 2010). The 2014 Continuous Multisectoral Survey (CMS) reveals that 40.1% of the Burkinabe population is poor [19]. As one of the poorest countries in the world, the country has been making economic progress in recent years thanks to relatively high annual economic growth (+6.51% in 2018). However, Burkina Faso has a long way to go on the road to development. The GDP per capita is only XOF444,817.96 (US$740.75 (1 XOF = 0.0017 US$ (April 2023)) (2018). This makes it difficult for people to access basic social services and increases unemployment. In addition, the country suffers from high morbidity and mortality, mainly due to acute infectious diseases (acute malaria, acute respiratory infections, diarrhea, etc.) and high infant and maternal mortality rates (World Health Organization, 2015; African Health Observatory, 2016). As a result, the country ranks 185 out of 188 countries on the 2016 Human Development Index (HDI) (United Nations Development Program, 2016) [20]. The healthcare structure is organized in three levels. The first level is the health district, which encompasses two parts. 2.2. The Free Care Policy for Children from 0 to 5 Years 2.2. The Free Care Policy for Children from 0 to 5 Years On 2 March 2016, Burkina-Faso adopted a policy of free care for children aged from 0 to 5 years, which was implemented on 2 April 2016, by the health districts of the Center, Sahel, and Hauts-Bassins regions. On 1 May 2016, the hospitals in the aforementioned regions also started the implementation. As of the 1 June 2016, the implementation was extended to all the other facilities in the other regions. Free care is offered in public health facilities and private health facilities that have signed an agreement with the Ministry of Health. The targeted populations benefit from free care whatever the medical or surgical specialty g p p g p y Healthcare for children aged from 0 to 5 years is preventive, diagnostic, and curative in both outpatient and inpatient/observation settings for all common conditions targeted by the IMCI (Integrated Management of Childhood Illness) strategy to reduce infant and child mortality [22]. 2.3. Data and Data Sources Data for this study were gathered from the Final Household Survey for the impact evaluation of the Results-Based Financing (Fbr), financed by the World Bank between April and June 2017. The sample is composed of 7935 households in 24 districts (intervention and control) in the six project regions (Boucle of Mouhoun, North-Central, West-Central, North, South-West, and East-Central). These households were selected in two phases: in the first phase, villages were selected randomly from the health areas. One village was randomly selected for each HSPC. In the second phase, 15 households were randomly selected in each village based on a complete list of households. This list consisted of households with at least one pregnant woman or one woman who had given birth in the last 24 months. For this study, we used the household module, namely the sections on socioeconomic and demographic characteristics of households, education, and health, particularly health- care expenditures for acute illnesses. In each household, the respondents were the head of the household, pregnant women, or women who had given birth in the last 24 months, and all children aged from 0 to 5 years. Our study therefore focuses on children aged from 0 to 5 years. 2.1. Framework of the Study The first level includes the Health and Social Promotion Centers (HSPC), which is the first contact point for a wide range of primary care services for children aged 0–5 years. The second level is the Medical and Surgical Centers (MSC). In 2020, there were 70 health districts with 2041 Health and Social Promotion Centers (HSPC) and 46 Medical and Surgical Centers (MSC) in operation. In 2020, the second level included nine Regional Hospital Centers (RHC) serving as references for the CMAs, and the third level consists of six University Hospital Centers. In addition, Burkina Faso has 641 private facilities concentrated in the cities of Ouagadougou and Bobo-Dioulasso [21]. The healthcare structure is organized in three levels. The first level is the health district, which encompasses two parts. The first level includes the Health and Social Promotion Centers (HSPC), which is the first contact point for a wide range of primary care services for children aged 0–5 years. The second level is the Medical and Surgical Centers (MSC). In 2020, there were 70 health districts with 2041 Health and Social Promotion Centers (HSPC) and 46 Medical and Surgical Centers (MSC) in operation. In 2020, the second level included nine Regional Hospital Centers (RHC) serving as references for the CMAs, and the third level consists of six University Hospital Centers. In addition, Burkina Faso has 641 private facilities concentrated in the cities of Ouagadougou and Bobo-Dioulasso [21]. Out-of-pocket health payments accounted for 35.8% of current health expenditures in 2018 (National Health Accounts 2018). This figure is high by WHO standards (the WHO stipulates that the percentage of out-of-pocket payments on current health expenditures should not exceed 20%). Healthcare 2023, 11, 1379 3 of 12 2.4. Description of the Sample We focused on children aged from 0 to 5 years who reported having a non-chronic illness or injury and whose parents sought care. The data allowed us to identify those children who reported contact with the formal public healthcare system for care as in previous studies [16]. This target was taken because we are interested in the free healthcare policy that is implemented in our study in public healthcare facilities in Burkina Faso. The identification steps of our sub-sample are visible in the flow chart (Figure 1). 2.5.1. Variable of Interest The “Out-of-pocket expenditure” is the main variable of interest. It aggregates all health expenditures made by the household for children aged from 0 to 5 who were sick in the last 24 months and who used healthcare in a public health facility. This package of care concerns only those in the free basket (including hospitalization) when a child aged 0–5 is cared for in a public health facility. These expenditures include consultation fees, laboratory/radiography and surgical fees (examinations), purchase of medicines, and hospitalization fees. Informal payments without receipts and transportation costs were therefore not included in the calculations of out-of-pocket health payments. Calculations were made at the individual, not the household, level. This avoids the risk of double- counting costs. Some of these costs might have been paid outside the health facility, namely those related to the purchase of drugs and examination fees. Expenditures were calculated in the local currency of the country, i.e., in XOF. Indirect costs were not considered. 4 of 12 Healthcare 2023, 11, 1379 1 Children under five years old: 15,323 No acute illness or injury: 14,308 acute illness or injury: 1015 Steps to get treatment : 889 No steps to get treatment: 126 contact with the formal public health care system: 807 Private and no contact with the formal public health care system: 82 Expenses for health care: 248 No expenses for health care: 559 Figure 1. Sample identification chart. 2.5.2. Explanatory (Control) Variables The research of factors associated with out-of-pocket expenditure highlights the demographic data of patients and their mothers (age, place of residence, mother’s le Children under five years old: 15 323 Children under five years old: 15,323 No acute illness or injury: 14,308 acute illness or injury: 1015 No steps to get treatment: 126 Steps to get treatment : 889 Steps to get treatment : 889 Private and no contact with the formal public health care system: 82 contact with the formal public health care system: 807 No expenses for health care: 559 Expenses for health care: Figure 1. Sample identification chart. 2.5.2. Explanatory (Control) Variables 1= (0–6); 2= (7–23); 3 =(24–59) 0 = Boy; 1 = Girl 0 = No effect on activities; 1 = Any effect on activities 0 = No; 1 = Yes 0= ≤5 km; 1= > 5 km 0 = Rural; 1 = Urban 0 = Other; 1 = Poor (Socio-economic status/quintile 1) 0= Uneducated; 1= Educated 0 = No; 1 = Yes 1 = Boucle du Mouhoun; 2 = Center est; 3 = Center nord; 4 = Center ouest; 5= Nord; 6 = Sud ouest Age (months) Sex Perceived illness severity Hospitalization Distance from household to nearest health facility (km) Place of residence Poverty status (SES) Mother’s level of education in the household District Fbr Region We categorized “disease severity” into no effect on activities and some effect on activities (leisure, school, being able to eat, etc.). 2.5.2. Explanatory (Control) Variables 2.5.2. Explanatory (Control) Variables 1 The research of factors associated with out-of-pocket expenditure highlights the socio- demographic data of patients and their mothers (age, place of residence, mother’s level of Healthcare 2023, 11, 1379 5 of 12 5 of 12 education, economic status) and those related to the health system (health district, region, distance from the health center) as control variables (Table 1). education, economic status) and those related to the health system (health district, region, distance from the health center) as control variables (Table 1). The “economic status” ranks households in the poorest quintile of socio-economic status (SES) against the other four richer quintiles. This approach follows the logic of the most vulnerable exemption policy that started its experimentation since 2008 with the collaboration of a German NGO (HELP). Socio-economic status (SES) was calculated as a continuous variable using the Multiple Component Analysis (MCA) method to aggregate information on assets, household housing characteristics, and other parameters, and was divided into quintiles [23,24]. Table 1. Variables and measurements. Mesurements and Categorization Variables of Interest Probability of out-of-pocket expenditure 0 = No; 1 = Yes Out-of-pocket expenditure [FRS CFA] Continuous Explanatory variables Age (months) 1= (0–6); 2= (7–23); 3 =(24–59) Sex 0 = Boy; 1 = Girl Perceived illness severity 0 = No effect on activities; 1 = Any effect on activities Hospitalization 0 = No; 1 = Yes Distance from household to nearest health facility (km) 0= ≤5 km; 1= > 5 km Place of residence 0 = Rural; 1 = Urban Poverty status (SES) 0 = Other; 1 = Poor (Socio-economic status/quintile 1) Mother’s level of education in the household 0= Uneducated; 1= Educated District Fbr 0 = No; 1 = Yes Region 1 = Boucle du Mouhoun; 2 = Center est; 3 = Center nord; 4 = Center ouest; 5= Nord; 6 = Sud ouest Table 1. Variables and measurements. 2.6. Analytical Approach Our objective was to identify how many children face an out-of-pocket expenditure, quantify its amount, and determine the associated factors. First, we computed mean values, standard deviation (SD), median, min and max values. To correct for outliers, we applied winsorizing, replacing 5 to 25% of outlier expenditure data items [25]. This method preserves the power of the sample in the regression analysis and avoids bias in the calculation of the mean value and variance by retaining higher values in the sample [26]. y g g p Second, we examined which factors were associated with a positive expenditure and with the magnitude of the expenditure. To address usual challenges related to the large number of zeros, skewness, and possible bias due to heteroscedasticity, several authors have recommended a two-part model approach [27]. Accordingly, the probability of facing a positive direct health payment was modeled first (Pr (Y > 0|X)) and followed by modeling the amounts of out-of-pocket health payments for those who paid (E (Y|Y > 0, X)) [27], as expressed in the equation below: E (Y|X) = Pr (Y > 0|X) × E (Y|Y > 0, X). Hence, for the first part, a logit regression was done to identify the “probability of incurring OOPE” because the interpretation of its results is quite simple. For the second part, the Box-Cox test (p = 0 for λ = 0) showed that the data are not suitable for the use of the generalized linear model (GLM) with a log link. Therefore, the OLS model with log transformation of Y was used to identify the “determinants of out-of-pocket health payments” in the second part. For the gross scale back transformation, the restrictive Healthcare 2023, 11, 1379 6 of 12 assumption of normal distribution of log scale errors was not imposed. The estimator of Duan (1983) was used in preference [27,28]. The data analysis was performed with STATA version 13. assumption of normal distribution of log scale errors was not imposed. The estimator of Duan (1983) was used in preference [27,28]. The data analysis was performed with STATA version 13. 3.2. Direct Childcare Services Payments 3.2. Direct Childcare Services Payments About 31% (n = 248) of those who had contact with the formal public healthcare system faced direct childcare service payments that averaged XOF3407.77 (US$ 5.67) (min: 100 frs and max: 10,000 frs) per illness episode (Table 2). The highest average expenditure was observed for hospitalization (concerning 4%), laboratory/radiology and surgical services (concerning 2%), and consultations (concerning 24%). The most frequent expenditures were for medical drugs (96%) and for consultation fees (24%). Additional expenses outside the free care package were noted. These are transportation expenses for 109 children (44%) whose parents declared that they had paid for transportation out of their own pockets with an average of XOF728 (US$1.21). This gives an indication of the financial burden on households. The highest variance is for hospitalization (SD = XOF16,358.74) and for consultation (XOF3459.1) Table 2. Adjusted out-of-pocket expenditures (OOPE) 1 among those who used formal. Table 2. Adjusted out-of-pocket expenditures (OOPE) 1 among those who used formal. j p p ( ) g N % Average (Frs CFA) SD (Frs CFA) Median (Frs CFA) Min (Frs CFA) Max (Frs CFA) Probability of OOPE among those who used formal services (n = 807) OOP = 0 559 69 NA NA NA NA NA OOP > 0 248 31 3407.77 2839.53 3200 100 10,000 Components of OOPE (n = 248) Consultation fees 59 24 3269.06 3459.1 1500 100 10,100 Laboratory/radiography and surgery costs (examinations) 5 2 4100 1341.64 5000 2000 5000 Drugs 237 96 2895.33 2388.14 2000 100 8000 Hospitalization costs 11 4 12,209.09 16,358.74 5050 750 50,000 Total direct health payments 248 100 3407.77 2839.53 3200 100 10,000 Transports 109 44 728.73 210.70 700 300 1000 SD: Standard Deviation. Corresponds to the costs of transport spent by those who made OOP. PS: these costs are not parts of the free health care basket. 2.7. Ethical Considerations The study received the favorable opinion of the ethics committee of the University of Heidelberg (S-272/2013) and the national ethics committee for health research of Burkina Faso (N◦2013-7-066 and N◦2015-5-071). Respondents gave their informed consent, and their confidentiality was ensured by the anonymity used in the data collection tools. 3.1. Characteristics of Sample The sample included a total of 15,323 children aged from 0 to 5 years (Figure 1). Of these, 1015 children reported a non-chronic illness or injury in the four weeks preceding the survey date. Of these, 807 sick children aged 0 to 5 years had contact with the formal public healthcare system. Most of these children did not come from poor households and lived in rural areas (n = 807, 90.46%) with an average distance from the household to the health facility of less than or equal to 5 km. These children were from FBR districts for 79.18% and went to primary healthcare facilities (HSPC, maternity) to receive care (97.40%). 3.3. Factors Associated with OOP Payments The percentage of children aged from 0 to 5 years who paid for care differed signif- icantly according to the child’s age group, severity of illness, economic status, place of residence, and region. The following factors have no impact on childcare service payments: mother’s level of education in the household, proximity to the health center, and district FBR. Table 3 presents the proportions of free and paid care services according to children Healthcare 2023, 11, 1379 7 of 12 7 of 12 aged from 0 to 5 years characteristics. This table allowed us to select the variables of the two-part model, taking variables as significant at the 20% level. aged from 0 to 5 years characteristics. This table allowed us to select the variables of the two-part model, taking variables as significant at the 20% level. Table 4 presents the adjusted results of the two-part model that included 807 obser- vations in the first part and 248 in the second part. In the logistic regression (first part), hospitalization, place of residence, region of residence, child’s age group, economic sta- tus, and severity of illness were significantly associated with out-of-pocket payments for children aged from 0 to 5 years. As a result, those who are hospitalized are 4.53 times more (95% CI= 1.92–8.88) likely to pay for childcare services than those not hospitalized. Compared with those in rural places, those in urban places paid for childcare services 3.47 times more often (95% CI = 1.88–5.34). People with an illness that affects any activity are 1.53 times more likely (95% CI = 1.07–2.09) to pay for childcare services than those whose illness does not affect their activities. Compared with the South-West region, those that lived in the East-Central and North-Central were 4.50 times (95% CI = 2.18–9.29) and 2.43 times (95% CI = 1.16–5.08) more likely to pay for childcare services for children aged from 0 to 5 years, respectively. In addition, children in the 7- to 23-month age group are 48 percent (95% CI= 0.35–0.83) less likely to pay for childcare services than those in the 0- to 6-month age group. The poorest section of the population (quintile 1) are 33 percent (95% CI= 0.44–1.07) less likely to pay for childcare services. Thus, the poor are protected. Table 3. A proportion of children aged 0–5 years who paid and who did not pay for services. 3.3. Factors Associated with OOP Payments Two-part model for the determinants of out-of-pocket expenditure (First part: logit, second part: OLS with log transformation; n = 807). In the log-transformed OLS regression (second part), hospitalization significantly increased the amount of out-of-pocket health payments for children aged from 0 to 5 years (coef = 0.78; p < 0.001). The amount was higher for people with an illness that affects any activity (coef = 0.24; p = 0.047). In addition, locations such as the East-Central, North-Central, and West-Central region saw increased the amounts of out-of-pocket health payments when there was a direct childcare services payment (coef= 0.60; 0.59; 0.76 and p = 0.029; 0.04; 0.01) compared with the South-West region. 3.3. Factors Associated with OOP Payments Characteristics Children Who Paid (n = 248) Children Who Did not Pay (n = 559) P n % n % Age groups (months) 0.012 (0–6) 58 40.28 86 59.72 (7–23) 119 27.17 319 72.83 (24–59) 71 31.56 154 68.44 Perceived illness severity 0.099 No effect 92 27.54 242 72.46 Effect 156 32.98 317 67.02 Poverty indices 0.009 Not poor 216 32.73 444 67.27 Poor (the poorest) 32 21.77 115 78.23 Mother’s level of education in the household 0.708 Uneducated 195 30.42 446 69.58 Educated 53 31.93 113 68.07 Place of residence 0.000 Rural 206 28.22 524 71.78 Urban 42 54.55 35 45.45 Proximity to a health center (distance in km) 0.472 ≤5 km 187 31.43 408 68.57 >5 km 61 28.77 151 71.23 District Fbr 0.621 No 49 29.17 119 70.83 Yes 199 31.14 440 68.86 Region 0.000 Boucle du Mouhoun 30 26.79 82 73.21 Center Est 67 48.2 72 51.8 Center Nord 44 32.35 92 67.65 Center Ouest 38 27.74 99 72.26 Nord 56 26.17 158 73.83 Sud Ouest 13 18.84 56 81.16 Table 3. A proportion of children aged 0–5 years who paid and who did not pay for services. Healthcare 2023, 11, 1379 8 of 12 Table 4. Two-part model for the determinants of out-of-pocket expenditure (First part: logit, second part: OLS with log transformation; n = 807). Part 1: Likelihood of Having a Direct Payment (n = 807) Part 2: Determinants of the Amount of OOPE (n = 248) Explanatory Variables OR 95% CI p-Value Coeff 95% CI p-Value Age group (months) (0–6 months) 1 0 (7–23 months) 0.52 0.35–0.83 0.003 *** −0.09 −0.39–0.19 0.51 (24–59 months) 0.62 0.39–1.01 0.052 * −0.015 −0.33–0.30 0.92 Hospitalization No 1 0 Yes 4.53 1.92–8.88 <0.001 *** 0.78 0.38–1.17 <0.001 *** Perceived illness severity No effect 1 0 Effect 1.53 1.07–2.09 0.018 ** 0.24 −0.003–0.49 0.047 ** Place of residence Rural 1 0 Urban 3.47 1.88–5.34 <0.001 *** 0.34 −0.032–0.66 0.031 ** Poverty Indices Not poor 1 0 Poor 0.67 0.44–1.07 0.098 * 0.09 −0.25–0.45 0.61 Regions South-West 1 0 Boucle du Mouhoun 1.51 0.70–3.28 0.288 −0.02 −0.63–0.58 0.945 Central-East 4.50 2.18–9.29 <0.001 *** 0.60 0.06–1.14 0.029 ** Central-North 2.43 1.16–5.08 0.018 ** 0.59 0.02–1.16 0.040 ** Centre-West 1.60 0.75–3.37 0.216 0.76 0.18–1.34 0.01 ** North 1.71 0.84–3.48 0.137 0.23 −32–0.78 0.409 * Significance at 10%; ** Significance at 5%; *** Significance at 1%. Table 4. 4. Discussion Our study is one of the first ones to estimate the level and determinants of out-of- pocket payments for care among children aged 0 to 5 years of age in the context of the gratuité, the free healthcare policy launched nationwide in 2016 in Burkina Faso. Our study makes an important contribution to the literature by providing evidence on the efficacy of the policy in removing user charges at point of use during its early implementation phase, building on a representative population-based sample and covering over a third of the country. Prior studies measuring OOP expenditure in the context of free healthcare policies in Burkina Faso have traditionally drawn from pilot experiences or focused on expenditures for maternal care [16,18]. p First, our results show that one year into the implementation, one third of all children aged 0 to 5 years of age who reported an episode of illness or injury and who sought care in the formal public healthcare system incurred direct health payments in the process of seeking care. Among those who incurred a payment, the amount averaged XOF 3407.77 (US$5.67) per episode of care. This amount is considerable in a country where, even in the formal sector, the minimum wage is equivalent to XOF 34,664 and where 44% of the population lives in extreme poverty on less than US$2 per day [29]. While our study has not investigated how families cope with these high payments, we can only speculate that past strategies (including asset erosion and borrowing) persist and contribute to further household impoverishment [30,31]. Our results are consistent with what has been observed in prior studies, suggesting that the introduction of free healthcare policies alone is not sufficient to remove all payments at point of use [12,16,32,33]. Prior research has indicated that challenges related to the implementation of healthcare policies, including insufficient knowledge among implementers and funding, which are often responsible for residual fees [34–36]. Further research is needed to investigate the root causes of our observations. 9 of 12 Healthcare 2023, 11, 1379 Second, our analysis shows that hospitalization, laboratory/radiology services, and surgery, although infrequent events, were key cost drivers. This suggests a failure on behalf of the system to provide free healthcare consistently across all levels of care. Similar patterns have been observed elsewhere in the presence of free healthcare policies. 4. Discussion For instance, in Zambia, almost all children accessed care free of charge after the introduction of the free healthcare policy, but nearly 10% were left to pay catastrophic amounts [9]. This suggests that healthcare systems are unable to implement the policy consistently and are unable to apply purchasing models that meet different needs, leading to a breakdown of supply chains. Further investments are needed a priori in the systems to not jeopardize the potential of free healthcare policies. p p Our findings indicate that expenditure on medications remained considerable at an average of XOF2, 895 (US$4.82). This observation is consistent with prior studies, having shown that in a context of free healthcare, frequent expenses are related to medications [12]. Several factors could explain why seeking care at public facilities still results in a high expenditure on medications. For instance, previous studies have suggested that stock-outs of medicines and medical consumables at public facilities push patients to purchase drugs at private facilities, driving expenditure on drugs. According to the Ministry of Health of Burkina Faso, only 60 percent of drug orders were fulfilled by the company responsible for supplying public health facilities with essential generic drugs in 2017. This is likely to have forced patients to resort to the private sector, resulting in direct payments in spite of a free healthcare setting in the public system [16,37]. Further research is needed to understand and strengthen the supply of stocks at the Centrale d’Achat des Médicaments Essentiels Génériques (CAMEG). Looking in-depth at the results of the two-part regression model, we noted that children have a higher probability of incurring a direct payment if they were hospitalized, live in an urban place, suffer from a severe condition, and live in the East-Central, North- Central, or West-Central region. More specifically, it is not surprising that a severe illness, since it limits daily activities and has a strong association with hospitalization, increases the likelihood of making an expenditure [11,38,39]. In line with prior studies [32,40,41], we found that OOP payments were higher among children of higher socio-economic status. This may reflect a higher ability to pay for items not directly covered by the free healthcare system, such as speciality instead of generic drugs [42,43]. 4. Discussion Likewise, OOP payments are higher in urban settings, possibly suggesting different costs between rural and urban settings [44] and access to more opportunities for spending on additional services in urban settings not covered by the free healthcare policy. Contrary to what has been observed in other settings [45,46], we observed higher spending on children of a younger age (0 to 6 month), suggesting that there may be more gaps in the policy coverage among this age group. g g p It also needs to be noted that beyond direct medical costs, 44% of the children who reported out-of-pocket expenditure for care also reported spending an average of XOF728 (US$1.21) for transportation. This finding underlines the high costs associated with seeking care beyond direct medical costs. A great deal has been written highlighting distance as one of the main barriers to accessing care in Burkina Faso, as well as in other developing countries [47]. In order to fully remove financial barriers to access, policy makers need to include a lump sum to cover transport to health facilities so that distance does not impose an additional cost. Methodological Considerations Beyond its policy contribution, we noted a few methodological limitations related to the nature of the data we used for our study. First, we acknowledge that the data we used were six years old by the time we submitted the article for publication. We are aware of the potential bias derived from the age of the data, as a lot could have changed in either direction, producing increases or decreases in OOP payments in Burkina Faso in the meantime. Nonetheless, we note that at the time of submission, no other large-scale Healthcare 2023, 11, 1379 10 of 12 10 of 12 population-based dataset was available in the country since the Demographic Health Survey has not been released for several years. Therefore, our estimates of OOP payments in the country remain the most relevant ones in the context of the gratuité. Second, the questionnaire was not developed to assess the determinants of spending for children aged 0 to 5 years of age [11]. As a result, information on the causes of the different sources of out-of-pocket payments is missing and could not be used to complement evidence from our analysis. Third, data were collected retrospectively, so information on out- of-pocket payments is likely to be less accurate because it is subject to recall bias [48]. Fourth, by considering children aged 0 to 5 years of age who had contact with the formal public healthcare system, we purposely truncated the sample to include only children who sought care in the public healthcare system. This is in line with our research question to determine the role of the gratuité in curbing OOP payments but may obviously lead to an underestimation of the overall magnitude of OPP for children under 5 in the country, since it captures only care encounters covered by the gratuité. Last, we recognize our inability to account for facility characteristics in our model as potential drivers of out-of-pocket expenditure due to the impossibility to link household survey data to facility data. This has limited the potential for causal inference on the role of health system characteristics in driving OOP payments under the gratuité. 5. Conclusions Conflicts of Interest: The authors declare no conflict of interest. Conflicts of Interest: The authors declare no conflict of interest. 1. Richard, F.; Witter, S.; de Brouwere, V. Innovative Approaches to Reducing Financial Barriers to Obstetric Care in Low-Income Countries. Am. J. Public Health 2010, 100, 1845–1852. [CrossRef] [PubMed] 5. Conclusions The study revealed that a considerable proportion of children aged from 0 to 5 years, who are the target of the current free healthcare policy, continue to pay for access to health- care. These payments are largely due to the purchase of drugs and medical consumables, probably due to stock-outs and the prescription of drugs not available in the pharmacy of public health facilities. Further research is needed to understand why these payments at point of use persist, and efforts are needed to ensure greater efficiency implementation to guarantee better financial protection. Author Contributions: Conceptualization, L.D.G.T., H.H. and M.D.A.; Methodology, L.D.G.T., M.Y. and M.D.A.; Validation, L.D.G.T., M.I.N., S.M.A.S., J.L. and S.H.; Formal analysis, L.D.G.T., M.Y., M.I.N., S.M.A.S., J.L., P.J.R. and M.D.A.; Data curation, L.D.G.T. and M.Y.; Writing—original draft, L.D.G.T.; Writing—review & editing, M.Y., M.I.N., S.M.A.S., J.L., P.J.R., S.H., H.H. and M.D.A.; Visualization, L.D.G.T., M.Y., M.I.N. and S.M.A.S.; Supervision, L.D.G.T., J.L., P.J.R., S.H., H.H. and M.D.A. All authors have read and agreed to the published version of the manuscript. Author Contributions: Conceptualization, L.D.G.T., H.H. and M.D.A.; Methodology, L.D.G.T., M.Y. and M.D.A.; Validation, L.D.G.T., M.I.N., S.M.A.S., J.L. and S.H.; Formal analysis, L.D.G.T., M.Y., M.I.N., S.M.A.S., J.L., P.J.R. and M.D.A.; Data curation, L.D.G.T. and M.Y.; Writing—original draft, L.D.G.T.; Writing—review & editing, M.Y., M.I.N., S.M.A.S., J.L., P.J.R., S.H., H.H. and M.D.A.; Visualization, L.D.G.T., M.Y., M.I.N. and S.M.A.S.; Supervision, L.D.G.T., J.L., P.J.R., S.H., H.H. and M.D.A. All authors have read and agreed to the published version of the manuscript. Funding: This study used data from the endline survey of the impact evaluation of the Performanc Based Financing Program in Burkina Faso, a study funded by the World Bank’s Health Results Innovation Trust Fund. All authors, however, contributed their own time towards preparation of this article. The World Bank provided no direct funding for preparation of this article. Institutional Review Board Statement: The study was conducted in accordance with the Declaration of Helsinki, and approved by the Ethics Committee of the University of Heidelberg (S-272/2013) and the national ethics committee for health research of Burkina Faso (N◦2013-7-066 and N◦2015-5-071). Informed Consent Statement: Informed consent was obtained from all subjects involved in the study. Data Availability Statement: Data is available on request for reasons of confidentiality and ethics. The data presented in this study are available on request from the principal investigators of the project who provided the data. 2. Shahrawat, R.; Rao, K.D. Insured yet vulnerable: Out-of-pocket payments and India’s poor. Health Policy Plan. 2012, 27, 213–221. [CrossRef] [PubMed] References 1. Richard, F.; Witter, S.; de Brouwere, V. Innovative Approaches to Reducing Financial Barriers to Obstetric Care in Low-Income Countries. Am. J. Public Health 2010, 100, 1845–1852. [CrossRef] [PubMed] 2. 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Mugisha, F.; Kouyate, B.; Gbangou, A.; Sauerborn, R. Examining out-of-pocket expenditure on health care in Nouna, Burkina Faso: Implications for health policy. Trop. Med. Int. Health 2002, 7, 10. [CrossRef] 45. Mugisha, F.; Kouyate, B.; Gbangou, A.; Sauerborn, R. Examining out-of-pocket expenditure on health care in Nouna, Burkina Faso: Implications for health policy. Trop. Med. Int. Health 2002, 7, 10. [CrossRef] 46. Hjortsberg, C. Why do the sick not utilise health care? The case of Zambia. Health Econ. 2003, 12, 755 770. [CrossRef] 47. Tey, N.; Lai, S. Correlates of and Barriers to the Utilization of Health Services for Delivery in South Asia and Sub-Saharan Africa. Sci. World J. 2013, 2013, 423403. [CrossRef] [PubMed] 47. Tey, N.; Lai, S. References Correlates of and Barriers to the Utilization of Health Services for Delivery in South Asia and Sub-Saharan Africa. Sci. World J. 2013, 2013, 423403. [CrossRef] [PubMed] 48. Heijink, R.; Xu, K.; Saksena, P.; Evans, D.; WHO. Validity and Comparability of Out of Pocket Health Expenditure from Household Surveys a Review of the Literature and Current Survey Instruments. 2011. Available online: http://www.who.int/health_ financing/documents/covdp_e_11_01oop_errors/en/ (accessed on 10 September 2018). 48. Heijink, R.; Xu, K.; Saksena, P.; Evans, D.; WHO. Validity and Comparability of Out of Pocket Health Expenditure from Household Surveys a Review of the Literature and Current Survey Instruments. 2011. Available online: http://www.who.int/health_ financing/documents/covdp_e_11_01oop_errors/en/ (accessed on 10 September 2018). Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.
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A Brain without Brakes: Reduced Inhibition Is Associated with Enhanced but Dysregulated Plasticity in the Aged Rat Auditory Cortex
ENeuro
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New Research Sensory and Motor Systems Sensory and Motor Systems Author Contributions: JMC and EdV designed research; JMC, LO, and BK performed research; JMC and EdV analyzed data; JMC and EdV wrote the paper. Received February 1, 2018; accepted June 29, 2018; First published August 21, 2018. The authors declare no competing financial interests. Abstract During early developmental windows known as critical periods (CPs) of plasticity, passive alterations in the quality and quantity of sensory inputs are sufficient to induce profound and long-lasting distortions in cortical sensory representations. With CP closure, those representations are stabilized, a process requiring the maturation of inhibitory networks and the maintenance of sufficient GABAergic tone in the cortex. In humans and rodents, however, cortical inhibition progressively decreases with advancing age, raising the possibility that the regulation of plasticity could be altered in older individuals. Here we tested the hypothesis that aging results in a destabilization of sensory representations and maladaptive dysregulated plasticity in the rat primary auditory cortex (A1). Consistent with this idea, we found that passive tone exposure is sufficient to distort frequency tuning in the A1 of older but not younger adult rats. However, we also found that these passive distortions decayed rapidly, indicating an ongoing instability of A1 tuning in the aging cortex. These changes were associated with a decrease in GABA neurotransmitter concentration and a reduction in parvalbumin and perineuronal net expres- sion in the cortex. Finally, we show that artificially increasing GABA tone in the aging A1 is sufficient to restore representational stability and improve the retention of learning. Key words: Aging; auditory cortex; cortical plasticity; GABA; inhibition; training DOI:http://dx.doi.org/10.1523/ENEURO.0051-18.2018 1Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal QC H3A 2B4, Canada and 2Centre for Research on Brain, Language, and Music, Montreal QC H3G 2A8, Canada Significance Statement In this study, we examined brain plasticity in the auditory cortex of young adult and older adult rats in the context of different types of auditory stimulation and training. Surprisingly, older brains retained an equal or even higher potential for plasticity compared to young adults. In older brains, however, changes elicited by auditory stimulation and training were rapidly lost, suggesting that such increased plasticity might be detrimental, as the older brains were unable to consolidate these changes. This increased but poorly regulated plasticity was associated with a reduction in cortical inhibition, which normally maintains the stability of sensory representations in the young adult brain. Importantly, increasing inhibition artificially with clinically available drugs restored stability and improved the retention of learning. rat primary auditory cortex (A1; Hensch, 2005; de Villers- Sidani et al., 2007). On closure of the CP, these experience-dependent alterations are consolidated, and A1 tuning becomes relatively resistant to passive sound J. Miguel Cisneros-Franco,1,2 Lydia Ouellet,1 Brishna Kamal,1 and Etienne de Villers-Sidani1,2 J. Miguel Cisneros-Franco,1,2 Lydia Ouellet,1 Brishna Kamal,1 and Etienne d DOI:http://dx.doi.org/10.1523/ENEURO.0051-18.2018 Received February 1, 2018; accepted June 29, 2018; First published August 21, 2018. The authors declare no competing financial interests. July/August 2018, 5(4) e0051-18.2018 1–15 Mapping the auditory cortex learning (Maffei and Turrigiano, 2008; Caroni et al., 2012). Cortical inhibitory circuits are almost invariably affected by natural aging, as evidenced by a reduction of inhibitory tone and specific inhibitory interneurons such as PV and somatostatin-positive (SST) cells in older brains (Cas- pary et al., 2008; Stanley et al., 2012; Ouellet and de Villers-Sidani, 2014). Given the importance of inhibitory processes in the regulation of plasticity and learning, it is reasonable to speculate that aging could have a signifi- cant impact on the mechanisms of learning in the brain (Caspary et al., 2008; Liguz-Lecznar et al., 2014). Loss of inhibition could lead to a state of cortical instability where sensory representations are easily distorted by nonspe- cific passive experiences, as is the case with the CP (Zhou et al., 2011). Such impairments could likely explain the noisy sensory processing and less effective learning and recovery observed in older rodents (Liguz-Lecznar et al., 2014) and humans (Boyke et al., 2008; Knoflach et al., 2012). Here, we tested these ideas using a combination of controlled passive pure tone exposure, pharmacological experiments, and behavioral training in young and old rats. We found that experience-dependent plasticity is paradoxically enhanced but unstable in old rats compared to young controls. Such instability was found even for relatively short 10 minute-long exposures and was paral- leled by a reduction in the number of PV cells and PNNs. Finally, we also demonstrated that this instability is asso- ciated with a more rapid decay of learning that can be reversed by artificially enhancing GABA tone in the brain. For A1 mapping, the rats were premedicated with dexa- methasone (0.2 mg/kg) to minimize brain edema. They were anesthetized with ketamine/xylazine/acepromazine (65/13/1.5 mg/kg, i.p.) followed by a continuous delivery of isoflurane 1% in oxygen delivered via endotracheal intubation and mechanical ventilation. Vital signs were monitored using a MouseOx device (Starr Life Sciences). Body temperature was monitored with a rectal probe and maintained at 37°C with a homeothermic blanket system. The rats were held by the orbits in a custom-designed head holder, leaving the ears unobstructed. The cisterna magna was drained of cerebrospinal fluid to further min- imize brain edema. The left temporalis muscle was re- flected, auditory cortex (AC) was exposed, and the dura was resected. The cortex was maintained under a thin layer of silicone oil to prevent desiccation. Cortical responses were recorded with 32–64-channel tungsten microelectrode arrays (Neuronexus). Gouvernement du Canada | Canadian Institutes of Health Research (CIHR) grant MOP-133426 to EdV, and CIHR Vanier Canada Graduate Scholarship and CONACYT fellowship to JMC. Acknowledgments: We are grateful to M. Thomas and P. Voss for useful comments on this manuscript. Correspondence should be addressed to J. Miguel Cisneros-Franco, 3801 University Rm 753, Montreal, QC, H3A2B4, Canada. E-mail: mike.cisneros- franco@mail.mcgill.ca. DOI:http://dx.doi.org/10.1523/ENEURO.0051-18.2018 Copyright © 2018 Cisneros-Franco et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license, which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed. Materials and Methods exposures. CP closure in sensory cortices is associated with the maturation of functional and structural inhibitory elements (Hensch, 2005; Fritschy and Panzanelli, 2014), including the maturation of parvalbumin positive (PV) interneurons (Kuhlman et al., 2013) and perineuronal nets (PNN; Wang and Fawcett, 2012). In the adult brain, plastic changes of the magnitude observed in the CP can be induced by down-regulating cortical inhibition (Fagiolini and Hensch, 2000) or disrupting elements involved in the stabilization of cortical representations such as PNNs (Pizzorusso et al., 2002; Carulli et al., 2010; Wang and Fawcett, 2012). Plastic changes of this magnitude other- wise still occur in the mature brain, but regulation mech- anisms restrict them mainly to the context of behavior (Blake et al., 2006; Polley et al., 2006; Caroni et al., 2012). This tight gating of plasticity and resulting relative stability in the mature brain contribute to the consolidation and retention of new perceptuo-motor skills acquired through learning (Maffei and Turrigiano, 2008; Caroni et al., 2012). All experimental procedures used in this study were approved by the Animal Care Committee and follow es- tablished guidelines. Twenty-three immature Long-Evans rats of either sex [age postnatal 10 days (P10) to P24], 24 Long-Evans young adult rats of either sex (age 6–8 mo), and 28 Long-Evans old adult rats of either sex (22–24 mo) were used for this study. Finally, we also demonstrated that this instability is asso- ciated with a more rapid decay of learning that can be reversed by artificially enhancing GABA tone in the brain. Passive sound exposure The tone pip-exposed rats were housed for 1 or 2 consecutive weeks (24 h/d, 7 d/wk) in a sound attenuated chamber equipped with a speaker. The exposure se- quences were generated using custom Matlab routines and contained repetitive trains of six 25-ms-long 5- or 10-kHz pips with 5-ms cosine gates presented at a rate of 5 p.p.s. at an intensity of 70 dB SPL. exposures. CP closure in sensory cortices is associated with the maturation of functional and structural inhibitory elements (Hensch, 2005; Fritschy and Panzanelli, 2014), including the maturation of parvalbumin positive (PV) interneurons (Kuhlman et al., 2013) and perineuronal nets (PNN; Wang and Fawcett, 2012). In the adult brain, plastic changes of the magnitude observed in the CP can be induced by down-regulating cortical inhibition (Fagiolini and Hensch, 2000) or disrupting elements involved in the stabilization of cortical representations such as PNNs (Pizzorusso et al., 2002; Carulli et al., 2010; Wang and Fawcett, 2012). Plastic changes of this magnitude other- wise still occur in the mature brain, but regulation mech- anisms restrict them mainly to the context of behavior (Blake et al., 2006; Polley et al., 2006; Caroni et al., 2012). This tight gating of plasticity and resulting relative stability in the mature brain contribute to the consolidation and retention of new perceptuo-motor skills acquired through learning (Maffei and Turrigiano, 2008; Caroni et al., 2012). Cortical inhibitory circuits are almost invariably affected by natural aging, as evidenced by a reduction of inhibitory tone and specific inhibitory interneurons such as PV and somatostatin-positive (SST) cells in older brains (Cas- pary et al., 2008; Stanley et al., 2012; Ouellet and de Villers-Sidani, 2014). Given the importance of inhibitory processes in the regulation of plasticity and learning, it is reasonable to speculate that aging could have a signifi- cant impact on the mechanisms of learning in the brain (Caspary et al., 2008; Liguz-Lecznar et al., 2014). Loss of inhibition could lead to a state of cortical instability where sensory representations are easily distorted by nonspe- cific passive experiences, as is the case with the CP (Zhou et al., 2011). Such impairments could likely explain the noisy sensory processing and less effective learning and recovery observed in older rodents (Liguz-Lecznar et al., 2014) and humans (Boyke et al., 2008; Knoflach et al., 2012). Here, we tested these ideas using a combination of controlled passive pure tone exposure, pharmacological experiments, and behavioral training in young and old rats. We found that experience-dependent plasticity is paradoxically enhanced but unstable in old rats compared to young controls. Such instability was found even for relatively short 10 minute-long exposures and was paral- leled by a reduction in the number of PV cells and PNNs. Introduction During early developmental epochs known as critical periods (CPs) of plasticity, passive exposure to environ- mental sounds profoundly shapes frequency tuning in the July/August 2018, 5(4) e0051-18.2018 1–15 New Research 2 of 15 Gouvernement du Canada | Canadian Institutes of Health Research (CIHR) grant MOP-133426 to EdV, and CIHR Vanier Canada Graduate Scholarship and CONACYT fellowship to JMC. DOI:http://dx.doi.org/10.1523/ENEURO.0051-18.2018 Acknowledgments: We are grateful to M. Thomas and P. Voss for useful comments on this manuscript. Copyright © 2018 Cisneros-Franco et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license, which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed. GABA microdialysis Immediately after craniotomy (see Methods: Electro- physiology), a microdialysis probe (CMA 12 Microdialysis probe, Harvard Apparatus) was implanted in the AC using the stereotaxic coordinates (Paxinos and Watson, 2007): bregma AP, –4.5 mm; ML, –7 mm; DV, 4.5 mm. The pump rate was set at 0.09 mL/h (PHD ultra 4400 Syringe pump, Harvard Apparatus). Samples were manually collected and frozen at –80°C until analysis with high performance liquid chromatography (Reinhoud et al., 2013). Normalized responses to standard and oddball tones were obtained by dividing the average firing rate recorded in the 50 ms after the occurrence of each tone presenta- tion by the average firing rate observed during the 50 ms after the first standard or oddball tone in the sequence. Asymptotes for standard and oddball responses were calculated by fitting exponential functions with a least squares method to the normalized response data from each recorded neuron. Simple linear regression of the normalized responses to the standard tone for the interval from event no. 150 to event no. 1200 was performed. The slope of the resulting best fit line was computed to deter- mine the level of adaptation for each recorded site. was classified as either “go” (producing a nose poke behavior) or “no-go.” For a given trial, the rat could elicit one of four reinforcements produced by the combinations of responses (go or no-go) and stimulus properties (target or nontarget). Go responses within 5 s of a target were scored as a hit; a failure to respond within this time window was scored as a miss; a go response within 5 s of a nontarget stimulus was scored as a false positive; the absence of a response was scored as a withhold. A hit triggered the delivery of a food pellet. A miss or false positive initiated a 5-s time-out period during which time the house lights were turned off and no stimuli were presented. A withhold did not produce a reward or a time-out. Psychometric functions and stimulus target rec- ognition indexes (D-prime) were calculated for each train- ing session by plotting the percentage of go responses as a function of the total number of target stimuli (i.e., hit ratio) and the percentage of false positives as a function of the total number of foils (i.e., false-positive ratio). Learning curves were reconstructed by plotting the D-prime mea- sure reached over successive days of training. pseudo-randomly distributed oddball frequencies presented 20% of the time with no repetition. The oddball frequencies in the train had a constant separation of 1 octave. Immunohistochemistry y Immediately following the end of recording sessions, rats received a high dose of pentobarbital (85 mg/kg i.p.) and were perfused intracardially with 4% paraformalde- hyde in 0.1 M PBS at pH 7.2. Immediately after perfusion, rat brains were removed and placed in the same fixative overnight for further fixation and then transferred to a 30% sucrose solution, snap-frozen, and stored at –80°C until sectioning. Fixed material was cut in the coronal plane along the tonotopic axis of A1 on a freezing microtome at 40 &micro;m. Tissue was incubated overnight at 4°C in either monoclonal or polyclonal antisera (for anti-PV: #P- 3088, dilution 1:10,000, Sigma-Aldrich; for PNN, fluores- cein wisteria floribunda lectin #FL-1351, dilution 1:200, Vector Laboratories). Tissue samples were always pro- cessed in pairs during immunostaining procedures to limit variables relative to antibody penetration, incubation time, and post-sectioning age/condition of tissue. A Zeiss LSM 510 Meta confocal microscope was used to assess fluo- rescence in the immunostained sections. Quantification of PV cells and PNN optical density was performed in ImageJ (National Institutes of Health) and MetaMorph imaging software (Molecular Devices Systems), respec- tively. Digital images of A1 cortical sections were taken with a 40 objective (Zeiss LSM 510). All quantification was assessed in 300–400-&micro;m-wide A1 sectors (rostral, middle, caudal) extending from layer 1 to the un- derlying white matter by an experimenter blind to the age of Electrophysiological data analysis The characteristic frequency (CF) of a cortical site was defined as the frequency at the tip of the V-shaped tuning curve. For flat-peaked tuning curves, the CF was defined as the midpoint of the plateau at threshold. For tuning curves with multiple peaks, the CF was defined as the frequency at the most sensitive tip (i.e., with lowest threshold). The CF and threshold were determined using an automated routine developed in the Matlab environ- ment (The MathWorks). To generate A1 maps, Voronoi tessellation (a Matlab routine) was performed to create tessellated polygons with electrode penetration sites at their centers. Each polygon was assigned the characteristics (i.e., CF) of the corresponding penetration site. In this way, every point on the surface of the AC was linked to the characteristics experimentally derived from its closest sampled cortical site. Primary AC (A1) was identified based on its rostral- to-caudal tonotopy, reliable short-latency tone-evoked neuronal responses, and relatively sharp V-shaped RF. To examine A1 map plasticity, we compared the percentage of A1 sites with CFs in 12 bins (width  octave) span- ning the spectrum of presented tones. Mapping the auditory cortex The micro- electrode array was lowered orthogonally into the cortex to a depth of 470–600 &micro;m (layers 4/5) where vig- orous stimulus-driven responses were obtained. The ex- tracellular neural action potentials were amplified, filtered (0.3–5 kHz), sorted, and monitored on-line. Acoustic stim- uli were generated using TDT System III (Tucker-Davis Technologies) and delivered in a free-field manner to the right ear through a calibrated speaker (Tucker-Davis Technologies). A software package (OpenEx; Tucker- Davis Technologies) was used to generate acoustic stim- uli, monitor cortical response properties on-line, and store data for off-line analysis. The evoked spikes of a single neuron or a small cluster of neurons were collected at each site. Frequency-intensity receptive fields were reconstructed by presenting pure tones of 63 frequencies (1–48 kHz; 0.1-octave increments; 25-ms duration; 5-ms ramps) at 8 sound intensities (0–70 dB SPL in 10-dB increments) to the contralateral ear at a rate of one stimulus per second. Ten-minute-long trains of 50-ms tone pips were pre- sented at 3 pulses per second at a sound intensity of 70 dB SPL. Each train had a commonly occurring frequency (standard) with a probability of occurrence of 80% and 5 eNeuro.org July/August 2018, 5(4) e0051-18.2018 New Research 3 of 15 Table 1. Statistical table. Such an exposure resulted in a significant overrepresentation of the exposure tone in A1 of immature rats (average % difference in the proportion of recording sites tuned within octave of exposure tone, relative to control: 9.77  1.54% increase, p  0.001a, with Tukey–Kramer correc- tion) but not in the young adult group (F(11,72)  4.02, p  0.001; 3.84  1.3% increase, p  0.87b, with Tukey– Kramer correction; Fig. 1B). Passive tone exposure, how- ever, resulted in a significant overrepresentation of the the animals. PV cells were classified into four subclasses as follows: low-PV, 0–0.8  105; intermediate low-PV, 8–1.6  105; intermediate high-PV, 1.6–2.4  105; high-PV, 2.4  105. PNNs were classified into four subclasses as follows: low PV, 0–1  104, intermediate low-PV, 1–2  105; inter- mediate high-PV, 2–3  105; high-PV, 3  105. Statistical analysis For normally distributed data, statistical significance was assessed using unpaired two-tailed t tests or two-way anal- ysis of variance with Tukey post hoc correction for multiple comparisons. Wilcoxon rank-sum test or Kruskal–Wallis test with Tukey post hoc correction for multiple comparisons were used for nonparametric data analysis. Data are pre- sented as mean  SEM or median  median absolute deviation (MAD). Superscript letters listed with p-values cor- respond to the statistical tests shown in Table 1. Table 1. Statistical table. Data structure Type of test Statistic and p value a Normal distribution 2-way ANOVA; Tukey–Kramer test F(11,168)  14.84, p  0.001; p  0.001 b Normal distribution 2-way ANOVA; Tukey–Kramer test F(11,72)  4.02, p  0.001; p  0.87 c Normal distribution 2-way ANOVA; Tukey–Kramer test F(11,72)  10.77, p  0.001; p  0.001 d Normal distribution 2-way ANOVA; Tukey–Kramer test F(11,72)  13.13, p  0.001; p  0.001, p  0.35 e Normal distribution 2-way ANOVA; Tukey–Kramer test F(11,72)  2.69, p  0.005; p  1, p  0.96 f Normal distribution 2-way ANOVA; Tukey–Kramer test F(11,72)  7.23, p  0.001; p  1, p  0.001 g Normal distribution 2-way ANOVA; Tukey–Kramer test F(11,132)  14.62, p  0; p  0.001, p  0.15 h Normal distribution 2-way ANOVA; Tukey–Kramer test F(11,120)  12.58, p  0; p  0.001, p  0.1 i Nonnormal distribution Wilcoxon rank-sum test z  –4.099, p  4.1  10–5 j Nonnormal distribution Wilcoxon rank-sum test z  –3.187, p  0.0014 K Normal distribution t test t(579)  5.64, p  0.001 l Normal distribution t test t(395)  3.35, p  9  10–4 m Normal distribution t test t(750)  0.75, p  0.45 n Normal distribution t test t(408)  0.64, p  0.52 o Normal distribution t test t(383)  2.55, p  0.011 p Nonnormal distribution Wilcoxon rank-sum test z  –4.4, p  1.1  10–5 q Nonnormal distribution Wilcoxon rank-sum test z  2.46, p  0.013 r Normal distribution t test t(720)  5.29, p  0.001 s Normal distribution t test t(345)  2.1, p  0.03 t Normal distribution t test t(690)  0.86, p  0.39 u Normal distribution t test t(308)  0.08, p  0.94 v Normal distribution t test t(18)  2.32, p  0.032 w Normal distribution 2-way ANOVA; Tukey–Kramer test F(11,72)  13.42, p  0.001; p  0.018 x Normal distribution 2-way ANOVA; Tukey–Kramer test F(11,72)  6.57, p  0.001; p  0.004, p  0.41 y Normal distribution t test t(6)  5.02, p  0.002 z Normal distribution 2-way ANOVA; Tukey–Kramer test F(11,72)  6.68, p  0.001; p  0.01 ab Normal distribution 2-way ANOVA; Tukey–Kramer test F(11,72)  1.41, p  0.18 ac Normal distribution 2-way ANOVA; Tukey–Kramer test F(11,72)  5.42, p  0.001; p  0.022 ad Normal distribution t test t(6)  2.53, p  0.04 ae Normal distribution t test t(6)  3.66, p  0.01 af Nonnormal distribution Kruskal–Wallis test; Tukey–Kramer post hoc test H(4)  14.52, p  0.0058; p  0.52, p  0.011, p  0.96, p  0.97 ag Nonnormal distribution Kruskal–Wallis test; Tukey–Kramer post hoc test H(4)  83.97, p  0.0001; p  0.0001, p  0.001, p  0.96, p  0.003 ah Nonnormal distribution Kruskal–Wallis test; Tukey–Kramer post hoc test H(4)  13, p  0.011; p  0.82, p  0.005, p  0.99, p  0.99 ai Nonnormal distribution Kruskal–Wallis test; Tukey–Kramer post hoc test H(4)  17.24, p  0.0017; p  0.48, p  0.04, p  0.004, p  0.8, p  0.99 aj Nonnormal distribution Kruskal–Wallis test; Tukey–Kramer post hoc test H(4)  22.06, p  0.001; p  0.004, p  0.039, p  0.99, p  0.85 ley et al., 2012; Ouellet and de Villers-Sidani, 2014; Steb- bings et al., 2016). Training B h i Behavior was shaped in three phases. During the first phase, rats were trained to make a nose poke response to obtain a food reward. During the second phase, rats were trained to make a nose poke only after presentation of an auditory stimulus. During the third phase, the actual training program, rats were trained to make a nose poke only for the target stimulus (a 5-kHz pure tone) and not for a foil nontar- get stimulus (10-kHz pure tone). The tones were presented at 60 dB SPL, stimulus presentation was randomized, and the probability of a target stimulus presentation was set at 20%. Training was performed in an acoustically transparent operant training chamber (60  45  35 cm, length  width  height) contained within a sound-attenuated chamber. Sound presentation and response recording were per- formed using OpenEx software and RZ6 auditory process- ing hardware from Tucker-Davis Technology and delivered in a free field manner through a calibrated loudspeaker. The intertrial interval was selected at random from a range of 4–6 s. A rat’s behavioral state at any point in time eNeuro.org July/August 2018, 5(4) e0051-18.2018 eNeuro.org New Research 4 of 15 Table 1. Statistical table. This raises the possibility that the old brain has in fact a higher plastic potential than its young adult counterpart. To test this hypothesis, we examined the effect of pure-tone exposure on spectral tuning in the aged A1. We exposed old adult rats (OA, 22–23 months old, n  4) to 5 kHz tone pips for 1 week. For comparison, the same exposure was used in young adult (YA, 6–8 months old, n  4) and immature rats in their CP window (I, P10–P17, n  8; Fig. 1A). We then compared the proportion of A1 neurons whose characteristic frequency was close to the exposure frequency. As expected, there was a clear effect of 5-kHz tone exposure on the CF of immature rats (two-way ANOVA, exposure group  fre- quency bin, F(11,168)  14.84, p  0.001a). Such an exposure resulted in a significant overrepresentation of the exposure tone in A1 of immature rats (average % difference in the proportion of recording sites tuned within octave of exposure tone, relative to control: 9.77  1.54% increase, p  0.001a, with Tukey–Kramer correc- tion) but not in the young adult group (F(11,72)  4.02, p  0.001; 3.84  1.3% increase, p  0.87b, with Tukey– Kramer correction; Fig. 1B). Passive tone exposure, how- ever, resulted in a significant overrepresentation of the ley et al., 2012; Ouellet and de Villers-Sidani, 2014; Steb- bings et al., 2016). This raises the possibility that the old brain has in fact a higher plastic potential than its young adult counterpart. To test this hypothesis, we examined the effect of pure-tone exposure on spectral tuning in the aged A1. We exposed old adult rats (OA, 22–23 months old, n  4) to 5 kHz tone pips for 1 week. For comparison, the same exposure was used in young adult (YA, 6–8 months old, n  4) and immature rats in their CP window (I, P10–P17, n  8; Fig. 1A). We then compared the proportion of A1 neurons whose characteristic frequency was close to the exposure frequency. As expected, there was a clear effect of 5-kHz tone exposure on the CF of immature rats (two-way ANOVA, exposure group  fre- quency bin, F(11,168)  14.84, p  0.001a). Table 1. Statistical table. Table 1. Statistical table. Passive tone exposure induces significant shifts in A1 tuning Aging is characterized by a progressive reduction in cortical inhibition to levels akin to those observed during developmental critical periods (Caspary et al., 2008; Stan- July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org B A Figure 1. Passive sound exposure alters frequency tuning in the aged A1. A, Representative A1 CF maps from naïve rats (top) and from rats exposed to 5-kHz pure tones during 1 week (bottom). D, dorsal; C, caudal; R, rostral; V, ventral. B, Difference in frequency tuning between naïve and exposed rats expressed as A1 percentage area and separated by CF for immature, young adult, and old adult groups. Immature group: n  8, recorded sites  389; YA: n  8, recorded sites  403; OA: n  8, recorded sites  382; immature-exposed: n  8, recorded sites  362; YA-exposed: n  4, recorded sites  177; OA-exposed: n  4, recorded sites  168. Values shown are mean, two-way ANOVA with Tukey–Kramer correction. New Research 5 of 15 New Research 5 of 15 A A B Figure 1. Passive sound exposure alters frequency tuning in the aged A1. A, Representative A1 CF maps from naïve rats (top) and from rats exposed to 5-kHz pure tones during 1 week (bottom). D, dorsal; C, caudal; R, rostral; V, ventral. B, Difference in frequency tuning between naïve and exposed rats expressed as A1 percentage area and separated by CF for immature, young adult, and old adult groups. Immature group: n  8, recorded sites  389; YA: n  8, recorded sites  403; OA: n  8, recorded sites  382; immature-exposed: n  8, recorded sites  362; YA-exposed: n  4, recorded sites  177; OA-exposed: n  4, recorded sites  168. Values shown are mean, two-way ANOVA with Tukey–Kramer correction. B B Figure 1. Passive sound exposure alters frequency tuning in the aged A1. A, Representative A1 CF maps from naïve rats (top) and from rats exposed to 5-kHz pure tones during 1 week (bottom). D, dorsal; C, caudal; R, rostral; V, ventral. B, Difference in frequency tuning between naïve and exposed rats expressed as A1 percentage area and separated by CF for immature, young adult, and old adult groups. Passive tone exposure induces significant shifts in A1 tuning Immature group: n  8, recorded sites  389; YA: n  8, recorded sites  403; OA: n  8, recorded sites  382; immature-exposed: n  8, recorded sites  362; YA-exposed: n  4, recorded sites  177; OA-exposed: n  4, recorded sites  168. Values shown are mean, two-way ANOVA with Tukey–Kramer correction. Enhancing cortical inhibition stabilizes frequency representation in the aged A1 exposure tone in the aged A1 group (F(11,72)  10.77, p  0.001, two-way ANOVA; 8.05  1.14% increase, p  0.001c, with Tukey–Kramer correction). Enhancing cortical inhibition stabilizes frequency representation in the aged A1 Having documented the existence of age-related tuning instability in A1, and considering the reduction of intra- cortical inhibition in sensory cortices associated with ad- vanced age (Lehmann et al., 2012; Wang and Fawcett, 2012), we hypothesized that increasing GABAergic tone would restore the excitatory/inhibitory (E/I) balance and prevent further plastic changes elicited by passive tone exposure. To determine the effect of enhancing inhibition on frequency tuning stability in aged rats, we systemically administered the GABAA agonist diazepam (1 mg/kg i.p., twice a day; n  4) during two consecutive pure-tone exposures as described above (10-kHz pure tones for 1 week followed by 5-kHz pure tones for 1 week; Fig. 2C). We found that diazepam administration resulted in an overrepresentation of the first (10-kHz) rather than the second (5-kHz) exposure tone (F(11,72)  7.23, p  To further document the extent of this tuning instability in older rats, we examined the effect of two consecutive pure-tone exposures over a 2-week period. Young (n  4) and old (n  4) adult rats were exposed to 10-kHz tone pips during the first week and to 5-kHz tone pips during the second week (Fig. 2A). This passive exposure proto- col resulted in an overrepresentation of the second (5- kHz) exposure tone in A1 of aged rats (F(11,72)  13.13, p  0.001, two-way ANOVA; 5 kHz: 8.81  1.7% in- crease, p  0.001; 10 kHz: 5.18  1.3% decrease, p  0.35d, with Tukey–Kramer correction) but did not alter the frequency tuning map of young adults (F(11,72)  2.69, p  0.005, two-way ANOVA; 5 kHz: 2.1  0.56% de- crease, p  1; 10 kHz: 3.4  0.57% decrease, p  0.96e, with Tukey–Kramer correction; Fig. 2B). eNeuro.org eNeuro.org eNeuro.org July/August 2018, 5(4) e0051-18.2018 New Research 6 of 15 D C B A Figure 2. Restoration of inhibition stabilizes frequency representation in the aged A1. Young and old adult rats were exposed to 10-kHz pure tones for 1 week, followed immediately by exposure to 5-kHz pure tones for 1 week. A, Representative A1 CF maps from young (left) and old (right) adult rats that received sham (saline) intraperitoneal injections during the 2-week passive exposure period. Enhancing cortical inhibition stabilizes frequency representation in the aged A1 B, Difference in frequency tuning between naïve and saline-treated rats expressed as A1 percentage area and separated by CF. C, Representative A1 CF map from an old adult rat that received diazepam (DZP) intraperitoneal injections during the 2-week passive exposure period. D, Difference in frequency tuning between naïve and DZP-treated rats. To investigate whether sequential exposure to pure tones would have a similar effect in immature rats, 2-week exposures were conducted starting on P10 as described in Fig. 2-1. YA-saline group: n  4, recorded sites  230; OA-saline: n  4, recorded sites  203; OA-diazepam: n  4; recorded sites  218. Values shown are mean, two-way ANOVA with Tukey–Kramer correction. Conventions as in Fig. 1. C A C C A D D D B B D Figure 2. Restoration of inhibition stabilizes frequency representation in the aged A1. Young and old adult rats were exposed to 10-kHz pure tones for 1 week, followed immediately by exposure to 5-kHz pure tones for 1 week. A, Representative A1 CF maps from young (left) and old (right) adult rats that received sham (saline) intraperitoneal injections during the 2-week passive exposure period. B, Difference in frequency tuning between naïve and saline-treated rats expressed as A1 percentage area and separated by CF. C, Representative A1 CF map from an old adult rat that received diazepam (DZP) intraperitoneal injections during the 2-week passive exposure period. D, Difference in frequency tuning between naïve and DZP-treated rats. To investigate whether sequential exposure to pure tones would have a similar effect in immature rats, 2-week exposures were conducted starting on P10 as described in Fig. 2-1. YA-saline group: n  4, recorded sites  230; OA-saline: n  4, recorded sites  203; OA-diazepam: n  4; recorded sites  218. Values shown are mean, two-way ANOVA with Tukey–Kramer correction. Conventions as in Fig. 1. 0.001, two-way ANOVA; 5 kHz: 2.23  1.45% increase, p  1; 10 kHz: 13.8  5.7% increase, p  0.001f, cor- rected with Tukey–Kramer test; Fig. 2D). (Hensch et al., 1998; Fagiolini and Hensch, 2000). July/August 2018, 5(4) e0051-18.2018 Enhancing cortical inhibition stabilizes frequency representation in the aged A1 In line with these observations, sequential tone exposure in im- mature rats treated with diazepam  (n  4) resulted in a significant expansion of the tone presented during the span of the CP; i.e., the first exposure tone (F(11,120)  12.58, p  0.001, two-way ANOVA; 5 kHz: 11.93  3.6% increase, p  0.018; 10 kHz: 6.11  1.1% decrease, p  0.1h, corrected with Tukey–Kramer test; Fig. 2-1A, B, right). To investigate whether sequential exposure to pure tones would have a similar effect in immature animals as in old adult animals, we used a sequential 2-week expo- sure paradigm starting at P10 (5 kHz pure tones for 1 week, followed by 10 kHz pure tones for 1 week, n  5). Previous experiments have shown that passive tone ex- posure outside the CP for frequency tuning (P10–P14) does not alter the A1 tonotopic map (de Villers-Sidani et al., 2007). For this reason, we predicted that such an exposure would result in an overrepresentation of the tone presented during the CP—the first exposure tone— regardless of any subsequent tone presentation. As ex- pected, and in contrast to the results observed in the OA group, we observed plasticity in response to the first exposure tone (F(11,132)  14.62, p  0, two-way ANOVA; 5 kHz: 13.27  3.4% increase, p  0.001; 10 kHz: 5.72  1.6% decrease, p  0.15g, corrected with Tukey–Kramer test; Fig. 2-1A, left) in the vehicle (saline) condition. Reversal of adaptation in the immature and aged A1 Auditory neurons continuously monitor the environ- ment, suppressing their response to repetitive sounds and making novel stimuli more salient (Ulanovsky et al., 2003; Malmierca et al., 2014). In the adult A1, such stimulus-specific adaptation prevents the overrepresen- tation of repetitive stimuli that drive plasticity during early development (Norena et al., 2006) and is also involved in the selection of A1 representations that should be selec- tively suppressed in the context of training (Froemke et al., 2013). With aging, however, receptive fields be- come less reliable across successive repetitions of the same set of stimuli (Turner et al., 2005). Enhancing cortical inhibition stabilizes frequency representation in the aged A1 Immature group: n  8, recorded sites  376; YA: n  4, recorded sites  205; OA: n  4, recorded sites  192; I-MDZ: n  8, recorded sites  346; OA-MDZ: n  4, recorded sites  155. Figure 3. Improved adaptation in the immature and aged A1 following administration of the GABAA agonist midazolam. A, Stimulation paradigm. Left, a standard (high-probability) tone was presented 80% of times. Five oddball (low-probability) tones distributed around the standard frequency (middle) were interspersed in the repetitive tone presentation (right). B, Representative normalized responses of individual A1 neurons to a standard tone (5 or 12 kHz at a repetition rate of 3 Hz) as function of tone position in the stimulus sequence. Red horizontal lines represent the average normalized firing rate in response to the standard tone during two different intervals in the stimulus sequence: early (T1, event 100–300; dashed line), and late (T2, event 900–1100; solid line). Note that adaptation is reduced in both immature (I) and old adult rats. C, Probability distribution plot of the slope of firing rate trace in response to the standard tone (interval from event no. 150–1200). Red dots denote the location of the median value for each group. Fig. 3-1 provides a summary of data related to adaptation in response to repetitive tones for all five groups. D, Frequency tuning of representative A1 neurons during T1 (dashed line) and T2 (solid line). The normalized spike rate is plotted for the standard tone (arrow) and each of the five deviant tones. Note the acute change in tuning after standard-oddball presentation in I and OA rats. E, Representative A1 activity maps depicting the change in firing rate at T2 relative to T1 (T2/T1 ratio of normalized firing rate). Warmer colors (white, yellow) denote neurons with reduced adaptation, notably in the I and OA groups. Same conventions apply for panels F–I, which show that midazolam improved adaptation and prevented changes in tuning in the immature and aged A1. Immature group: n  8, recorded sites  376; YA: n  4, recorded sites  205; OA: n  4, recorded sites  192; I-MDZ: n  8, recorded sites  346; OA-MDZ: n  4, recorded sites  155. 376; OA, 0.11  0.02  10 4, p  0.0014, z  –3.187j, number of recorded cortical sites  192; Wilcoxon rank- sum test; Fig. 3B, C). Enhancing cortical inhibition stabilizes frequency representation in the aged A1 Immature group: n  8, recorded sites  376; YA: n  4, recorded sites  205; OA: n  4, recorded sites  192; I-MDZ: n  8, recorded sites  346; OA-MDZ: n  4 recorded sites  155 A D B E C D E C B H F H G H I I F G I n in the immature and aged A1 following administration of the GABAA agonist midazolam. A, Stimulation e 3. Improved adaptation in the immature and aged A1 following administration of the GABAA agonist mid Figure 3. Improved adaptation in the immature and aged A1 following administration of the GABAA agonist midazolam. A, Stimulation paradigm. Left, a standard (high-probability) tone was presented 80% of times. Five oddball (low-probability) tones distributed around the standard frequency (middle) were interspersed in the repetitive tone presentation (right). B, Representative normalized responses of individual A1 neurons to a standard tone (5 or 12 kHz at a repetition rate of 3 Hz) as function of tone position in the stimulus sequence. Red horizontal lines represent the average normalized firing rate in response to the standard tone during two different intervals in the stimulus sequence: early (T1, event 100–300; dashed line), and late (T2, event 900–1100; solid line). Note that adaptation is reduced in both immature (I) and old adult rats. C, Probability distribution plot of the slope of firing rate trace in response to the standard tone (interval from event no. 150–1200). Red dots denote the location of the median value for each group. Fig. 3-1 provides a summary of data related to adaptation in response to repetitive tones for all five groups. D, Frequency tuning of representative A1 neurons during T1 (dashed line) and T2 (solid line). The normalized spike rate is plotted for the standard tone (arrow) and each of the five deviant tones. Note the acute change in tuning after standard-oddball presentation in I and OA rats. E, Representative A1 activity maps depicting the change in firing rate at T2 relative to T1 (T2/T1 ratio of normalized firing rate). Warmer colors (white, yellow) denote neurons with reduced adaptation, notably in the I and OA groups. Same conventions apply for panels F–I, which show that midazolam improved adaptation and prevented changes in tuning in the immature and aged A1. Enhancing cortical inhibition stabilizes frequency representation in the aged A1 To examine the Although treatment with diazepam accelerates the clos- ing of the CP (Iwai et al., 2003), it does not prevent experience-dependent plasticity from taking place July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org eNeuro.org New Research 7 of 15 E I H G F D C B A Figure 3. Improved adaptation in the immature and aged A1 following administration of the GABAA agonist midazolam. A, Stimulation paradigm. Left, a standard (high-probability) tone was presented 80% of times. Five oddball (low-probability) tones distributed around the standard frequency (middle) were interspersed in the repetitive tone presentation (right). B, Representative normalized responses of individual A1 neurons to a standard tone (5 or 12 kHz at a repetition rate of 3 Hz) as function of tone position in the stimulus sequence. Red horizontal lines represent the average normalized firing rate in response to the standard tone during two different intervals in the stimulus sequence: early (T1, event 100–300; dashed line), and late (T2, event 900–1100; solid line). Note that adaptation is reduced in both immature (I) and old adult rats. C, Probability distribution plot of the slope of firing rate trace in response to the standard tone (interval from event no. 150–1200). Red dots denote the location of the median value for each group. Fig. 3-1 provides a summary of data related to adaptation in response to repetitive tones for all five groups. D, Frequency tuning of representative A1 neurons during T1 (dashed line) and T2 (solid line). The normalized spike rate is plotted for the standard tone (arrow) and each of the five deviant tones. Note the acute change in tuning after standard-oddball presentation in I and OA rats. E, Representative A1 activity maps depicting the change in firing rate at T2 relative to T1 (T2/T1 ratio of normalized firing rate). Warmer colors (white, yellow) denote neurons with reduced adaptation, notably in the I and OA groups. Same conventions apply for panels F–I, which show that midazolam improved adaptation and prevented changes in tuning in the immature and aged A1. Direct application of midazolam (1 g/&micro;l at a rate of 0.5 l/min) to the cortex resulted on average in the progressive suppression of A1 responses to repetitive tones in the immature and older groups (median slope of normalized response rate: I, –0.13  0.02  10 4, p  1.1  10 5, z  –4.4p, number of recorded cortical sites  346; OA, –0.01  0.04  10 4, p  0.013, z  –2.46q, number of recorded cortical sites  155; Wilcoxon rank- sum test; Fig. 3F, G and Fig. 3-1A). It also resulted in a significant decrease in response to the high-probability tone in these groups (change in normalized firing rate in response to the standard tone, T2 minus T1; I: –0.12  0.04, p  0.001, t(720)  5.29r; OA: –0.09  0.06, p  0.03, t(345)  2.1s; t test). The overall response to the standard-oddball stimulus remained constant from T1 to T2 for both groups (difference in mean area under the curve between T1 and T2: I, 6.08  4.55, p  0.39, t(690)  0.86t; OA, 1.63  5.52, p  0.94, t(308)  0.08u; t test; Fig. 3H, I). A summary of A1 responses to repetitive tones and oddballs is provided in Fig. 3-1B. To determine the retention of learning and persistence of training-related A1 retuning, we characterized trained younger (YA-Tdelay, n  4) and older (OA-Tdelay, n  4) rats after a 4-week delay period following completion of train- ing (Fig. 4D, top). On average, younger rats maintained a significantly better performance than older when resum- ing training (YA-Tdelay: d=  2.8  0.12; OA-Tdelay: d=  0.96  0.48, p  0.002 t(6)  5.02y; Fig. 4D, bottom). A1 CF maps were reconstructed in another group of younger and older rats after the delay period (Fig. 4E). In these we found that the target tone representation in A1 had per- sisted in the younger but not older group (YA-Tdelay: F(11,72)  6.68, p  0.001, two-way ANOVA; 5 kHz: 10.37  2.3% increase, p  0.01z, corrected with Tukey– Kramer test; OA-Tdelay: F(11,72)  1.41, p  0.18ab, two- way ANOVA; 5 kHz: 4.72  2.1% increase; Fig. 4F). Interestingly, the sum of responses to high and low probability tones remained constant in the immature and young adult groups, while it increased for the old adult group (differ- ence in mean area under the curve between T1 and T2: I, 6.2  3.3, p  0.45, t(750)  0.75m; YA, 4.78  5, p  0.52, t(408)  0.64n; OA, 13.83  2.71, p  0.011, t(383)  2.55o; paired t test; Fig. 3D, E). neurons in the immature and old adult groups exhibited a significant increase in response to the high-probability tone from T1 to T2, while the opposite was seen in the young adult group (change in normalized firing rate, T2 minus T1: YA, –0.19  0.05; I, 0.18  0.04, p  0.001, t(579)  5.64k, relative to YA; OA, 0.15  0.09 p  9  10 4, t(395)  3.35l, relative to YA; t test). Interestingly, the sum of responses to high and low probability tones remained constant in the immature and young adult groups, while it increased for the old adult group (differ- ence in mean area under the curve between T1 and T2: I, 6.2  3.3, p  0.45, t(750)  0.75m; YA, 4.78  5, p  0.52, t(408)  0.64n; OA, 13.83  2.71, p  0.011, t(383)  2.55o; paired t test; Fig. 3D, E). In immature rats, short periods of auditory stimulation readily modify frequency tuning in A1, likely because of a disrupted E/I balance following the onset of hearing (Dorrn et al., 2010). Additionally, considering that GABAA- mediated inhibition regulates SSA (Duque et al., 2014), we hypothesized that transiently increasing inhibitory tone would improve adaptation in both the immature and aged A1. To test this possibility, we administered the short- acting GABAA agonist midazolam during the presentation of the same repetitive stimulus. Given the different time scales between our adaptation (10 min) and passive ex- posure (1–2 weeks) experiments, we decided to use midazolam as opposed to the long-acting GABAA agonist diazepam. Finally, to test whether pharmacologically increasing GABA inhibition would improve the retention of training- induced plastic changes, we treated a subgroup (n  4) of older rats with diazepam (1 mg/kg i.p., twice a day) during the delay period post-training. A1 mapping in this group revealed a persistent target tone overrepresentation not significantly different from what had been observed im- mediately following training (F(11,72)  5.42, p  0.001, two-way ANOVA; 5 kHz: 7.64  2.8% increase, p  0.022ac, corrected with Tukey–Kramer test; Fig. 4F). 8 of 15 et al., 2008; Lustig et al., 2009). To examine the impact of age on the retention of training-related plastic changes in A1, we compared the performance of young (n  8) and older (n  12) adult rats on an auditory discrimination task and then measured training-induced A1 changes at the end of training and after a 4-week delay. Both groups were trained on a two-tone discrimination task (target tone: 5 kHz, non-target tone: 10 kHz). Training ended once the rats’ discrimination reached a sustained value of D-prime (d=) 1 for two consecutive days; Fig. 4A, top). Older rats required on average more training sessions to reach criterion than younger adults (YA: 8.4  0.8 ses- sions; OA: 11.9  1.1, p  0.032, t(18)  2.32v; t test; Fig. 4A, bottom). At the end of training, A1 CF maps were obtained from a subgroup of young (YA-T, n  4) and a subgroup of old adult rats (OA-T, n  4; Fig. 4B). Two-way analysis of variance revealed a significant effect of training  frequency bin for both YA-T and OA-T groups (F(11,72)  13.42, p  0.001w; F(11,72)  6.57, p  0.001x; re- spectively). Compared to age-matched controls, both groups exhibited an increase in the number of neurons tuned to the target tone by the end of the training period (average % difference in the proportion of recording sites tuned within octave of exposure tone, relative to control: YA-T: 12.25  1.5% increase, p  0.029w; OA-T: 8.06  2.25% increase, p  0.004x, corrected with Tukey– Kramer test; Fig. 4C). We also found, as previously re- ported (Voss et al., 2016), that the nontarget frequency was underrepresented in the trained YA but not in the OA group (YA-T: 11.54  3.5% decrease, p  0.018w; OA-T: 6.7  2.2% decrease, p  0.41x, corrected with Tukey– Kramer test; Fig. 4C). neurons in the immature and old adult groups exhibited a significant increase in response to the high-probability tone from T1 to T2, while the opposite was seen in the young adult group (change in normalized firing rate, T2 minus T1: YA, –0.19  0.05; I, 0.18  0.04, p  0.001, t(579)  5.64k, relative to YA; OA, 0.15  0.09 p  9  10 4, t(395)  3.35l, relative to YA; t test). Enhancing cortical inhibition stabilizes frequency representation in the aged A1 extent to which aging A1 neurons exhibit SSA, we used 10-min-long trains of pure tones (Fig. 3A). As expected, we found a progressive decrease in A1 neuron responses to repetitive tones in younger adults (median slope of normalized response rate: YA, –0.14  0.03  10 4, number of recorded cortical sites  205) but an increase in responses to repetitive tones in the imma- ture and old adult groups relative to YA (median slope of normalized response rate: I, 0.09  0.03  10 4, p  4.1  10 5, z  –4.099i, number of recorded cortical sites  Tuning stability in the same A1 neurons was examined by interspersing five oddball (low-probability) tones cov- ering the hearing range during the repetitive (high- probability) tone presentation (see Methods). Using this method, coarse tuning curves could be constructed over two time intervals during the tone train exposure (T1, from 60 to 120 s; T2, from 400 to 460 s). On average, A1 July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org New Research 8 of 15 New Research July/August 2018, 5(4) e0051-18.2018 Impact of aging and dysregulated plasticity on auditory learning Our results using passive sound exposure over different time scales suggest that age-related loss of inhibition could return the cortex into a state of instability where sensory representations are continuously distorted by nonspecific passive experience. If the deleterious effects of age-related loss of inhibition observed on passive ex- perience extend to goal-oriented behavior, it is conceiv- able that reduced inhibition might contribute to make learning slower, harder, and more susceptible to decay, as has been clinically observed in older patients (Boyke July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org New Research 9 of 15 F E D C B A Figure 4. Aging and decay of training-induced A1 plasticity. Young and old adult rats were trained on a two-tone discrimination task (target tone: 10 kHz, nontarget: 5 kHz). A, Top: Experimental protocol. Bottom: Older adult rats needed on average more training sessions to reach criterion than young adult rats (D-prime 1; YA no. of sessions  8.4  1.1; OA  11.9  1.4, p  0.03). B, Representative A1 characteristic frequency (CF) maps from trained young (left) and old (right) adult rats. Bolded polygons have a CF at the target tone 0.3 octaves. Hatched polygons have a CF at the nontarget tone 0.3 octaves. C, Difference in frequency tuning between naïve and exposed rats expressed as A1 percentage area and separated by CF. The full arrows point to the target frequency; the hatched arrows points to the nontarget frequency. D, Top: To determine the persistence of learning and training-induced A1 map plasticity, a subgroup of YA-T and two subgroups of OA-T rats were subjected to a 4-week delay after reaching criterion, followed by behavioral re-assessment and A1 mapping. Bottom: From the first session of the reassessment onwards, young adult rats performed above criterion, while old adult rats performed above criterion from the second session onwards. E, Representative A1 characteristic frequency (CF) maps from trained rats that received daily sham (saline) or diazepam (DZP) injections during the delay period. F, Difference in A1 area tuned to various frequencies between each experimental group and untrained age-matched controls. YA-T group: n  4, recorded sites  212; OA-T: n  4, recorded sites  209; YA-Tdelay: n  4; recorded sites  192; OA-Tdelay: n  4; recorded sites  203; OA-Tdelay(DZP): n  4; recorded sites  189. Tonic GABAergic inhibition is reduced in the aged A1 Tonic GABAergic inhibition is reduced in the aged A1 Tonic GABAergic inhibition is reduced in the aged A1 To study the anatomic correlates of frequency tuning instability and impaired training performance, we sampled GABA concentration using microdialysis and quantified PV/PNN expression in A1 through immunohistochemistry. As documented in previous research (Morrison and Bax- ter, 2012; Rozycka and Liguz-Lecznar, 2017), we found that GABA concentration in A1 interstitial fluid was 25% lower in older adult rats (OA, 24 months old, n  4) than in young adult controls (YA, 6 months old, n  4) when measured in silence (YA, 100  7.9%; OA, 75.2  5.8% relative to YA; p  0.04, t(6)  2.53ad, t test; Fig. 5-1A). This difference was more pronounced during continuous sound presentation (see Methods). In the latter experi- mental condition, a relative reduction close to 40% was noted (YA-stim, 124  7.7%; OA-stim, 88.2  6.0% relative to YA-stim; p  0.01, t(6)  3.66ae, t test; Fig. 5-1B). ; y ; g g ) Further examination revealed that staining intensity of individual PV cells could be divided into four subgroups: low, intermediate low, intermediate high, and high inten- sity (Donato et al., 2013). We found a smaller proportion of high-intensity PV cells in older rats compared to young adults (H(4)  13, p  0.011aj, Kruskal–Wallis test; fraction of PV cells with low staining intensity and p-value relative to YA, per group: Ilow  16  7.1%, p  0.82; YAlow  14  3.2%; OAlow  2.9  0.4%, p  0.005; IDlow  12.1  1.7%, p  0.99; OADlow  14.2  3.2%, p  0.99ah; Tukey–Kramer test; Fig. 5C and Fig. 5-4B). A similar anal- ysis was performed on PNNs, which could also be divided into four staining intensity groups. Tonic GABAergic inhibition is reduced in the aged A1 We found on average a higher proportion of low-intensity PNNs in aged rats com- pared to young adults (H(4)  17.24, p  0.0017, Kruskal– Wallis test; fraction of low-intensity PNNs and p-value relative to YA, per group: Ilow  55  8.1%, p  0.48; YAlow  34  2.2%; OAlow  55  1.7%, p  0.04ai, Tukey–Kramer test) and a decrease in the high-intensity PNN subgroup in immature and aged rats compared to young adults (H(4)  22.06, p  0.001, Kruskal–Wallis test; fraction of high-intensity PNNs and p-value relative to YA, per group: Ihigh  3.5  1.7%, p  0.004; YAhigh  26  1.9%; OAhigh  9.3  2.7%, p  0.039aj; Tukey– Kramer test). Notably, following diazepam treatment, the proportion of low-intensity PNNs in older rats decreased, whereas the proportion of high-intensity PNNs in both immature and older rats increased, resulting in an inten- sity staining distribution that resembled that of the control (YA) group (fraction of PNN as a function of staining intensity and p-value relative to YA, per group: IDlow  31.1  1.9%, p  0.8; OADlow  47  3.1%, p  0.99ai; IDhigh  27.2  0.5%, p  0.99; OADhigh  21.2  3.5%, p  0.85aj; Tukey–Kramer test; Fig. 5E and Fig. 5-4D). Impact of age on perineuronal nets and PV neurons in A1 PV- and SST-positive cells constitute the two largest interneuron subpopulations throughout the cortex. In par- ticular, PV neurons and associated PNNs are important regulators of experience-dependent plasticity throughout life (Caroni et al., 2012; Wang and Fawcett, 2012). Re- duced cortical staining of PV and PNN are both associ- ated with cortical immaturity and increased instability of cortical representations (Pizzorusso et al., 2002; McRae et al., 2007; Wang and Fawcett, 2012; Donato et al., 2013). To assess whether age-related representational insta- bility would be paralleled by a reduction in these plasticity-regulating structural elements, we first charac- terized the expression of the main interneuron subpopu- lations in the context of total cell counts for the three age groups—immature, young adult, and older adult—in- cluded in the present study (see Fig. 5-2 and Fig. 5-3 for cell counts and representative micrographs of interneu- rons, respectively). This analysis confirmed previous re- search showing a decrease in PV and SST cell counts associated with aging (Ouda et al., 2008; Ouellet and de Villers-Sidani, 2014). We then examined PV and PNN staining intensity in our different experimental groups (I, n  6; YA, n  6; OA, n  6; ID, n  3; OAD, n  3; Fig. 5A). In line with previous reports (Hilbig et al., 2002; Ouda et al., 2008), we found decreased PV staining intensity with aging, which was recovered with 2-week-long diaz- epam treatment [median staining intensity  MAD per PV cell, arbitrary confocal units (au)  105; H(4)  14.52, p  0.0058, Kruskal–Wallis test; I: 1.17  0.85, p  0.52, relative to YA; YA: 1.19  0.69; OA: 1  0.53, p  0.011, relative to YA; ID: 1.3  0.66, p  0.96, relative to YA; OAD: 1.1  0.76, p  0.97af, relative to YA; Tukey–Kramer test; Fig. 5B and Fig. 5-4A]. PNN staining intensity, in contrast, showed a more contrasting lifetime trajectory, increasing from immature to young adult age and then reversing course with aging (Fig. 5D). Like our findings on PV cells, diazepam treatment resulted in recovery of New Research 10 of 15 PNN intensity staining for immature and older adult rats (median staining intensity per PNN, au  105; H(4)  83.97, p  0.0001, Kruskal–Wallis test; I: 0.7  0.79, p  0.0001, relative to YA; YA: 1.64  1.37; OA: 0.76  1.04, p  0.001, relative to YA; ID: 1.79  1.39, p  0.96, relative to YA; OAD: 1.11  1.33, p  0.003ag, relative to YA; Tukey–Kramer test; Fig. 5D and Fig. 5-4C). Impact of aging and dysregulated plasticity on auditory learning Values shown are mean  SEM, t test, two-way ANOVA with A C B B A A B C C D F E E D E F Figure 4. Aging and decay of training-induced A1 plasticity. Young and old adult rats were trained on a two-tone discrimination task (target tone: 10 kHz, nontarget: 5 kHz). A, Top: Experimental protocol. Bottom: Older adult rats needed on average more training sessions to reach criterion than young adult rats (D-prime 1; YA no. of sessions  8.4  1.1; OA  11.9  1.4, p  0.03). B, Representative A1 characteristic frequency (CF) maps from trained young (left) and old (right) adult rats. Bolded polygons have a CF at the target tone 0.3 octaves. Hatched polygons have a CF at the nontarget tone 0.3 octaves. C, Difference in frequency tuning between naïve and exposed rats expressed as A1 percentage area and separated by CF. The full arrows point to the target frequency; the hatched arrows points to the nontarget frequency. D, Top: To determine the persistence of learning and training-induced A1 map plasticity, a subgroup of YA-T and two subgroups of OA-T rats were subjected to a 4-week delay after reaching criterion, followed by behavioral re-assessment and A1 mapping. Bottom: From the first session of the reassessment onwards, young adult rats performed above criterion, while old adult rats performed above criterion from the second session onwards. E, Representative A1 characteristic frequency (CF) maps from trained rats that received daily sham (saline) or diazepam (DZP) injections during the delay period. F, Difference in A1 area tuned to various frequencies between each experimental group and untrained age-matched controls. YA-T group: n  4, recorded sites  212; OA-T: n  4, recorded sites  209; YA-Tdelay: n  4; recorded sites  192; OA-Tdelay: n  4; recorded sites  203; OA-Tdelay(DZP): n  4; recorded sites  189. Values shown are mean  SEM, t test, two-way ANOVA with Tukey–Kramer correction. July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org Discussion Our findings indicate that experience-dependent plas- ticity increases with aging following a natural reduction in cortical inhibition. Such increased plasticity may facilitate changes elicited by experience but also impair the brain’s capacity to crystallize such changes. Brain aging is characterized by a down-regulation of cortical inhibition, which contributes to a range of func- tional deficits such as reduced selectivity of receptive fields, degraded temporal processing, heightened re- sponses to noise, and reduced adaptation to repetitive stimuli (Turner et al., 2005; Hua et al., 2006; Caspary et al., 2008; Liguz-Lecznar et al., 2014; Schreiner and Polley, 2014). What are the mechanisms of age-related reduction in inhibition? Recent findings suggest that reduced inhibi- tion might not be a result of aging itself (Gourevitch et al., July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org New Research 11 of 15 B C A D E Figure 5. Impact of age on structural inhibitory elements in the auditory cortex. A, High-power microphotographs of representative sections immunolabeled for perineuronal nets (PNN) and parvalbumin (PV) from immature (I), young adult (YA), old adult, immature  diazepam treatment (IA), and old adult  diazepam treatment (OAD) rats. B, D, Group fluorescence optical density for (B) PV and (D) PNN staining for each age group (all cortical layers; green boxes represent median values). C, E, Distribution of (C) PV cell and (E) PNN intensity staining for each age group. Fig. 5-1 compares A1 GABA concentration between YA and OA rats. Cell count per field for different neuronal types and age groups are detailed in Fig. 5-2. Fig. 5-3 shows representative micrographs of PV- and SST-positive cells. A summary of the cumulative distribution of staining intensity and interindividual variability for all groups is provided in Fig. 5-4. Number of hemispheres examined: I  12, YA  12, OA  12, ID  6, OAD  6; total cell count per group: I  418, YA  343, OA  236, ID  156, OAD  231. Values shown are mean  SEM. p  0.05 relative to YA; Kruskal–Wallis test, corrected for multiple comparisons using Tukey–Kramer test. New Research 11 of 15 B B C A C C A B E D D E Figure 5. Impact of age on structural inhibitory elements in the auditory cortex. Discussion A, High-power microphotographs of representative sections immunolabeled for perineuronal nets (PNN) and parvalbumin (PV) from immature (I), young adult (YA), old adult, immature  diazepam treatment (IA), and old adult  diazepam treatment (OAD) rats. B, D, Group fluorescence optical density for (B) PV and (D) PNN staining for each age group (all cortical layers; green boxes represent median values). C, E, Distribution of (C) PV cell and (E) PNN intensity staining for each age group. Fig. 5-1 compares A1 GABA concentration between YA and OA rats. Cell count per field for different neuronal types and age groups are detailed in Fig. 5-2. Fig. 5-3 shows representative micrographs of PV- and SST-positive cells. A summary of the cumulative distribution of staining intensity and interindividual variability for all groups is provided in Fig. 5-4. Number of hemispheres examined: I  12, YA  12, OA  12, ID  6, OAD  6; total cell count per group: I  418, YA  343, OA  236, ID  156, OAD  231. Values shown are mean  SEM. p  0.05 relative to YA; Kruskal–Wallis test, corrected for multiple comparisons using Tukey–Kramer test. 2014). Young rats housed in a noisy auditory environment exhibit auditory perceptual deficits that mirror those ob- served in aging (Kamal et al., 2013; Gourevitch et al., 2014), alongside reduced GABA and interneuron expres- sion (Zhou et al., 2011; Zhou and Merzenich, 2012). These impairments, however, are observed exclusively in rats exposed to continuous nonmodulated noise, but not after amplitude-modulated noise exposure (Thomas et al., 2018), suggesting that it is the lack of structured in- puts—as opposed to noise per se—that drives maladap- tive plasticity in the auditory cortex (Voss et al., 2017). It is therefore possible that age-related maladaptive plastic changes are a consequence of continuous, nonstructured “noisy” inputs, whether originating from the environment or resulting from conductive, sensorineural, or strial hear- ing loss (Jayakody et al., 2018). Prolonged exposure to distorted inputs might destabilize the activity of local neural circuits (Gourevitch et al., 2014) and trigger com- pensatory homeostatic changes (Burrone and Murthy, 2003; Dean et al., 2005; Turrigiano, 2011) that ultimately amplify excitatory inputs and reduce inhibition (Rothman et al., 2009; Tyagarajan et al., 2011). 2014). Discussion In the present study, this deficit was evident on a 10-min-long exposure to repetitive tones (Fig. 3B–E). We found impaired adap- tation and tuning instability in the aged A1, whereas in- creasing inhibition with a short-acting GABAA agonist improved adaptation and reversed the tendency of aged A1 neurons to increase their tuning to the repetitive tone (Fig. 3F–I). Although there might be differences in the physiologic response to anesthesia between aged and adult animals, it should be noted that SSA is a property found in A1 and subcortical auditory nuclei that is mini- mally affected by anesthesia (Richardson et al., 2013; Duque and Malmierca, 2015). Tuning instability was further confirmed by the fact that a short 1-week pip tone exposure sufficed to produce an overrepresentation of the exposure tone in older rats, as previously seen in immature rats (Fig. 1). However, this increased plasticity in the aged auditory cortex does not seem to be limited to a short time window, as is the case with the CP. In the present study, immature rats exposed successively to two different pure tones exhibited plastic- ity in response to the first tone, most likely because only the first tone exposure overlapped with the CP (Fig. 2A). Whereas a rapid and sustained increase in inhibition (Fa- giolini and Hensch, 2000; Iwai et al., 2003; Hensch, 2005) ends the CP and prevents additional alterations due to passive sound exposure, a subsequent 1-week exposure to a different tone resulted in the overrepresentation of the latter tone in aged rats. Interestingly, boosting GABA inhibition consolidated frequency tuning representation and made the aging A1 again resistant to further altera- tions, thus “closing” this period of maladaptive increased plasticity (Fig. 2C). Follow-up studies may want to rule out the possibility, although unlikely, that diazepam selec- tively affects the processing of frequency tones in the 10-kHz range by presenting a lower frequency tone (e.g. 5 kHz) before the 10-kHz tone during diazepam treatment. Taken together, these findings suggest that the aging A1 appears to be in a permanent state of heightened plas- ticity to levels akin to those observed during early devel- opment. Discussion Proposed model of the impact of age on A1 plasticity. During periods of life characterized by a low inhibitory tone, passive exposure alters the A1 CF map. Plastic changes to the immature A1 are long lasting: as inhibition increases, the CP ends and sensory representations become stable. In contrast, plastic changes to the aged A1 are short-lived, as these cannot be consolidated due to a persistent low inhibitory tone. New Research 12 of 15 New Research 12 of 15 Figure 6. Proposed model of the impact of age on A1 plasticity. During periods of life characterized by a low inhibitory tone, passive exposure alters the A1 CF map. Plastic changes to the immature A1 are long lasting: as inhibition increases, the CP ends and sensory representations become stable. In contrast, plastic changes to the aged A1 are short-lived, as these cannot be consolidated due to a persistent low inhibitory tone. The slower rate of learning in aged rats supports previous findings showing that age-related cortical pro- cessing deficits contribute to degraded behavioral perfor- mance (Barnes et al., 1997; Gazzaley et al., 2005; Samson and Barnes, 2013; Fig. 4A–C). According to the map expansion-renormalization model, initial sensory map ex- pansion is necessary for discrimination learning (Taka- hashi et al., 2010; Reed et al., 2011). However, once subjects become experts at a task and reach a plateau in performance, their maps return to their previous state (Reed et al., 2011). In the present study, training was suspended before rats reached this plateau, and both groups exhibited typical training-induced map changes (Blake et al., 2006; Polley et al., 2006; Zhou et al., 2010). Learning becomes more susceptible to decay with aging (Lustig et al., 2009), which was evident after a 1-month delay period (Fig. 4D-F). Interestingly, training-induced map changes were preserved in the old rats treated with diazepam during the delay period between end of training and cortical mapping. Although map expansion was still present after this relatively short delay period, we did not measure the behavioral implications or the extent of this persistence beyond 1-month follow-up. Further studies will be necessary to fully understand the behavioral rele- vance of sustained map plasticity for learning. Functional deficits in the aged A1 include slowed and incomplete suppression of background distractors, which further impairs the detection of novel stimuli (de Villers- Sidani et al., 2010; Mishra et al., 2014). July/August 2018, 5(4) e0051-18.2018 Discussion Young rats housed in a noisy auditory environment exhibit auditory perceptual deficits that mirror those ob- served in aging (Kamal et al., 2013; Gourevitch et al., 2014), alongside reduced GABA and interneuron expres- sion (Zhou et al., 2011; Zhou and Merzenich, 2012). These impairments, however, are observed exclusively in rats exposed to continuous nonmodulated noise, but not after amplitude-modulated noise exposure (Thomas et al., 2018), suggesting that it is the lack of structured in- puts—as opposed to noise per se—that drives maladap- tive plasticity in the auditory cortex (Voss et al., 2017). It is therefore possible that age-related maladaptive plastic changes are a consequence of continuous, nonstructured “noisy” inputs, whether originating from the environment or resulting from conductive, sensorineural, or strial hear- ing loss (Jayakody et al., 2018). Prolonged exposure to distorted inputs might destabilize the activity of local neural circuits (Gourevitch et al., 2014) and trigger com- pensatory homeostatic changes (Burrone and Murthy, 2003; Dean et al., 2005; Turrigiano, 2011) that ultimately The aforementioned studies strongly suggest that age- related anatomic and functional deficits can be modeled in noise-exposed young adult rats. Furthermore, rats ex- posed to nonstructured noise recover normal function when returned to their normal environment (Zhou and Merzenich, 2012; Kamal et al., 2013). Taken together, these observations suggest that perceptual deficits ob- served in the aged cortex have a significant activity- dependent component, rather than being purely age- related, and are thus at least partially reversible (Hilbig et al., 2002; Zhou and Merzenich, 2012; Liguz-Lecznar et al., 2014). For instance, GABA agonists increase selec- tivity of receptive fields in the primary visual cortex (Lev- enthal et al., 2003; Hua et al., 2006), classic conditioning enhances the expression of GABAergic markers in the barrel cortex (Liguz-Lecznar et al., 2014), and operant conditioning results in increased PV expression in A1 (de Villers-Sidani et al., 2010). July/August 2018, 5(4) e0051-18.2018 eNeuro.org eNeuro.org Figure 6. Proposed model of the impact of age on A1 plasticity. During periods of life characterized by a low inhibitory tone, passive exposure alters the A1 CF map. Plastic changes to the immature A1 are long lasting: as inhibition increases, the CP ends and sensory representations become stable. In contrast, plastic changes to the aged A1 are short-lived, as these cannot be consolidated due to a persistent low inhibitory tone. New Research 12 of 15 Figure 6. eNeuro.org New Research 13 of 15 needed. Similarly, interventions that delay cortical matu- ration during early development (Chang and Merzenich, 2003; de Villers-Sidani et al., 2008) and those that impair auditory processing during adulthood (Martin del Campo et al., 2012; Zhou and Merzenich, 2012) result in de- creased PV staining and increased plasticity. In line with these observations, we found a moderate increase in the low-PV fraction in the immature and aged A1, the age groups that showed increased experience-dependent plasticity. Moreover, the high-PV fraction was significantly diminished in the aged (Fig. 5B, C), which could account for the inadequate consolidation of newly formed sensory representations (Caroni et al., 2012; Donato et al., 2013). PNNs are extracellular matrix deposits produced jointly by neurons and astrocytes, particularly around PV cells (McRae et al., 2007; Nakamura et al., 2009), forming both a structural and functional barrier that limits plasticity (Pizzorusso et al., 2002; Berardi et al., 2004; Wang and Fawcett, 2012). We found age-related changes in PNNs that mirrored those documented for PV cells; namely, a lower average staining density of PNNs in the extremes of life, characterized by an increase in the low-PNN fraction and a decrease in the high-PNN fraction. Interestingly, while age-related PNN intensity differences were more striking than those observed for PV cells, diazepam treatment in both cases resulted in a redistribution of the low- and high-intensity subgroups in immature and older adult rats toward values that resembled those of the young adult group (Fig. 5D, E). The disparity in histology results between PV cells and associated PNNs in imma- ture rats supports the idea that PV cell development predates PNN assembly (Baker et al., 2017), suggesting that adequate PV cell functioning is required for PNN formation (Yamada et al., 2015; Quattromani et al., 2017). The present study contributes to the understanding of how plasticity is regulated in the aged brain. Whereas previous studies have shown that GABAergic inhibition declines with age (Leventhal et al., 2003; Caspary et al., 2008; Liguz-Lecznar et al., 2014) and that passive sound exposure can alter cortical response properties in adult- hood (Norena et al., 2006; Pienkowski et al., 2011), our study is the first one to show that A1 experience-de- pendent plasticity increases with aging. Further targeted In the human research domain, our findings may be particularly relevant to studies that are currently underway and that have potential clinical applications. Interestingly, while age-related PNN intensity differences were more striking than those observed for PV cells, diazepam treatment in both cases resulted in a redistribution of the low- and high-intensity subgroups in immature and older adult rats toward values that resembled those of the young adult group (Fig. 5D, E). The disparity in histology results between PV cells and associated PNNs in imma- ture rats supports the idea that PV cell development predates PNN assembly (Baker et al., 2017), suggesting that adequate PV cell functioning is required for PNN formation (Yamada et al., 2015; Quattromani et al., 2017). Traditionally, aging has been regarded as a period of limited plasticity. However, our experiments suggest that this idea is unlikely to be correct in detail, as the aged brain is in some ways more plastic than the young adult brain. We propose that the inhibitory regulation of plas- ticity, rather than plasticity per se, is reduced in the aged brain (Fig. 6). Researchers and clinicians may build on this knowledge to develop rehabilitation strategies with at least two complementary objectives in mind: first, taking advantage of increased plasticity to enhance seniors’ functional recovery after neurologic injury, and second, regulating plasticity to preserve the benefits of rehabilita- tion and promote long-lasting recovery. The present study contributes to the understanding of how plasticity is regulated in the aged brain. Whereas previous studies have shown that GABAergic inhibition declines with age (Leventhal et al., 2003; Caspary et al., 2008; Liguz-Lecznar et al., 2014) and that passive sound exposure can alter cortical response properties in adult- hood (Norena et al., 2006; Pienkowski et al., 2011), our study is the first one to show that A1 experience-de- pendent plasticity increases with aging. Further targeted manipulations of GABAergic function will be necessary to pinpoint the exact mechanisms underlying this age-related dysregulation of plasticity and to understand whether altered excitatory neurotransmission during aging (Benali et al., 2008) also plays a role. Discussion g Our findings of reduced PV and SST expression sup- port numerous reports of reduced interneuron cell counts associated with aging (Rozycka and Liguz-Lecznar, 2017), suggesting that inhibitory deficits may be related to the dysfunction of specific interneuron cell subtypes (Cha et al., 1997; Ouda et al., 2008; Fish et al., 2013). Recent research, however, has focused on PV expression as a proxy for cellular function and has shown that cortical PV staining intensity is tightly correlated with the degree of experience-dependent plasticity (Zhou et al., 2011; Ca- roni, 2015). As a case in point, recent studies by Donato et al. (2013, 2015) demonstrate the impact of reduced PV staining on cell function. High-intensity PV cells are found on completion of learning and immediately after fear conditioning, situations in which stable, long-lasting sensory representations are warranted (Donato et al., 2013). Conversely, low-intensity PV cells are abundant during learning and following environmental enrichment, situations in which a more flexible cortical network is July/August 2018, 5(4) e0051-18.2018 eNeuro.org In the ab- sence of region-selective drugs to modulate GABAergic neurotransmission, studies using noninvasive brain stim- ulation (NIBS) are exploring the effects of manipulating cortical E/I balance on learning in the elderly (Opie and Cirillo, 2017). For instance, Opie et al. (2017) used two modalities of transcranial magnetic stimulation to alter cortical excitability before a motor learning task but found no benefit in healthy aged volunteers. In contrast, a sub- sequent study using transcranial direct current stimulation found that increasing inhibition before testing, followed by decreasing inhibition during testing, resulted in greater skill improvement in older adults (Fujiyama et al., 2017). We posit that a follow-up experiment using NIBS could be used to test our hypotheses of the role of inhibition in the acquisition and retention of learning—specifically, to test whether reducing inhibition early during training increases plasticity and facilitates learning, and whether increasing inhibition after learning facilitates the crystallization of newly acquired skills. needed. Similarly, interventions that delay cortical matu- ration during early development (Chang and Merzenich, 2003; de Villers-Sidani et al., 2008) and those that impair auditory processing during adulthood (Martin del Campo et al., 2012; Zhou and Merzenich, 2012) result in de- creased PV staining and increased plasticity. In line with these observations, we found a moderate increase in the low-PV fraction in the immature and aged A1, the age groups that showed increased experience-dependent plasticity. Moreover, the high-PV fraction was significantly diminished in the aged (Fig. 5B, C), which could account for the inadequate consolidation of newly formed sensory representations (Caroni et al., 2012; Donato et al., 2013). representations (Caroni et al., 2012; Donato et al., 2013). PNNs are extracellular matrix deposits produced jointly by neurons and astrocytes, particularly around PV cells (McRae et al., 2007; Nakamura et al., 2009), forming both a structural and functional barrier that limits plasticity (Pizzorusso et al., 2002; Berardi et al., 2004; Wang and Fawcett, 2012). 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Multi Gigabit Wireless Data Transfer in Detectors at Future Colliders
Frontiers in physics
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REVIEW REVIEW published: 16 June 2022 doi: 10.3389/fphy.2022.872691 Multi Gigabit Wireless Data Transfer in Detectors at Future Colliders R. Brenner 1*, C. Dehos 2 and E. Locci 3 1Uppsala University, Uppsala, Sweden, 2CEA, Leti, Université Grenoble-Alpes, Grenoble, France, 3Gangneung-Wonju National University, Gangneung, South Korea The WADAPT (Wireless Allowing Data And Power Transmission) consortium has been formed to identify the specific needs of different projects that might benefit from wireless communication technologies with the objective of providing a common platform for research and development in order to optimize effectiveness and cost. Wireless technologies have developed extremely fast over the last decade and are now mature enough to be a promising alternative to cables and optical links, with a possibility of revolutionizing detector design. Although wireless readout has the qualities and properties to be used in many collider detectors, this article focuses on the transmission of large amount of data from vertex detectors at high rate, low power budget and in potential high radiation environment. For vertex detectors, the 60 GHz band has proven to be adequate and commercial products are already available, providing 6 Gbps data links. This technology allows efficient partitioning of detectors in topological regions of interest, with the possibility of adding intelligence on the detector to perform four-dimensional reconstruction of the tracks and vertices online, in order to attach the tracks to their vertex with great efficiency even in difficult experimental conditions, and conveniently substitutes a mass of materials (cables and connectors). Early transceiver module products have been successfully tested for signal confinement, crosstalk, electromagnetic immunity and resistance to radiation. In the long run, emerging 140 GHz bands could also be used for higher data rates (>100 Gbps) at future high energy and luminosity hadron colliders. INTRODUCTION The WADAPT consortium [1] chose to firstly investigate the relevance of wireless techniques for data transfer within vertex detectors, where commercially-available products in the 60 GHz band [2] would be adequate. The present ATLAS [3] and CMS [4] experiments have been designed for nominal operation at luminosity of 2 × 1034 cm−2s−1 and 60 interactions per beam crossing. Pileup lead to a number of mismeasured or misidentified tracks, and add extra energy to calorimeter measurements. Pileup confuses the trigger and also the offline reconstruction and interpretation of events. It also increases the execution time for the reconstruction of events in the High Level Trigger and the offline analysis. Specialty section: This article was submitted to Radiation Detectors and Imaging, a section of the journal Frontiers in Physics Specialty section: This article was submitted to Radiation Detectors and Imaging, a section of the journal Frontiers in Physics Received: 09 February 2022 Accepted: 21 April 2022 Published: 16 June 2022 *Correspondence: R. Brenner *Correspondence: R. Brenner Richard.Brenner@cern.ch Keywords: wireless, data transfer, WADAPT, vertex detector, collider Edited by: Petra Merkel, Fermi National Accelerator Laboratory (DOE), United States Reviewed by: David Christian, Fermi National Accelerator Laboratory (DOE), United States Jingbo Ye, Reviewed by: David Christian, Fermi National Accelerator Laboratory (DOE), United States Jingbo Ye, Southern Methodist University, United States Keywords: wireless, data transfer, WADAPT, vertex detector, collider Citation: The High Luminosity LHC (HL-LHC) is potentially able to deliver a luminosity up to 7.5 × 1034cm−2s−1, increasing the interaction rate and collision pileup beyond existing or envisioned data readout technologies. The detector systems in the experiment will currently need a trigger to sustain a pileup up to 200 interactions per 25 ns beam crossing. The first event selection and data reduction is typically done by a fast trigger decision within 3–6 microseconds after a collision where 40 million Brenner R, Dehos C and Locci E (2022) Multi Gigabit Wireless Data Transfer in Detectors at Future Colliders. Front. Phys. 10:872691. doi: 10.3389/fphy.2022.872691 June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 1 Multi Gigabit Data Transfer Brenner et al. events per second are currently reduced to about 100 kHz and at HL-LHC this will be increased by an order of magnitude. In present experiments this decision is based on information from all detector systems except the tracker. For HL-LHC the CMS experiment has developed a data reduction method with pT filtering in the tracker which opens for the use of tracking data in the trigger [5]. installation and repair, and reductions in detector dead material. These two last aspects are especially important in tracking detectors and they may become particularly important in case of limited access or/and hostile environment. For a full exploitation of the advantages of integrating a wireless point-to-point readout, new architectures will be necessary. The tracker is the most granular detector system in the experiment that is used to associate charged particles with the correct interaction vertices. The tracking detector would ideally read out all information for every single bunch crossing, perform reconstruction in real time, and then apply trigger criteria to filter events or if possible directly process the data in an event filter farm. The challenge is however to read out the very granular detector in time for the fast trigger decision or before data in the pipelined front-end electronics gets overwritten. The data rate needed to read out all hit clusters of 1-2 pixels in the next generation pixel detectors is between 50 and 100 Tbps1. Data from tracking detectors at the two big LHC experiments are today transferred with optical links. The main benefit with optical links compared to wire links is that they are electrically decoupled and free from crosstalk. Citation: The weakness of optical links is the size of the connectors, their alignment constrains, and the sensitivity to mechanical damage. Wire/copper links suffer from bandwidth limitation at higher data rates. Furthermore, the tracker is built in a modular way that does not follow the topology of the physics event. The readout is bound to the modularity of the tracker, which is not optimal for a fast trigger decision based on event topology. The advantage of wireless technology is that it is not constrained to the mechanical modularity of the tracker. The technology offers already today data rate comparable with present optical links and no connectors are needed. The next generation of hadron colliders, which might be the envisioned, FCC, would even be more challenging with a peak luminosity of 30 × 1035 cm−2s−1, leading to a pileup up to 1,000 interactions per 25 ns beam crossing, and more granular detectors. Although the current electron-positron colliders do not introduce stringent requirements on the trigger capabilities, the experiments would certainly benefit from the wireless technology. For both types of collider experiments, minimizing the amount of material in the region of the tracking detectors will reduce multiple scattering and nuclear interactions that degrade the precision on the measurement of track momentum and interaction vertices, and in addition will reduce the number of fake hits arising from secondaries. Both CMS and ATLAS upgrades aim at reducing passive material by embedding serial powering [7] or by using DC-DC converters with reduced mass [8]. 2Here the signal to noise ratio is defined as the average received signal over the bandwidth, and the noise is defined as the average noise or interference power over the bandwidth. 1The latest description of the pixel detector layout, including the number of staves per barrel and endcap layer, the number of sensors per stave and the estimated data rates per chip can be found in [6]. MILLIMETER WAVE WIRELESS TECHNOLOGY Data Rates and Frequency Band According to the Shannon-Hartley theorem, the physical data rate at which information can be transmitted over a communication channel is limited by the channel bandwidth and the signal-to- noise ratio2. The fast development of the wireless technologies is linked to the improvements made in the electronics, especially the semiconductor devices and the new simulation capacity [9–15]. This technological evolution is expected to continue in the coming years. Some of the main strategies to improve the performance of radio communication systems are the following: Over the last decade the spectral efficiency, meaning the data rate of the physical layer that could be transmitted in a given radio frequency bandwidth, has been increased by a factor 100. This efficiency is obtained by the use of higher order modulation coding scheme and multiple data streams (MIMO). The use of these advanced techniques requires intensive digital signal processing, increasing the complexity of the chipset design, the size, as well as the power consumption. The recent progress in terms of computing capability and energy per operation brought by the advanced FinFET and FDSOI technologies comes along with this increase in signal processing complexity, containing the power consumption, heat dissipation and manufacturing cost. According to the Shannon-Hartley theorem, another strategy to increase the throughput is to increase the spectrum bandwidth. Since the radio frequency frontend and antenna have a bandwidth limited in a proportion of the carrier frequency (typically a maximum of 15–20%), then larger signal bandwidths require transmission at higher frequency, which became feasible, once again, with the progresses made on the electronics. Over the last decade the spectral efficiency, meaning the data rate of the physical layer that could be transmitted in a given radio frequency bandwidth, has been increased by a factor 100. This efficiency is obtained by the use of higher order modulation coding scheme and multiple data streams (MIMO). The use of these advanced techniques requires intensive digital signal processing, increasing the complexity of the chipset design, the size, as well as the power consumption. The recent progress in terms of computing capability and energy per operation brought by the advanced FinFET and FDSOI technologies comes along with this increase in signal processing complexity, containing the power consumption, heat dissipation and manufacturing cost. According to the Shannon-Hartley theorem, another strategy to increase the throughput is to increase the spectrum bandwidth. MILLIMETER WAVE WIRELESS TECHNOLOGY Since the radio frequency frontend and antenna have a bandwidth limited in a proportion of the carrier frequency (typically a maximum of 15–20%), then larger signal bandwidths require transmission at higher frequency, which became feasible, once again, with the progresses made on the electronics. According to the Free Space Path Loss equation, the attenuation of a 60 GHz transmission at 1 m is about 68 dB, which is 21.6 dB higher than a 5 GHz transmission. Consequently at constant transmit power and using a given modulation scheme, the communication range will be 12 times shorter. This shorter signal range has the benefit that it will mitigate co-channel interference making a high-density channel-reuse design possible. The higher frequencies lead to smaller sizes of the RF passive components, including antennae, which can be easily integrated into electronic systems. The application-related antenna must be carefully chosen according to many parameters such as directivity/gain, angle aperture, Well-chosen detector technology and geometry, combined with wireless techniques might help in reducing the amount of cables and optimizing their path, and thus minimizing the geometrical inefficiency. The total or even partial removal of cables and connectors will result in cost reductions, simplified 2Here the signal to noise ratio is defined as the average received signal over the bandwidth, and the noise is defined as the average noise or interference power over the bandwidth. 1The latest description of the pixel detector layout, including the number of staves per barrel and endcap layer, the number of sensors per stave and the estimated data rates per chip can be found in [6]. June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 2 Brenner et al. Multi Gigabit Data Transfer FIGURE 1 | Coherent (A) and non-coherent (B) RF architecture schematics. FIGURE 1 | Coherent (A) and non-coherent (B) RF architecture schematics. (mmw) band. Non- coherent architecture brings high data rate (up to 10 Gbps at 60 GHz) and low power (<10 pJ/bit) for short- range applications [17]. Recent advance in antenna and packaging design allows the integration of the mmw antenna on chip [17] or in package [18] with good efficiency. Commercial products are now available for mass market applications with 3 main competitors (Lattice (SiBeam), Molex (Keyssa) and STMicroelectronics (Figure 2), proposing different integration schemes function of the application. Transceiver Architectures Two main transceiver architectures may be considered at mmw frequencies (Figure 1). Coherent architecture requires precise frequency synthesis (using Phase Locked Loop), and time and frequency synchronization mechanism achieved by digital base-band circuit [16]. This architecture allows complex amplitude and phase modulations, achieving high spectral efficiency, but leads to high power consumption. Research is progressing [20] towards very high data rate wireless communication systems, using channel aggregation or channel bonding in W or D-band (110–170 GHz), where huge bandwidths (35 GHz aggregated) are available for short range communications. Channel bonding is particularly relevant for the aggregation of data from multiple detectors. A total of 16 channels of 7 Gbps each can be aggregated in a D-band transceiver, reaching 100 Gbps. The data can be sent over a few tens of meter range using directive planar antennas, such as transmit arrays [21], or over light plastic waveguide material [22]. On the contrary non-coherent architecture allows amplitude modulation only (On Off Keying, Amplitude Shift Keying or Pulse Amplitude Modulation). The receiver can implement a simple envelope detector, a comparator and digital interface, without any frequency reference or digital base band processing. The quadratic envelope detector provides negative gain, so that the overall receiver noise figure increases and affects the receiver sensitivity. For this reason, this architecture is more dedicated to short range and low power communication. MILLIMETER WAVE WIRELESS TECHNOLOGY Strong efforts have also been put on the compatibility with high/low speed digital protocols (USB3, PCIe, Gig Ethernet, UART) for a seamless cable replacement. In parallel a HEP dedicated 60 GHz Integrated Chip was under development in Heidelberg, using 130 nm SiGe BICMOS technology [19] in order to assess the feasibility and performance of the wireless link and establish solid foundation for designing the final reading system. The first prototype was designed to handle a data rate of 4.5 Gbps over a link distance of 1 m. Estimated power consumption for a first full prototype readout is about 150 mW. bandwidth, etc. A wide range of antenna topologies can be produced on chip, in package or on advanced printed circuits boards. The use of RF lenses to increase the gain and the directivity of the antenna is also a possibility at this frequency. Improvements lie in carefully selecting the communication protocol. For a radio communication channel to work, a large amount of the transmission time is devoted to transmitter and receiver synchronisation, medium access, medium sensing, legacy standard-protection mechanism or transmission error compensation. The distribution of a system clock in particle physics detectors will facilitate the transmitter-receiver synchronisation. Frontiers in Physics | www.frontiersin.org TOWARDS WIRELESS INTEGRATION IN A DETECTOR The results of these studies are reported in Sections 3.1–3.4. More recently, tests have been conducted using non-coherent transceiver prototypes from STMicroelectronics [28], especially for latency, connectivity and radiation hardness. These features, the high path loss, high material penetration loss, narrow beam-width, Line-Of-Sight (LOS) mode of propagation, and operation in a controlled environment, makes the 60 GHz band optimal for short range operation as in the considered detector, where the signal propagates over a 10 cm distance between layers. In addition, the use of the high carrier frequency translates into small form factor for passives (antenna), which will reduce the material budget. This provides an extremely desirable frequency re-use that can handle a large number of transceivers in a small area as in the HEP detectors and other detector systems. Signal is routed through each layer from the bottom receiver to the transmitter at top side. This multi-hop concept requires that the wave front stay confined between the two considered layers, and does not crosstalks with neighbours. FIGURE 3 | Proposal of a radial readout for the tracking detector of the ATLAS experiment. Feasibility studies regarding the integration of the 60 GHz wireless technologies in silicon tracking detector were performed [26], based on a commercial coherent transceiver from Hittite [27]. Several aspects relevant for the implementation of 60 GHz links were studied: transmission losses, interference effects, absorbing materials and the influence of the antenna design and directivity, power consumption. The results of these studies are reported in Sections 3.1–3.4. More recently, tests have been conducted using non-coherent transceiver prototypes from STMicroelectronics [28], especially for latency, connectivity and radiation hardness. experiments and low energy experiments at the intensity frontier for a large range of particle physics detectors. The first step taken by the WADAPT consortium is to bring the proof of concept in the context of data transmission through a typical vertex detector. g yp Present and future collider experiments require more and more bandwidth for the handling of ever increasing data rates. It is especially true for highly granular tracking detectors operated at high beam luminosities. The performance is currently limited because of insufficient readout bandwidth. An example is the ATLAS Phase II New Inner Tracker Pixel Detector with five- barrel layers, four end-cap rings and a silicon strip detector with four layers and six end-cap disks, in 1 m radius. TOWARDS WIRELESS INTEGRATION IN A DETECTOR The readout should operate at up to 4 MHz (25 µs) L0 rate. At downlink a broadcast trigger and control signal will be sent at 160 Mbps while Frontiers in Physics | www.frontiersin.org TOWARDS WIRELESS INTEGRATION IN A DETECTOR In the last decade there has been tremendous advances in silicon technologies that have made it possible to build high performance RF transceivers operating in the millimeter-wave Possible wireless applications encompass HEP experiments at high- energy colliders, neutrino physics experiments, astroparticle-physics June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 3 Brenner et al. Multi Gigabit Data Transfer FIGURE 2 | ST Microelecronics ST60 contactless connectivity transceiver in BGA. FIGURE 2 | ST Microelecronics ST60 contactless connectivity transceiver in BGA. FIGURE 3 | Proposal of a radial readout for the tracking detector of the ATLAS experiment. 10k up-links will transmit data at a rate of 5 Gbps. The data readout problematic, based on wired transmission strategy, is addressed in [23]. Different cabling schemes are evaluated with the goal of 5 Gbps data transmission per cable, while reducing as much as possible the material within the small detector volume. The proposed alternative for future colliders is to replace the innermost dense wired network by a multi-hop point-to-point wireless network, streaming the data radially from the centre to outer enclosure (Figure 3) [24]. The worldwide license-free 60 GHz band (57–66 GHz) [25] is very attractive in order to achieve high data rate transfer. y g These features, the high path loss, high material penetration loss, narrow beam-width, Line-Of-Sight (LOS) mode of propagation, and operation in a controlled environment, makes the 60 GHz band optimal for short range operation as in the considered detector, where the signal propagates over a 10 cm distance between layers. In addition, the use of the high carrier frequency translates into small form factor for passives (antenna), which will reduce the material budget. This provides an extremely desirable frequency re-use that can handle a large number of transceivers in a small area as in the HEP detectors and other detector systems. Signal is routed through each layer from the bottom receiver to the transmitter at top side. This multi-hop concept requires that the wave front stay confined between the two considered layers, and does not crosstalks with neighbours. Feasibility studies regarding the integration of the 60 GHz wireless technologies in silicon tracking detector were performed [26], based on a commercial coherent transceiver from Hittite [27]. Several aspects relevant for the implementation of 60 GHz links were studied: transmission losses, interference effects, absorbing materials and the influence of the antenna design and directivity, power consumption. Transmission and Reflection Tests The data throughput of a wireless read-out system, as depicted in Figure 3, is maximized when links with maximum bandwidth are June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 4 Multi Gigabit Data Transfer Brenner et al. FIGURE 4 | (A) The ATLAS SCT barrel module under test. Positions for frequency scans are denoted by (A), (B) and (C). A position scan is performed along the black arrow. (B) Transmission loss of the barrel module averaged over the frequency band for a position scan (along the arrow in panel 4A) and the noise limited sensitivity of the spectrum analyzer. The uncertainties represent the RMS of the average measurements [26]. FIGURE 5 | (A) The ATLAS SCT endcap module under test. Positions for frequency scans are denoted by (A), (B) and (C). A position scan is performed along the black arrow. (B) Transmission loss of the endcap module averaged over the frequency band for a position scan (along the arrow in panel 5A) [26]. FIGURE 4 | (A) The ATLAS SCT barrel module under test. Positions for frequency scans are denoted by (A), (B) and (C). A position scan is performed along the black arrow. (B) Transmission loss of the barrel module averaged over the frequency band for a position scan (along the arrow in panel 4A) and the noise limited sensitivity of the spectrum analyzer. The uncertainties represent the RMS of the average measurements [26]. FIGURE 4 | (A) The ATLAS SCT barrel module under test. Positions for frequency scans are denoted by (A), (B) and (C). A position scan is performed along the black arrow. (B) Transmission loss of the barrel module averaged over the frequency band for a position scan (along the arrow in panel 4A) and the noise limited sensitivity of the spectrum analyzer. The uncertainties represent the RMS of the average measurements [26]. FIGURE 5 | (A) The ATLAS SCT endcap module under test. Positions for frequency scans are denoted by (A), (B) and (C). A position scan is performed along the black arrow. (B) Transmission loss of the endcap module averaged over the frequency band for a position scan (along the arrow in panel 5A) [26]. FIGURE 5 | (A) The ATLAS SCT endcap module under test. Positions for frequency scans are denoted by (A), (B) and (C). A position scan is performed along the black arrow. Transmission and Reflection Tests (B) Transmission loss of the endcap module averaged over the frequency band for a position scan (along the arrow in panel 5A) [26]. densely packed. The main challenge is to avoid crosstalk between parallel and subsequent chained links. transmission loss as function of the position on the module (Figure 5B) is −20 dB to −40 dB in the electronics region due to the assembly hole and the gap between hybrid and flex print. As expected the silicon strip region is opaque for the millimeter waves. Transmission and reflection tests have been performed with a spare silicon strip detector module from the ATLAS barrel detector (Figure 4A). The module is mounted on a 2D movable stage and placed in line of sight of two horn antennas for transmission and reception. The module is irradiated with linearly polarized waves in the range from 57.3 to 61.3 GHz. A spectrum analyzer measures the power transmitted through the module in the radio frequency band without down conversion. The transmitted power is normalized to the power in the absence of module in-between. Figure 4B shows the transmission loss averaged over the chosen frequency band for a few positions along the module. Most of the signal is absorbed by the silicon material, and small reflections may occur due to metallization of the chip and PCB. In some configurations these reflections might induce crosstalk. Absorbing materials (e.g., graphite foam) may be used to attenuate reflections [26]. Link Density Studies with Al-Kapton® horn antennas installed on both sides, links can be placed as close as 2 cm next to each other without significant interference effects. Without using any directive antennas crosstalk can be reduced just by absorber shields. This has been tested by equipping all transmitters and receivers with 1 cm long, hollow graphite foam cylinders on top of the waveguide apertures to shield lateral radiation. Then shielded links can be placed as close as 4 cm next to each other. The different methods for reducing crosstalk discussed in the previous section have been experimentally studied by measuring how close two parallel 60 GHz links can be placed without interfering (Figure 6). The parameter S/N is defined as the ratio of the signals from transmitter #1 (useful signal) over transmitter #2 (interfering signal) measured with the spectrum analyzer at the antenna of the receiver #1. The link quality is considered to be acceptable when S/N is higher than 20 dB, which corresponds to a theoretical bit error rate (BER) of 10–12, for high order modulation scheme decoding and forward error correction. For OOK the required S/N is in the range 30–35 dB function of the total jitter requirement. p The Bit Error Rate (BER) measures the performance of a data transmission device. With the setup described above the BER is measured for a data rate of 1.76 Gbps using Minimum Shift Keying (MSK) as modulation scheme. Both links use the same polarization state and the same carrier frequency. Figure 8 shows the BER measured as function of the pitch in different configurations. With horn antennas bit error rates smaller than 10–12 are achieved for all considered pitches. The distance between transmitters and receivers is set at 10 cm (expected distance between layers) and both links have identical polarization. S/N is measured as a function of the antenna spacing for different setups (Figure 7). For reference non-directive waveguide apertures are used, for which S/N increases linearly as a function of the pitch. In a real tracking detector 60 GHz radiation can be partially reflected between the silicon detector layers, generating multipath and crosstalk. The silicon detector environment can be simulated by enclosing the volume with aluminium plates (Figure 6). The distance between the links is set to 5, 10 and 15 cm. Reduction of Crosstalk All wireless links in a tracking detector are installed in stationary positions. Therefore, wireless readout systems can be designed and optimized in order to minimize the interference effects The measurement is repeated with a spare ATLAS SCT endcap module (Figure 5A). The frequency averaged June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 5 Brenner et al. Multi Gigabit Data Transfer FIGURE 6 | Sketch of the setup to measure crosstalk with two links between highly reflective aluminium layers. LOS crosstalk is indicated as purple wave [26]. FIGURE 6 | Sketch of the setup to measure crosstalk with two links between highly reflective aluminium layers. LOS crosstalk is indicated as purple wave [26]. FIGURE 7 | S/N in the radio frequency spectrum with LOS induced crosstalk as function of the antenna pitch for different setups [26]. between different links. Nevertheless crosstalk may be an issue for extremely high link densities. However different actions can be combined to reduce crosstalk, if necessary. One of them is acting on the antenna pattern, using directive antennas with high gain, small beam width and low secondary lobes. By increasing the gain of the antenna, the transmitted power can be decreased while keeping the signal over noise ratio (S/N) in the receiver constant. In addition the antenna linear or circular polarization direction can be exploited. Crosstalk between adjacent links can be significantly reduced by using orthogonal polarization states. Furthermore low mass absorbing material can be used to attenuate the spurious reflections without increasing the material budget. Finally a tunable voltage controlled oscillator (VCO) with sharp filters or low bandwidth antennas may be used to divide the frequency band in different channels. Spreading (CDMA) is also an option with the drawback of reducing the data rate [26]. FIGURE 7 | S/N in the radio frequency spectrum with LOS induced crosstalk as function of the antenna pitch for different setups [26]. Frontiers in Physics | www.frontiersin.org Link Density Studies FIGURE 9 | S/N for two parallel links operated between two fully reflective aluminium layers at a distance of 10 cm. Results are shown for parallel polarization states (top, white background) and orthogonal polarization states (bottom, grey background) [26]. Link Density Studies FIGURE 9 | S/N for two parallel links operated between two fully reflective aluminium layers at a distance of 10 cm. Results are shown for parallel polarization states (top, white background) and orthogonal polarization states (bottom, grey background) [26]. FIGURE 10 | Measured BER of two parallel-operated links at a pitch of 2.6 cm as function of the carrier frequency offset. The links are operated with MSK at up to 1.76 Gbps. No directive antennas are used. The 3 dB bandwidth of the Hititte transceivers (1.8 GHz) is indicated as red line, twice the bandwidth as a blue line [26]. FIGURE 10 | Measured BER of two parallel-operated links at a pitch of 2.6 cm as function of the carrier frequency offset. The links are operated with MSK at up to 1.76 Gbps. No directive antennas are used. The 3 dB bandwidth of the Hititte transceivers (1.8 GHz) is indicated as red line, twice the bandwidth as a blue line [26]. FIGURE 10 | Measured BER of two parallel-operated links at a pitch of 2.6 cm as function of the carrier frequency offset. The links are operated with MSK at up to 1.76 Gbps. No directive antennas are used. The 3 dB bandwidth of the Hititte transceivers (1.8 GHz) is indicated as red line, twice the bandwidth as a blue line [26]. FIGURE 8 | Influence of LOS crosstalk on the BER of a wireless data transmission, shown as function of the pitch between two parallel links. Distance between transmitter and receiver is set to 10 cm. Both links are operated at the same carrier frequency [26]. FIGURE 8 | Influence of LOS crosstalk on the BER of a wireless data transmission, shown as function of the pitch between two parallel links. Distance between transmitter and receiver is set to 10 cm. Both links are operated at the same carrier frequency [26]. FIGURE 10 | Measured BER of two parallel-operated links at a pitch of 2.6 cm as function of the carrier frequency offset. The links are operated with MSK at up to 1.76 Gbps. No directive antennas are used. The 3 dB bandwidth of the Hititte transceivers (1.8 GHz) is indicated as red line, twice the bandwidth as a blue line [26]. FIGURE 10 | Measured BER of two parallel-operated links at a pitch of 2.6 cm as function of the carrier frequency offset. Link Density Studies The measurements relative to all antenna setups In the absence of any mitigation a minimum pitch of about 8 cm is necessary to achieve a S/N of 20 dB. With one highly directive (17 dBi) Al-Kapton® horn antenna on the transmitting or receiving side, the minimum pitch is reduced to 4 cm, while June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 6 Multi Gigabit Data Transfer Brenner et al. 5 cm is possible for all studied configurations. For orthogonal polarization of neighbouring links, a good S/N is obtained for all tested setups even without directive antennas and a distance smaller than 5 cm seems to be possible. The combination of directive antennas and absorbing foam can increase the S/N ratio further. Thus using directive antennas, polarization, absorber materials, alone or in combination allows the operation of 60 GHz links between highly reflective materials even at a small pitch. A transmitter chip with tunable carrier frequency allows the use of frequency channeling. The BER has been measured as a function of the carrier offset when two parallel links are positioned at a pitch of 2.6 cm using the same polarization state. Foam cylinders on top of the waveguide apertures provide a minimum shielding. The carrier frequency offset is varied in steps of 500 MHz. Figure 10 shows that with this setup, using 3 frequency channels in parallel within the full 60 GHz band seems possible. Drawing full benefit from channeling necessitates filters with very sharp cutoff frequencies. An estimate on the possible link density can be derived from above results. Assuming a tracking detector environment with distances of 10 cm between layers and a minimum pitch of 3.5 cm between links., OOK as modulation scheme with a spectral efficiency of ρOOK ≈0.5 bps/Hz, and using the full 9 GHz bandwidth per channel yields a data rate of 4.5 Gbps per link, the resulting data rate area density is about 3.7 Tbps/m2. This is a theoretical limit, which cannot be realistically reached experimentally. The estimated experimental data rate density is rather around 1.2 Tbps/m2 [26]. FIGURE 8 | Influence of LOS crosstalk on the BER of a wireless data transmission, shown as function of the pitch between two parallel links. Distance between transmitter and receiver is set to 10 cm. Both links are operated at the same carrier frequency [26]. Link Density Studies The links are operated with MSK at up to 1.76 Gbps. No directive antennas are used. The 3 dB bandwidth of the Hititte transceivers (1.8 GHz) is indicated as red line, twice the bandwidth as a blue line [26]. FIGURE 9 | S/N for two parallel links operated between two fully reflective aluminium layers at a distance of 10 cm. Results are shown for parallel polarization states (top, white background) and orthogonal polarization states (bottom, grey background) [26]. 5 cm is possible for all studied configurations. For orthogonal polarization of neighbouring links, a good S/N is obtained for all tested setups even without directive antennas and a distance smaller than 5 cm seems to be possible. The combination of directive antennas and absorbing foam can increase the S/N ratio further. Thus using directive antennas, polarization, absorber materials, alone or in combination allows the operation of 60 GHz links between highly reflective materials even at a small pitch. A transmitter chip with tunable carrier frequency allows the use of frequency channeling. The BER has been measured as a function of the carrier offset when two parallel links are positioned at a pitch of 2.6 cm using the same polarization state. Foam cylinders on top of the waveguide apertures provide a minimum shielding. The carrier frequency offset is varied in steps of 500 MHz. Figure 10 shows that with this setup, using 3 frequency channels in parallel within the full 60 GHz band seems possible. Drawing full benefit from channeling necessitates filters with very sharp cutoff frequencies. An estimate on the possible link density can be derived from above results. Assuming a tracking detector environment with distances of 10 cm between layers and a minimum pitch of 3.5 cm between links., OOK as modulation scheme with a spectral efficiency of ρOOK ≈0.5 bps/Hz, and using the full 9 GHz bandwidth per channel yields a data rate of 4.5 Gbps per link, the resulting data rate area density is about 3.7 Tbps/m2. This is a theoretical limit, which cannot be realistically reached experimentally. The estimated experimental data rate density is rather around 1.2 Tbps/m2 [26]. FIGURE 9 | S/N for two parallel links operated between two fully reflective aluminium layers at a distance of 10 cm. Results are shown for parallel polarization states (top, white background) and orthogonal polarization states (bottom, grey background) [26]. Connectivity A non-coherent transceiver was interfaced with Minimum Ionizing MOnolithic Active pixel Sensors (MIMOSA) from IPHC Strasbourg (Figure 14), which use the epitaxial layer of standard CMOS (TowerJazz High Resistivity 180 nm technology [29]) processes as detecting sensitive volume. The pixel detector board provides 5 μs refreshment rate and generates up to 3 Gbps data rate. Signal integrity tests were carried out with the detector feeding a wireless link. No error was reported at oscilloscope. Different materials were then introduced between the antennas. Signals well passed through the non-metallized area of the thin flex Kapton PCB that embeds chips, but not through low-density carbon foam that holds the detector. These results validate the proposed readout architecture, whose principle is to isolate every detector layer and export data through multiple hops between layers. At longer term, the RF transceiver may be integrated within the detector chip. The antenna could also be part of the chip with good efficiency, assuming the high resistivity substrate of the CMOS backend material. Pixel detectors still need to receive a clock or trigger reference from the network. It could then be worth modifying the 60 GHz transceiver, so that the clock is also transmitted wirelessly from chip to chip on the carrier by harmonic injection locking. FIGURE 11 | Block diagram of the setup used for the irradiation test at Freiburg. A, B, C and D indicate different antenna positions used in the test. The 12 readout chips are illustrated as brown boxes on the orange readout hybrid [26]. as cut-off frequencies of sensors and readout chips for silicon detectors are typically below a few GHz, no interference between the 60 GHz links and tracking detector modules is expected. To demonstrate this, 60 GHz irradiation tests are performed for different silicon strip and pixel detectors. Two ATLAS Binary Chip-Next (ABCN) endcap electronics hybrid prototypes for the Phase-2 upgrade of the silicon tracking-detector for the ATLAS experiment are tested using the setup shown on Figure 11. One is a bare electronics hybrid, while the other one is connected to short silicon strip sensors with a strip length of 2.4 cm. Each prototype includes 12 fully functional ABCN readout chips. Noise is measured for each channel of the readout ASICs under wireless irradiation. The hybrid module is irradiated using a 20 dBi horn antenna from an distance of 1 cm resulting in a irradiated power of about −1 dBm. Radiation Hardness A first irradiation experiment with protons was performed at Åbo Akademi University, Turku, Finland [30]. Figure 15 shows a scheme and a picture of the setup. The radiation hardness of the V-band TRX chip in 65 nm CMOS, acting both in TX and RX modes, was FIGURE 12 | Noise distribution of all channels of the 12 ABCN readout chips without strip sensors under irradiation. The reference measurement was performed without 60 GHz irradiation. Mean μ and width σ of the Gaussian fits are given. No significant difference is observed [26]. These results indicate that there should not be any obstacle to wireless data transmission in the 60 GHz band with respect to the operation and performance of current silicon tracking detector sensors [26]. FIGURE 12 | Noise distribution of all channels of the 12 ABCN readout chips without strip sensors under irradiation. The reference measurement was performed without 60 GHz irradiation. Mean μ and width σ of the Gaussian fits are given. No significant difference is observed [26]. FIGURE 12 | Noise distribution of all channels of the 12 ABCN readout chips without strip sensors under irradiation. The reference measurement was performed without 60 GHz irradiation. Mean μ and width σ of the Gaussian fits are given. No significant difference is observed [26]. Connectivity Four different components are irradiated (Figure 11) with carrier frequencies of 57, 60 and 63 GHz: (A) the power converter, (B) and (C) the readout chips, and (D) the bonding wires. The noise level distribution of a reference measurement and a measurement with 60 GHz irradiation are compared in Figure 12 for the electronics hybrid without silicon strips and no significant differences are found in the mean and width of the noise distributions. Similarly no significant noise increase for the second prototype connected to silicon strips is observed. As expected, no influence of the wireless signal on the noise level is found at any carrier frequency. Noise Pickup with both polarization states (parallel and orthogonal) between the two links are displayed in Figure 9. With directive antennas, stable data transmission at a pitch of The pickup of noise from 60 GHz communications is a potential worry for the operation of wireless links inside the detector. However, June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 7 Multi Gigabit Data Transfer Brenner et al. FIGURE 11 | Block diagram of the setup used for the irradiation test at Freiburg. A, B, C and D indicate different antenna positions used in the test. The 12 readout chips are illustrated as brown boxes on the orange readout hybrid [26]. low directivity antenna (Figure 13). The transmitter was fed by a SLVS 8b/10b encoded signal from pseudo random binary sequence at 5 Gbps. At the receiver output the binary signal showed less than 75 ps total jitter, less than 35 ps 20–80% rising/falling time and less than 1 ns latency (without the cables). A range of 10 cm can be obtained using 10 dB gain antenna. Signal Integrity The performance of non-coherent chips described in [2] was measured at 1–5 cm range between transmitter and receiver using June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 8 FIGURE 13 | Emitted waveform (left) and received eye diagramm (right) for 5 Gbps wireless link. FIGURE 14 | Wireless data transmission interfacing with MIMOSA detector. FIGURE 15 | irradiation tests at Turku Cyclotron. Brenner et al. Multi Gigabit Data Transfer Multi Gigabit Data Transfer Brenner et al. FIGURE 13 | Emitted waveform (left) and received eye diagramm (right) for 5 Gbps wireless link. FIGURE 13 | Emitted waveform (left) and received eye diagramm (right) for 5 Gbps wireless link. FIGURE 13 | Emitted waveform (left) and received eye diagramm (right) for 5 Gbps wireless link. FIGURE 14 | Wireless data transmission interfacing with MIMOSA detector. FIGURE 14 | Wireless data transmission interfacing with MIMOSA detector. FIGURE 14 | Wireless data transmission interfacing with MIMOSA detector. FIGURE 14 | Wireless data transmission interfacing with MIMOSA detector. FIGURE 15 | irradiation tests at Turku Cyclotron. FIGURE 15 | irradiation tests at Turku Cyclotron. experiment presents a first investigation of radiation hardness that gives encouraging results despite the fact that the devices were not specifically radiation hardened by either design or process. A second campaign of irradiation with electrons was carried out at the CLEAR (CERN Linear Electron Accelerator for Research) facility at CERN [31]. The TX and RX were exposed to a TID of 3.14 and 2.70 MGy respectively. The pre- and post-irradiation characterization of the chips revealed a 80 MHz upshift in the centre frequency. An overall link budget degradation of 10 dB was observed, which is a sum of 4 dB reduced TX output power and 6 dB degraded receiver sensitivity. Besides, circuit bandgap (voltage reference) were degraded, which affected the transceivers internal biasings and so investigated after 17 MeV proton irradiation. TID and fluence used during the experiment were 74 and 42 kGy and 1.4 × 10 14Neq/cm2 and 0.8 × 1014Neq/cm2 for the RX and the TX, respectively. Transmission performance was measured before, during and after irradiation. The RX experienced higher loss of sensitivity than the TX power loss, accordingly to the respective TID and fluence. However, both the RX and the TX were found operational through over-the-air measurements at 5 Gbps after irradiation. Signal Integrity If some transmission errors were observed during the irradiation, the chip recovered error free transmission after irradiation with small gain degradation. experiment presents a first investigation of radiation hardness that gives encouraging results despite the fact that the devices were not specifically radiation hardened by either design or process. A second campaign of irradiation with electrons was carried out at the CLEAR (CERN Linear Electron Accelerator for Research) facility at CERN [31]. The TX and RX were exposed to a TID of 3.14 and 2.70 MGy respectively. The pre- and post-irradiation characterization of the chips revealed a 80 MHz upshift in the centre frequency. An overall link budget degradation of 10 dB was observed, which is a sum of 4 dB reduced TX output power and 6 dB degraded receiver sensitivity. Besides, circuit bandgap (voltage reference) were degraded, which affected the transceivers internal biasings and so Although the radiation levels expected in the real experiment at HL-LHC or future hadron colliders are much higher, this June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 9 Multi Gigabit Data Transfer Brenner et al. antennas are particularly relevant for the considered innermost part of the readout network, based on multi-hop transmission. Early feasibility tests with prototypes and commercial products have demonstrated that crosstalk is not an issue for high density of links and that no pickup noise is to be expected. The projected theoretical limit with current technology is 3.7 Tbps/m2 and <10 pJ/ bit. Although the commercial products were not designed nor manufactured as radiation hard components, they showed good behaviour under irradiation with protons and electrons. They could be easily hardened to be able to sustain radiation levels expected at future hadron colliders. There is no show-stopper to the early deployment and proof of concept using hardened RFICs and associated electronics in HEP experiments. The mmw technological roadmap shows soaring data rates using higher frequency bands above 100 GHz, challenging optical links for data aggregation and routing at short to medium range. the transmitter and receiver gains. Despite the mentioned degradation, the chips were found operational in the post-irradiation characterization. Moreover, margins have been taken in chip design in order to guarantee performance through P,V,T variations and production yield, so that calibration means can restore part of the chip performance. 4R. Brenner, D. Dancila, C. Dehos, P. De Lurgio, Z. Djurcic, G. Drake, J.L. Gonzalez Jiménez, L. Gustafsson, D.W. Kim, E. Locci, U. Pfeiffer, D. Röhrich, D. Rydberg, A. Schöning, A. Siligaris, H.K. Soltveit, K. Ullaland, P. Vincent, P.R. Vasquez, D. Wiedner, S. Yang. 5J. Baudot, G. Claus, M. Goffe. Future Developments and Test At long term, the integration of wireless technologies in tracking detector would certainly require the design of a dedicated radiation hardened mmw transceiver IP, to be integrated either as a companion chip or within silicon trackers. For this purpose the ST C65SPACE radiation hardened ASIC technology or 45 nm Partially Depleted SOI technologies seem good candidates. The latter would allow the integration of antenna directly on the High Resistivity substrate of its back-end. For a better and versatile interfacing, the transceiver IP could also contain serializer/deserializer. External antennas or focusing lenses should be envisaged with the objectives of extending the range and ease crosstalk management. The crosstalk can be further improved by alternating antennas radiating in vertical and horizontal polarization for better isolation. The antenna should radiate a vertical beam (normal to the PCB plane) in order to fit easily in the detector. Well-chosen detector technology and geometry, combined with flexible wireless techniques might help in minimizing dead material by reducing the amount of cables and connectors. The absence of constrain to mechanical structures allows radial readout following the event topology that would be optimal for a fast trigger decision and would enhance on-detector intelligence, which could also open up new possibilities of communication between chips. Technologies should be mature enough to be envisaged as a part of the readout network of future detectors at future colliders. ACKNOWLEDGMENTS The present document is based on the work of the whole WADAPT consortium4, which has been partly presented at the 40th International Conference on High Energy physics—ICHEP2020 [2]. The authors are grateful to their colleagues of the Heidelberg University, Sebastian Dittmeier, André Schöning, Hans Kristian Soltveit, Dirk Wiedner, for giving them the permission to use in extenso large parts of their publication [26] for the sake of the completeness of this review. Special thanks are due to Sebastian Dittmeier for the tests of the Hittite transceiver, to Imran Aziz for the irradiation tests, to Frederic Lagrange from STMicroelectronics for providing equipment and support, to our colleagues5 of the Institut Pluridisciplinaire Hubert Curien, Strasbourg, France for the tests of connectivity to MIMOSA sensors as well as to Åbo Akademi University, Finland for use of their irradiation facility. Warm thanks go to Hans Kristian Soltveit for the careful reading of this document. AUTHOR CONTRIBUTIONS All authors listed have made a substantial, direct, and intellectual contribution to the work and approved it for publication. At shorter term is envisaged the integration of the available non coherent mmw transceivers BGA with external antennas, as System In Package or System On Board. The antenna shall provide a narrow beam broadside for dense wireless links. As a proof of concept, a three (or four) layer silicon detector will be build3, as shown on Figure 3. This mock-up of a central tracker will be equipped with the transceiver chip in BGA package. This will allow to study the added noise and data transmission quality (impact on eye diagram, Jitter, Bit Error Rate) over the different layers and get the antenna specifications: gain, polarization, bandwidth and radiation robustness. Then we will integrate the detectors to the setup to check the readout capabilities while using multi-hop wireless link. Eventually a multilink scenario will be considered to check if the isolation between channels is sufficient for the considered application. This would bring us closer to the full scale implementation and would help specify and integrate the future wireless systems in detectors at future colliders. Signal Integrity Indeed TX power can be increased by 3dB by changing the settings, while LNA gain can be boosted also to restore the sensitivity. Radiation hardening shall however be considered on C65SPACE (which includes libraries with hardened cells, tested up to 0.3 Mrad dose but could handle higher radiations) or more advanced SOI technology for the highest radiation levels expected at future colliders such as HL-LHC or FCC-hh. 3This project is supported by AIDAinnova. REFERENCES High Energy Physics — PoS(EPS-HEP2017); October 2017 (2017). doi:10. 22323/1.314.0520 High Energy Physics — PoS(EPS-HEP2017); October 2017 (2017). doi:10. 22323/1.314.0520 20. Gonzalez-Jimenez JL, Dehos C, Cassiau N, Siligaris A, Clemente A, D’Errico R, et al. Channel-bonding CMOS Transceiver for 100 Gbps Wireless point-to- point Links. EURASIP J Wireless Commun Networking, 2020 (2020). p. 117. doi:10.1186/s13638-020-01741-1 1. Brenner R, Ceuterickx S, Dehos C, De Lurgio P, Djurcic Z, Drake G, et al. Development of Wireless Techniques in Data and Power Transmission Application for Particle-Physics Detectors. 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Multigigabit Wireless Transfer of Trigger Data through Millimetre Wave Technology. J Instrumentation (2010) 5:c07002. doi:10.1088/ 1748-0221/5/07/c07002 7. Sguazzoni G. The CMS Pixel Detector for the High Luminosity LHC. Nucl.Instrum.Meth.A (2019) 958:162089. doi:10.1016/j.nima.2019.04.043 25. REFERENCES Dehos C, González JL, De Domenico A, Kténas D, Dussopt L. Millimeter-wave Access and Backhauling: the Solution to the Exponential Data Traffic Increase in 5G mobile Communications Systems? IEEE Commun Mag (2014) 52(9): 88–95. doi:10.1109/MCOM.2014.6894457 8. Affolder A, Allongue B, Blanchot G, Faccio F, Fuentes C, Greenall A, et al. DC-DC Converters with Reduced Mass for Trackers at the HL-LHC. J Inst (2011) 6:C11035. doi:10.1088/1748-0221/6/11/c11035 9. Rappaport TS, Murdock JN, Gutierrez F. State of the Art in 60-GHz Integrated Circuits and Systems for Wireless Communications. Proc IEEE (2011) 99(No. 8):1390–436. doi:10.1109/jproc.2011.2143650 26. 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Wideband Low-Loss Linear and Circular Polarization Transmit-Arrays in V-Band. IEEE Trans Antennae Propagation (2011) 59:2513–23. doi:10.1109/tap.2011.2152331 31. Aziz I. Ultra-wideband Millimeter-waveAntenna Arrays and Front-End SystemsFor High Data Rate 5G and High Energy Physics. PhD Thesis Digital Compr Summ Uppsala Dissertations Fac Sci Tech (2021) 2005:68. 14. Pfeiffer UR, Goren D. CONCLUSION The recent advances in mmw technologies allows low latencies, high data rates and low power wireless data transmission at short range. The association of non-coherent RF architecture and directive June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 10 Multi Gigabit Data Transfer Brenner et al. REFERENCES A 20 dBm Fully-Integrated 60 GHz SiGe Power Amplifier with Automatic Level Control. IEEE J Solid-state Circuits (2007) 42(7):1455–63. doi:10.1109/jssc.2007.899116 15. Reynolds SK, Floyd BA, Pfeiffer UR, Beukema T, Grzyb J, Haymes C, et al. A Silicon 60-GHz Receiver and Transmitter Chipset for Broadband Communications. IEEE J Solid-state Circuits (2006) 41:2820–31. doi:10.1109/jssc.2006.884820 Conflict of Interest: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. 16. Diet A, Villegas M, Baudoin G, Robert F. Radio-communications Architectures. In: A Bazzi, editor. Radio Communications. Sciyo: Intech (2010). p. 1–35. ffhal-00553229f. Publisher’s Note: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher. 17. Siligaris A, Deparis N, Pilard R, Gloria D, Loyez C, Rolland N, et al. A 60 GHz UWB Impulse Radio Transmitter with Integrated Antenna in CMOS65nm SOI Technology. In: Proceeding of the 2011 IEEE 11th Topical Meeting on Silicon Monolithic Integrated Circuits in RF Systems; Jan. 2011; Phoenix, AZ. IEEE (2011). p. 153–6. doi:10.1109/SIRF.2011.5719303 Copyright © 2022 Brenner, Dehos and Locci. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. 18. Dussopt L, Lamy Y, Joblot S, Lanteri J, Salti H, Bar P, et al. Silicon Interposer with Integrated Antenna Array for Millimeter-Wave Short-Range Communications. In: Proceeding of the 2012 IEEE/MTT-S International Microwave Symposium Digest; June 2012; Montreal QC. IEEE (2012). p. 1–3. doi:10.1109/MWSYM.2012.6259424 19. Soltveit HK. Multi-Gigabit Wireless Data Transfer for High EnergyPhysics Applications. In: Proceedings of The European Physical Society Conference on June 2022 | Volume 10 | Article 872691 Frontiers in Physics | www.frontiersin.org 11
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11C-methionine PET aids localization of microprolactinomas in patients with intolerance or resistance to dopamine agonist therapy
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1 Cambridge Endocrine Molecular Imaging Group, Metabolic Research Laboratories, Wellcome–MRC Institute of Metabolic Science, University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK * M. Gurnell mg299@medschl.cam.ac.uk 11C‑methionine PET aids localization of microprolactinomas in patients with intolerance or resistance to dopamine agonist therapy W. A. Bashari1 · M. van der Meulen1 · J. MacFarlane1 · D. Gillett1,2 · R. Senanayake1 · L. Serban1 · A. S. Powlson1 · A. M. Brooke3 · D. J. Scoffings4 · J. Jones4 · D. G. O’Donovan5 · J. Tysome6 · T. Santarius7 · N. Donnelly6 · I. Boros8 · F. Aigbirhio8 · S. Jefferies9 · H. K. Cheow1,2,4 · I. A. Mendichovszky1,2,4 · A. G. Kolias7 · R. Mannion7 · O. Koulouri1 · M. Gurnell1 W. A. Bashari1 · M. van der Meulen1 · J. MacFarlane1 · D. Gillett1,2 · R. Senanayake1 · L. Serban1 · A. S. Powlson1 · A. M. Brooke3 · D. J. Scoffings4 · J. Jones4 · D. G. O’Donovan5 · J. Tysome6 · T. Santarius7 · N. Donnelly6 · I. Boros8 · F. Aigbirhio8 · S. Jefferies9 · H. K. Cheow1,2,4 · I. A. Mendichovszky1,2,4 · A. G. Kolias7 · R. Mannion7 · O. Koulouri1 · M. Gurnell1 Accepted: 3 May 2022 / Published online: 24 May 2022 © The Author(s) 2022 Accepted: 3 May 2022 / Published online: 24 May 2022 © The Author(s) 2022 2 Department of Nuclear Medicine, University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK 3 Macleod Diabetes and Endocrine Centre, Royal Devon and Exeter Hospital, Exeter, UK Abstract Purpose  To assess the potential for 11C-methionine PET (Met-PET) coregistered with volumetric magnetic resonance imag- ing (Met-PET/MRCR) to inform clinical decision making in patients with poorly visualized or occult microprolactinomas and dopamine agonist intolerance or resistance. Patients and methods  Thirteen patients with pituitary microprolactinomas, and who were intolerant (n = 11) or resistant (n = 2) to dopamine agonist therapy, were referred to our specialist pituitary centre for Met-PET/MRCR between 2016 and 2020. All patients had persistent hyperprolactinemia and were being considered for surgical intervention, but standard clini- cal MRI had shown either no visible adenoma or equivocal appearances. Results  In all 13 patients Met-PET/MRCR demonstrated a single focus of avid tracer uptake. This was localized either to the right or left side of the sella in 12 subjects. In one patient, who had previously undergone surgery for a left-sided adenoma, recurrent tumor was unexpectedly identified in the left cavernous sinus. Five patients underwent endoscopic transsphenoidal selective adenomectomy, with subsequent complete remission of hyperprolactinaemia and normalization of other pituitary function; three patients are awaiting surgery. In the patient with inoperable cavernous sinus disease PET-guided stereotactic radiosurgery (SRS) was performed with subsequent near-normalization of serum prolactin. Two patients elected for a further trial of medical therapy, while two declined surgery or radiotherapy and chose to remain off medical treatment. C l i I ti t ith d i i t i t l i t d i d t i t it it MRI l l (f f Conclusions  In patients with dopamine agonist intolerance or resistance, and indeterminate pituitary MRI, molecular (func- tional) imaging with Met-PET/MRCR can allow precise localization of a microprolactinoma to facilitate selective surgical adenomectomy or SRS. Keywords  11C-methionine PET · Microprolactinoma · Dopamine agonist intolerance/ resistance * M. Pituitary (2022) 25:573–586 https://doi.org/10.1007/s11102-022-01229-9 Pituitary (2022) 25:573–586 https://doi.org/10.1007/s11102-022-01229-9 Abstract Gurnell mg299@medschl.cam.ac.uk 1 Cambridge Endocrine Molecular Imaging Group, Metabolic Research Laboratories, Wellcome–MRC Institute of Metabolic Science, University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK 2 Department of Nuclear Medicine, University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK 3 Macleod Diabetes and Endocrine Centre, Royal Devon and Exeter Hospital, Exeter, UK 4 Department of Radiology, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK 5 Department of Neuropathology, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK 6 Department of Otolaryngology, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK 7 Department of Neurosurgery, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK 8 Wolfson Brain Imaging Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK 9 Department of Oncology, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK 7 Department of Neurosurgery, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK 8 Wolfson Brain Imaging Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK 9 Department of Oncology, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK 9 Department of Oncology, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK 3 Macleod Diabetes and Endocrine Centre, Royal Devon and Exeter Hospital, Exeter, UK :(0123 1 3456789) 3 3456789) 3 574 Pituitary (2022) 25:573–586 adenomas and has been successfully used to facilitate curative (including repeat) TSS in acromegaly and Cush- ing Disease when MRI is indeterminate [32–34]. Several PET radiotracers have been trialled for imaging prolactino- mas, including 11C-raclopride and 11C-N-methylspiperone (dopamine D2 receptor ligands) [35, 36], 18F-fluorodeox- yglucose (metabolic activity as per the Warburg effect) [37, 38], and 11C-methionine [taken up via the L-type amino acid transporter 1 (LAT1) at sites of peptide syn- thesis] [38–41]. 11C-methionine PET (Met-PET) has been reported to have high sensitivity for the detection of func- tioning pituitary adenomas, including prolactinomas [38, 42]. Moreover, compared to other pituitary adenoma sub- types, prolactinomas show particularly avid 11C-methio- nine uptake [41, 43]. We have therefore reviewed our recent experience with Met-PET coregistered with volu- metric MRI (Met-PET/MRCR) in patients with suspected microprolactinomas who are being considered for pituitary surgery due to intolerance or resistance to dopamine ago- nist therapy, but in whom standard clinical MRI has not conclusively identified a discrete lesion. Abstract Here, we show that functional imaging can confirm or refute the suspected site of a microprolactinoma queried on clinical MRI and reveal the location of an adenoma when MRI is negative. Patients Thirteen patients with microprolactinomas were referred to our tertiary center for consideration of surgery, because of dopamine agonist intolerance (n = 11) or resistance (n = 2), between April 2016 and March 2020. In all cases, the diag- nosis of a prolactinoma was originally based on typical symptoms (e.g. galactorrhea and/or gonadal dysfunction) in the presence of confirmed raised serum prolactin levels (females > 29 ng/ml, males > 18 ng/ml). Conventional pitui- tary MRI (T1 spin echo with and without intravenous con- trast and, where available, T2 fast spin echo) was deemed equivocal (one or more possible abnormalities identified, but low confidence to confirm site of the adenoma) or negative (no abnormality seen). Each patient underwent Met-PET and volumetric MRI with co-registration to yield hybrid images (Met-PET/MRCR) as described in the following sections. The study received institutional approval (CUH QSIS 2020: 3039). Introduction Prolactinomas are the most common functioning pitui- tary adenomas [1]. Microprolactinomas typically mani- fest with galactorrhea and hypogonadism [2, 3], which can have significant adverse effects on quality of life [4]. The mainstay of treatment remains medical therapy with dopa- mine agonists [5]. These are generally well tolerated [6], but may cause side effects including postural dizziness, daytime somnolence, gastro-intestinal upset and cardiac valvular fibrosis [7–9], although risk of the latter when using low dosages (as is typically required for prolacti- nomas) is still debated [10]. In recent years, attention has also focussed on potential psychological adverse effects, including impulse control disorders (ICDs), which have been reported in 8–24% of patients with prolactinomas receiving treatment with dopamine agonists [11–15], and which can have devastating consequences for patients and their families [16].f When adverse effects prevent a successful treatment trial (either with respect to drug dosage and/or duration of therapy), patients are considered intolerant to dopa- mine agonist therapy [3]. This should be distinguished from dopamine agonist resistance, which is preferred when there is failure to normalize serum prolactin and/or achieve significant tumor shrinkage (in macroprolactino- mas) despite good tolerance and concordance with stand- ard clinical dosages [17, 18]. For patients with intolerance or resistance to medical therapy, transsphenoidal surgery (TSS) is an alternative treatment option [5], with several recent reports suggesting a higher long-term remission rate [19–24] and improved cost-effectiveness compared with dopamine agonist therapy [25, 26]. As evidence for the efficacy and safety of transsphenoidal surgery (TSS) accrues, there is increasing discussion about the earlier deployment of surgery for selected cases [27, 28]. How- ever, even in experienced hands, TSS may be complicated by cerebrospinal fluid leakage and new-onset hypopitui- tarism (including diabetes insipidus) [19]. Careful preop- erative appraisal must therefore balance the probability of achieving surgical cure with these risks. High qual- ity magnetic resonance imaging (MRI) of the sella and parasellar regions is central to effective decision-making and may provide important information regarding the likelihood of achieving complete surgical resection [29]. Nonetheless, it is not always possible to reliably localize the causative microadenoma, and MRI findings may be considered equivocal or negative even prior to a trial of medical therapy [30, 31]. Standard and 3D gradient echo MRI MR imaging was performed on clinical 1.5 T or 3 T sys- tems (GE Healthcare, Waukesha, WI, USA) using a circu- larly polarised head coil. Coronal T1 spin echo (SE) images were obtained before and after intravenous injection of 0.1 mmol/kg gadobutrol. A fast spoiled gradient recalled echo (FSPGR) acquisition sequence was performed to opti- mise co-registration with the PET-CT dataset (Met-PET/ MRCR). In brief, sagittal T1-weighted FSPGR images [TR (repetition time) 11.5 ms, TE (echo time) 4.2 ms, slice thick- ness 1 mm, 0 mm gap, 256 × 256 matrix] of the whole head were obtained following intravenous injection of 0.1 mmol/ kg gadobutrol. Image processing and analysis The PET tracer, L-[methyl-11C]-methionine, was synthe- sised in compliance with good manufacturing practice using a captive solvent in loop methylation method without preparative HPLC, adapted from methods published pre- viously [45–47]. Briefly, ­[11C]CO2 was produced using a PETtrace cyclotron (GE Healthcare, Milwaukee, WI, USA) via the 14 N(p,훼)11C reaction before conversion to ­[11C]MeI in the MeI MicroLab (GE Healthcare). This was then trans- ferred to the HPLC loop of a modified TracerLabFXC (GE Healthcare) synthesiser containing an L-homocysteine pre- cursor solution (0.5 M aqueous NaOH solution in ethanol). 11C-methionine was produced in yields averaging 376 MBq with a radiochemical purity of > 96% and specific activity between 263 and 452.5 MBq. Image processing was performed using open source soft- ware 3D Slicer [48] (version 4.10.2, 05–2019). PET images (GE SharpIR reconstruction) were prepared for visualiza- tion by creating ratio PET (SUVr) images. SUVr images were created by dividing each voxel in the image by the mean value found in a region of interest (ROI) positioned in the subject’s cerebellum. Each subject’s SUVr images were displayed with identical colour scales (ColdToHotRainbow), colour ranges (1.0–4.0), and threshold levels to remove low level background uptake (< 1.0). SUVr images were regis- tered with volumetric MRI images (FSPGR sequence) using rigid registration with 6 degrees of freedom, a maximum number of iterations of 1500 and a sample ratio of 0.01. Following registration, the SUVr images were overlaid on the MRI images. Clinical care Molecular (functional) imaging using positron emis- sion tomography-computed tomography (PET-CT) can aid localization of de novo, residual or recurrent pituitary Patients were managed according to local approved pitui- tary care pathways, which are consistent with international clinical guidelines [5]. Pituitary function tests [including 3 3 Pituitary (2022) 25:573–586 575 prolactin, cortisol, free thyroxine (FT4), thyroid stimulat- ing hormone (TSH), luteinizing hormone (LH), follicle stimulating hormone (FSH), estrogen or testosterone, and insulin-like growth factor 1 (IGF-1)] were performed on serum samples collected between 8 and 9AM. All biochemi- cal measurements (Siemens Medical Solutions Diagnostics Ltd.) were performed in a Clinical Pathology Accreditation Ltd. laboratory (CPA) with relevant internal and external quality assurance as required by the CPA. Each patient pro- vided informed consent for Met-PET. All patients remained off dopamine agonist therapy for at least one month prior to performing functional imaging to minimise the risk of a false negative scan due to residual suppression of tumor activity. Treatment decisions were made on a case-by-case basis, considering patient preference, after discussion by a specialist pituitary multidisciplinary team consisting of pituitary neurosurgeons, endocrinologists, otolaryngolo- gists, radiation oncologist, neuropathologist, and neurora- diologists, who had full access to the Met-PET/MRCR scans to inform clinical decision-making. Transsphenoidal pitui- tary surgery or radiotherapy were performed as previously described [34, 44]. 3D iterative reconstruction algorithms (three iterations, 24 subsets, 2 mm Gaussian post-filter) incorporating ToF and resolution recovery software (VUE Point FX and Sharp IR) to a 3.27 mm slice thickness. CT images were reconstructed at 1.25 mm slice thickness. Met-PET studies were indepen- dently reviewed by nuclear medicine physicians with exper- tise in PET-CT on the Xeleris workstation (GE Healthcare, Amersham, Buckinghamshire, UK). 11C‑methionine PET‑CT imaging Images were acquired on a GE Discovery 690 PET-CT scan- ner (GE Healthcare). All patients fasted for 4 h before PET- CT scanning. An intravenous injection of 264–423 MBq of L-[methyl-11C]-methionine was given prior to each scan. The uptake time for PET-CT was standardized at 20 min. An attenuation correction (low dose) CT was performed (140 kV, 220 mA, 0.5 s rotation, and 0.984 mm pitch) followed by a single bed position PET acquisition of the head. Time-of-flight (ToF) PET data were acquired for a total acquisition time of twenty minutes. PET images were reconstructed with CT attenuation correction using fully Results Thirteen patients, all of reproductive age, were included in the study [twelve women, one man; mean age at time of Met-PET scan 34 years (range 20–45)]. Eleven patients were referred for Met-PET because of intolerance to DA therapy, and two because of DA resistance (Table 1). All had expe- rienced several years (in some instances > 10 years) of sub- optimal disease control (Fig. 1). Results In seven subjects (Cases 2, 5, 7, 8, 11, 12, 13), findings on pituitary MRI at the time of 1 Pituitary (2022) 25:573–586 576 576 Pituitary (2022) 25:573 586 1 3 Table 1   Clinical, biochemical and radiological features at initial presentation, at the time of Met-PET, and following further treatment Case Sex Baseline biochemistry MRI findings at diagnosis Previous treatment DA side effects or resistance MRI findings following previous treatment Met-PET/ MRCR find- ings PRL at time of PET (ng/ ml) * Further treat- ment Biochemistry following further treatment Latest PRL (ng/ ml)* PRL (ng/ml)* Pituitary deficits PRL (ng/ml)* Pituitary deficits 1 F 203 G Infundibulum central; possible right-sided lesion C, B, Q Low mood Infundibulum central; possible bilateral non- enhancing lesions Focal high tracer uptake adjacent to left CS 107 TSS 10 None 24 2 F 67 G Subtle left infun- dibular deviation; possible bilateral non-enhanc- ing lesions C Low mood Subtle left infun- dibular deviation; possible bilateral non-enhanc- ing lesions Focal high tracer uptake within right sella 74 TSS 5 None 5 3 F 172 G Possible right infun- dibular deviation; no discrete lesion C, B, Q Low mood, headache Right infun- dibular deviation; no discrete lesion Focal high tracer uptake just to left of infun- dibulum inferiorly 73 TSS 15 None 8 4 F 48 G Unavailable C, Q Low mood Infundibulum central; possible right sided lesion with subtle depression of sella floor Focal high tracer uptake within right sella 49 TSS 3 None 6 5 F 109 None Infundibulum central; no discrete lesion C, A** Low mood Infundibulum central; no discrete lesion Focal high tracer uptake within right sella 100 Awaiting TSS NA NA 100 6 M 191 G Infundibulum central; possible left-sided lesion C, B, Q Aggression, increased libido Infundibulum central; no discrete lesion Focal high tracer uptake within left sella 61 Nil NA G 46 Pituitary (2022) 25:573–586 577 ) Baseline biochemistry MRI findings at diagnosis Previous treatment DA side effects or resistance MRI findings following previous treatment Met-PET/ MRCR find- ings PRL at time of PET (ng/ ml) * Further treat- ment Biochemistry following further treatment Latest PRL (ng/ ml)* PRL (ng/ml)* Pituitary deficits PRL (ng/ml)* Pituitary deficits 52 None Infundibulum central; minor depression of left sella floor; no discrete lesion C, B, Q Low mood Infundibulum central; minor depression of left sella floor; no discrete lesion Focal high tracer uptake within sella inferiorly to the left of midline 49 Awaiting TSS NA N/A 49 56 G Infundibulum central; minor inferior depression of right sella floor; possible right micro- adenoma C, Q Nausea Infundibulum central; minor inferior depression of right sella floor; possible right micro- adenoma Focal high tracer uptake within right sella inferiorly 36 TSS 6 None 6 75 G Infundibulum central; no discrete lesion C Headache Infundibulum central; possible area of reduced enhance- ment in left side of sella Focal high tracer uptake within left sella 46 C 29 None 35 470 G Unavailable; presumed left-sided adenoma (site of previous TSS) C, TSS Raynaud phenom- enon Post- operative changes; no definite residual/ recurrence Focal high tracer uptake within left CS 82 SRS 86 None 40 65 G Infundibulum central; possible bilateral non- enhancing lesions C Nausea, increased libido Infundibulum central; possible bilateral non- enhancing lesions Focal high tracer uptake within right sella 55 C 15 None 8 3 Pituitary (2022) 25:573–586 578 ole for a concomitant mental health condition riptine, BP blood pressure, C cabergoline, CS cavernous sinus, DA dopamine agonist, F female, G hypogonadism, M male, NA not available, PRL prolactin, Q quina- adiosurgery, TSS transsphenoidal surgery (endoscopic) 1 3 Case Sex Baseline biochemistry MRI findings at diagnosis Previous treatment DA side effects or resistance MRI findings following previous treatment Met-PET/ MRCR find- ings PRL at time of PET (ng/ ml) * Further treat- ment Biochemistry following further treatment Latest PRL (ng/ ml)* PRL (ng/ml)* Pituitary deficits PRL (ng/ml)* Pituitary deficits 12 F 120 G Possible subtle left Infun- dibular deviation; no discrete lesion seen C Resistance Possible subtle left Infun- dibular deviation; no discrete lesion seen Focal high tracer uptake within left sella 111 Nil NA NA 35 13 F 84 G Possible subtle left Infundibu- lar devia- tion with right-sided lesion in superior aspect of gland C Resistance Possible subtle left Infundibu- lar devia- tion with right-sided lesion in superior aspect of gland Focal high tracer uptake within right sella 39 Awaiting TSS NA NA 37 *Prolactin references ranges: female (3–29 ng/ml), male (2–18 ng/ml) **Treated with aripiprazole for a concomitant mental health condition A aripiprazole, B bromocriptine, BP blood pressure, C cabergoline, CS cavernous sinus, DA dopamine agonist, F female, G hypogonadism, M male, NA not available, PRL prolactin, Q quina- golide, SRS stereotactic radiosurgery, TSS transsphenoidal surgery (endoscopic) Pituitary (2022) 25:573–586 579 Fig. Results 1   Schematic representation of the clinical courses for each of the thirteen patients prior to and following Met-PET. DA dopamine ago- nist, Met-PET/MRCR 11C-methionine PET coregistered with volumet- ric (FSPGR) MRI, PET Positron Emission Tomography, PRL prolac- tin, SRS stereotactic radiosurgery, TSS transsphenoidal surgery, ULN upper limit of normal Fig. 1   Schematic representation of the clinical courses for each of the thirteen patients prior to and following Met-PET. DA dopamine ago- nist, Met-PET/MRCR 11C-methionine PET coregistered with volumet- ric (FSPGR) MRI, PET Positron Emission Tomography, PRL prolac- tin, SRS stereotactic radiosurgery, TSS transsphenoidal surgery, ULN upper limit of normal effects, with one achieving a normal serum prolactin level, while two patients have elected to remain off all treatment with ongoing hyperprolactinemia (Fig. 1).i referral to our service were similar to those reported at initial presentation (Table 1). In three patients initial MRI appear- ances were either less informative regarding the suspected site of the adenoma (Cases 3, 9) or incorrectly identified a possible abnormality on the contralateral side to where the adenoma was subsequently resected (Case 1) (Table 1). In a single patient (Case 6), MRI at diagnosis identified a pos- sible adenoma that was not readily visualized on repeat MRI at the time of referral for Met-PET (Table 1). In two patients (Cases 4, 10), initial imaging was unavailable for review. Met-PET identified a focus of increased tracer uptake in all thirteen cases (Figs. 2–4 and Supplementary Fig. 1). Five patients underwent uncomplicated PET-guided TSS with intra-operative and, in four cases, histological confirmation of PET findings. All had subsequent complete remission of hyperprolactinemia, which has been maintained off medical treatment, and all have normal pituitary function (Figs. 1–3). Three patients are awaiting surgery. One patient was deemed to have unresectable lateral disease, and therefore received stereotactic radiosurgery (SRS), with subsequent near nor- malization of hyperprolactinemia (Table 1; Figs. 1 and 4). Four patients had a clear abnormal focus of tracer uptake on Met-PET but chose not to undergo surgical intervention after further consideration of the risks and benefits of sur- gery (Table 1; Supplementary Fig. 1). Two of these patients have returned to cabergoline therapy despite ongoing side referral to our service were similar to those reported at initial presentation (Table 1). Results In three patients initial MRI appear- ances were either less informative regarding the suspected site of the adenoma (Cases 3, 9) or incorrectly identified a possible abnormality on the contralateral side to where the adenoma was subsequently resected (Case 1) (Table 1). In a single patient (Case 6), MRI at diagnosis identified a pos- sible adenoma that was not readily visualized on repeat MRI at the time of referral for Met-PET (Table 1). In two patients (Cases 4, 10), initial imaging was unavailable for review. Met-PET identified a focus of increased tracer uptake in all thirteen cases (Figs. 2–4 and Supplementary Fig. 1). Five patients underwent uncomplicated PET-guided TSS with intra-operative and, in four cases, histological confirmation of PET findings. All had subsequent complete remission of hyperprolactinemia, which has been maintained off medical treatment, and all have normal pituitary function (Figs. 1–3). Three patients are awaiting surgery. One patient was deemed to have unresectable lateral disease, and therefore received stereotactic radiosurgery (SRS), with subsequent near nor- malization of hyperprolactinemia (Table 1; Figs. 1 and 4). Four patients had a clear abnormal focus of tracer uptake on Met-PET but chose not to undergo surgical intervention after further consideration of the risks and benefits of sur- gery (Table 1; Supplementary Fig. 1). Two of these patients have returned to cabergoline therapy despite ongoing side The five patients who underwent selective adenomectomy and the single patient who underwent SRS, guided by the findings on Met-PET, are presented in more detail below. Case 1 (Table 1 and Figs. 1–2) A young woman presented with secondary amenorrhea and was found to have significant hyperprolactinemia (serum prolactin 203  ng/ml). Initial and subsequent MRI did not identify a clear adenoma, although a pos- sible right-sided lesion was queried. Over the course of 15 years, several DAs were trialled, including bromocrip- tine (maximum tolerated dosage 5 mg/day), cabergoline (0.5 mg/week), and quinagolide (75 μg/day). Normopro- lactinaemia was never achieved, and the patient experi- enced recurrent episodes of low mood while on treat- ment (Fig. 1). Repeat T1 SE MRI remained equivocal, highlighting possible abnormalities on both sides of the gland (Fig. 2). Met-PET identified a focus of intense 11C-methionine uptake in the left lateral sella (Fig. 2). The patient proceeded to endoscopic TSS, with selective resection of a left-sided tumour which was histologically 1 3 580 Pituitary (2022) 25:573–586 Fig. 2   MRI and Met-PET findings with 3D reconstruction of the sella and parasellar regions in case 1. A–B Pre- and post-contrast coronal T1 SE MRI demonstrates equivocal appearances, with two possible areas of reduced enhancement (arrows). C Met-PET/MRCR reveals avid focal tracer uptake in the left side of the gland adjacent to the cavernous sinus (arrow). D–I 3D reconstructed images, com- bining PET, CT and FSPGR MRI datasets, allows appreciation of the location of the tumor (yellow) with respect to the normal gland (turquoise) and proximity of the tumor to key adjacent structures including the intracavernous cartoid artery (red). At transsphenoi- dal surgery, a microadenoma abutting the left cavernous sinus was resected and confirmed histologically to be a prolactinoma. Postop- eratively the patient remains normoprolactinemic and eupituitary. CT computed tomography, FSPGR fast spoiled gradient recalled echo, Gad gadolinium, MRI magnetic resonance imaging, Met-PET/MRCR 11C-methionine PET-CT coregistered with volumetric (FSPGR) MRI, PET positron emission tomography, SE spin echo Fig. 2   MRI and Met-PET findings with 3D reconstruction of the sella and parasellar regions in case 1. A–B Pre- and post-contrast coronal T1 SE MRI demonstrates equivocal appearances, with two possible areas of reduced enhancement (arrows). C Met-PET/MRCR reveals avid focal tracer uptake in the left side of the gland adjacent to the cavernous sinus (arrow). D–I 3D reconstructed images, com- bining PET, CT and FSPGR MRI datasets, allows appreciation of the location of the tumor (yellow) with respect to the normal gland (turquoise) and proximity of the tumor to key adjacent structures including the intracavernous cartoid artery (red). Case 1 (Table 1 and Figs. 1–2) At transsphenoi- dal surgery, a microadenoma abutting the left cavernous sinus was resected and confirmed histologically to be a prolactinoma. Postop- eratively the patient remains normoprolactinemic and eupituitary. CT computed tomography, FSPGR fast spoiled gradient recalled echo, Gad gadolinium, MRI magnetic resonance imaging, Met-PET/MRCR 11C-methionine PET-CT coregistered with volumetric (FSPGR) MRI, PET positron emission tomography, SE spin echo Case 3 (Table 1 and Fig. 3) confirmed as a lactotroph pituitary adenoma. She remains in remission off all treatment at 3 years follow-up, with otherwise normal pituitary function. A young woman was found to have a raised serum prol- actin level (172 ng/ml) during investigation for secondary amenorrhea. A diagnosis of a presumed microprolacti- noma was made, although T1 gadolinium-enhanced SE MRI did not identify a discrete lesion. Trials of cabergo- line (0.5 mg/week), bromocriptine (10 mg/day) and quina- golide (150 µg/day) each allowed restoration of normopro- lactinemia, but all resulted in intolerable side effects with low mood and headaches. Repeat T1 gadolinium-enhanced SE MRI showed subtle infundibular deviation to the right but no discrete lesion (Fig. 3). Met-PET revealed a focus of high tracer uptake inferiorly and just to the left of mid- line (Fig. 3), which corresponded with a small area of abnormal tissue at TSS. Although histology was unable to confirm an adenoma (insufficient sample), immediately following surgery the patient’s serum prolactin was nor- mal, and she remains in remission 2 years after surgery with no pituitary hormone deficits. 3 Case 2 (Table 1 and Fig. 3) A young woman developed secondary amenorrhea, bilateral galactorrhea, and low libido. Serum prolac- tin was raised at 67 ng/ml. T1 gadolinium-enhanced SE and FSPGR MRI failed to demonstrate a convinc- ing adenoma, although possible focal reduced contrast enhancement was queried bilaterally (Fig. 3). Cabergo- line therapy (maximum tolerated dosage 0.75 mg/week) was associated with depressive symptoms and failure to normalize serum prolactin (Fig. 1). Met-PET revealed a focus of intense 11C-methionine uptake in the right side of the pituitary gland. The patient underwent endoscopic TSS with selective resection of a right-sided lactotroph adenoma (with confirmatory histology). She remains in remission 3 years later, with normal pituitary function. 3 581 Pituitary (2022) 25:573–586 Fig. 3   MRI and Met-PET findings in cases 2, 3, 4 and 8. A–H Pre- and post-contrast coronal T1 SE MRI show equivocal appearances in four patients, identifying either no abnormality or possible single or multiple lesions (arrows). I–L In contrast, in all four subjects Met-PET/MRCR demonstrates a single focus of intense tracer uptake which was subsequently confirmed at transsphenoidal surgery to be the site of a microprolactinoma. Postoperatively, all patients remain normoprolactinemic and eupituitary. FSPGR fast spoiled gradient recalled echo, Gad gadolinium, MRI magnetic resonance imaging, Met-PET/ MRCR 11C-methionine PET-CT coregistered with volumetric (FSPGR) or SE MRI, PET positron emission tomography, SE spin echo Fig. 3   MRI and Met-PET findings in cases 2, 3, 4 and 8. A–H Pre- and post-contrast coronal T1 SE MRI show equivocal appearances in four patients, identifying either no abnormality or possible single or multiple lesions (arrows). I–L In contrast, in all four subjects Met-PET/MRCR demonstrates a single focus of intense tracer uptake which was subsequently confirmed at transsphenoidal surgery to be the site of a microprolactinoma. Postoperatively, all patients remain normoprolactinemic and eupituitary. FSPGR fast spoiled gradient recalled echo, Gad gadolinium, MRI magnetic resonance imaging, Met-PET/ MRCR 11C-methionine PET-CT coregistered with volumetric (FSPGR) or SE MRI, PET positron emission tomography, SE spin echo Case 4 (Table 1 and Fig. 3) A–B Post- contrast coronal T1 SE and FSPGR MRI demonstrate indeterminate appearances in a patient who had previously undergone transsphenoi- dal surgery for a left-sided microprolactinoma. C Axial FSPGR MRI shows possible recurrent tumor in the left cavernous sinus (yellow arrow). D–E Coronal and axial Met-PET/MRCR confirm avid tracer uptake at the site of the suspected recurrence (yellow arrow); tracer Fig. 4   PET–guided stereotactic radiosurgery in case 10. A–B Post- contrast coronal T1 SE and FSPGR MRI demonstrate indeterminate appearances in a patient who had previously undergone transsphenoi- dal surgery for a left-sided microprolactinoma. C Axial FSPGR MRI shows possible recurrent tumor in the left cavernous sinus (yellow arrow). D–E Coronal and axial Met-PET/MRCR confirm avid tracer uptake at the site of the suspected recurrence (yellow arrow); tracer uptake within the remaining normal gland is also seen (white arrow). F Treatment plan for PET-guided SRS. Three years later serum prol- actin was near-normalized (1.4 × ULN). FSPGR fast spoiled gradient recalled echo, Gad gadolinium, MRI magnetic resonance imaging, Met-PET/MRCR 11C-methionine PET-CT coregistered with volumet- ric (FSPGR) MRI, PET positron emission tomography, PTV Planning Target Volume, SE spin echo, ULN upper limit of normal uptake within the remaining normal gland is also seen (white arrow). F Treatment plan for PET-guided SRS. Three years later serum prol- actin was near-normalized (1.4 × ULN). FSPGR fast spoiled gradient recalled echo, Gad gadolinium, MRI magnetic resonance imaging, Met-PET/MRCR 11C-methionine PET-CT coregistered with volumet- ric (FSPGR) MRI, PET positron emission tomography, PTV Planning Target Volume, SE spin echo, ULN upper limit of normal Fig. 4   PET–guided stereotactic radiosurgery in case 10. A–B Post- contrast coronal T1 SE and FSPGR MRI demonstrate indeterminate appearances in a patient who had previously undergone transsphenoi- dal surgery for a left-sided microprolactinoma. C Axial FSPGR MRI shows possible recurrent tumor in the left cavernous sinus (yellow arrow). D–E Coronal and axial Met-PET/MRCR confirm avid tracer uptake at the site of the suspected recurrence (yellow arrow); tracer uptake within the remaining normal gland is also seen (white arrow). F Treatment plan for PET-guided SRS. Three years later serum prol- actin was near-normalized (1.4 × ULN). FSPGR fast spoiled gradient recalled echo, Gad gadolinium, MRI magnetic resonance imaging, Met-PET/MRCR 11C-methionine PET-CT coregistered with volumet- ric (FSPGR) MRI, PET positron emission tomography, PTV Planning Target Volume, SE spin echo, ULN upper limit of normal Case 4 (Table 1 and Fig. 3) A young woman developed oligomenorrhea and bilateral galactorrhea. Serum prolactin was raised at 56 ng/ml. Ini- tial T1 gadolinium-enhanced SE MRI was considered sug- gestive of a possible right-sided pituitary microadenoma, with subtle depression of the sella floor. Cabergoline (0.5 mg/week) was initiated; however, she developed sig- nificant nausea, which did not improve despite changing to quinagolide (75 μg/day). Her symptoms recurred on subsequent rechallenging with dopamine agonist therapy and surgery was therefore considered. Repeat T1 SE MRI identified a suspected lesion in the right side of the pitui- tary gland (Fig. 3). The possibility of proceeding direct to surgery based on the MRI findings alone was considered but, following discussion with the patient, Met-PET was performed to confirm a functioning lesion at this loca- tion. This demonstrated focal increased 11C-methionine uptake in the anterior-inferior aspect of the pituitary fossa, concordant with the site suspected on MRI (Fig. 3). The patient underwent PET-guided TSS, with histological con- firmation of a prolactinoma at this location. She remains in remission postoperatively (at 12 months), with otherwise normal pituitary function. A young woman with secondary amenorrhea was found to have mild hyperprolactinemia (serum prolactin 48 ng/ ml). The findings from initial T1 gadolinium-enhanced SE MRI were unavailable for review. The patient was com- menced on cabergoline but was unable to tolerate even the lowest dosage (0.25 mg/week) due to mood disturbance. Thereafter, quinagolide (75 µg/day) was tried but resulted in return of depressive symptoms and the patient elected to discontinue DA therapy. Several years later, she sought further advice about possible surgical treatment of her prolactinoma given her persistent symptoms and ongoing hyperprolactinemia. Repeat T1 gadolinium-enhanced SE MRI identified a possible right-sided pituitary microade- noma (Fig. 3). Whilst surgery could have been undertaken based on these MRI findings alone, after discussion with the patient molecular imaging was performed to increase confidence that the suspected lesion was indeed func- tioning. Met-PET showed intense 11C-methionine tracer uptake within the right side of the sella (Fig. 3). At TSS, a right-sided adenoma was resected, with histological con- firmation of a lactotroph adenoma. Thereafter, serum pro- lactin levels have normalized, with restoration of regular menses (and maintained for > 12 months). 1 3 Pituitary (2022) 25:573–586 582 Fig. 4   PET–guided stereotactic radiosurgery in case 10. Discussion A young woman was found to have hyperprolactinemia (serum prolactin 470 ng/ml) while being investigated for secondary amenorrhea. The findings of MRI at ini- tial presentation were not available. She was treated with cabergoline in increasing dosages (up to 4 mg/week), with varying control of hyperprolactinemia. During this time, the patient developed marked Raynaud phenomenon and dopamine agonist therapy was discontinued. She then pro- ceeded to TSS, and a left-sided lactotroph microadenoma was resected (confirmed histologically). Following a short period of normoprolactinemia, her symptoms returned, and serum prolactin was again elevated (82 ng/ml). How- ever, T1 gadolinium-enhanced SE MRI could not reliably identify recurrent adenoma tissue (Fig. 4). Unexpectedly, Met-PET revealed a small focus of avid 11C-methionine uptake within the left cavernous sinus (Fig. 4). A small hypointense abnormality could be appreciated at exactly the same location on axial FSPGR MRI (Fig. 4). As the recurrent tumour was considered inoperable, the patient underwent SRS. Prolactin levels have decreased to 40 ng/ ml, at 3  years following SRS, with no new pituitary deficits. We report our initial experience with Met-PET/MRCR in 13 patients with microprolactinomas and dopamine agonist intolerance or resistance, in whom standard clinical MRI was considered indeterminate or negative. In all 13 cases, Met-PET demonstrated a focus of increased (often intense) tracer uptake (Figs. 2–4 and Supplementary Fig. 1). In some instances, this correlated with an area that had been identi- fied on MRI as possibly in keeping with an adenoma, but in other subjects Met-PET did not support MRI findings and/ or revealed a previously undisclosed abnormality (Table 1; Figs. 1–4 and Supplementary Fig. 1). In all five patients who proceeded to surgery, complete and sustained biochemi- cal remission was achieved, often for the first time in many years, with histology confirming a lactotroph adenoma in four cases. In the fifth patient, an obvious abnormality was found at surgery at the site identified on Met-PET, but his- tology was not confirmatory of a prolactinoma; however, this likely reflected a small tumor with total resection as evidenced by restoration and maintenance of normal serum prolactin following surgery—analogous to surgical/histolog- ical findings in some corticotroph tumors. In the patient with recurrent hyperprolactinemia following previous TSS (Case 1 3 3 Pituitary (2022) 25:573–586 583 10), in whom recurrent tumor was localized within the left cavernous sinus, SRS was followed by a progressive fall in serum prolactin to near normal levels (1.4 × ULN) (Table 1 and Figs. 1 and 4). Importantly, in all patients undergo- ing surgery, normal pituitary function was maintained or restored, and there were no other surgical complications. undergoing surgery because of resistance or intolerance to dopamine agonists, or patient preference, and reported that 38% achieved sustained remission without further treatment (66% of microprolactinomas, 22% of macroprolactinomas), while 62% achieved remission with adjunctive dopamine agonist therapy [64]. , g p Traditonally, dopamine agonist therapy has been consid- ered the cornerstone of management of patients with prolac- tinoma [5, 49]. In particular, cabergoline is recommended as it has superior efficacy in achieving normoprolactinemia and tumour shrinkage, when compared with bromocriptine and quinagolide. However, two important factors merit consider- ation before embarking on medical therapy: (1) the potential need for long-term treatment and (2) possible adverse effects of dopamine agonist therapy. With respect to treatment dura- tion, two recent systematic reviews concluded that following withdrawal of medical therapy, which is usually undertaken after two years of treatment, only approximately one-third of patients will achieve sustained remission [50, 51]. As a result, many patients require long-term (even > 10 years) treatment [16]. Although dopamine agonists are generally considered safe, a longer duration of treatment means that there is an extended exposure window in which the patient may experience side effects, and which may have particular relevance, for example, when considering the risk of car- diac valvular fibrosis [8, 10]. In addition, in recent years, concerns have surfaced regarding the possible adverse psy- chological effects, and in particular the previously unrecog- nized high prevalence of impulse control disorders (ICDs), in those treated with dopamine agonists [11–15, 52], which were not fully appreciated when earlier guidelines were pub- lished [5]. Accordingly, recent guidelines acknowledge that surgery can be considered as a first line treatment option for microprolactinomas where complete resection is deemed possible following specialist neurosurgical evaluation [53]. As the majority of prolactinomas are microadenomas [49], selective and complete adenomectomy, which deliv- ers long-term remission without causing additional pituitary deficits (and where possible correcting exisiting deficits), should be the goal of transsphenoidal surgery. 3 This is par- ticularly important for young women considering repro- duction, who are the group most commonly affected by microprolactinomas. To facilitate selective adenomectomy, accurate preoperative localisation of the adenoma is impor- tant, to minimise the need for more extensive exploration of the gland, and thereby potentially reducing the risk of new pituitary deficiencies or other (e.g. neurovascular) complica- tions. Nonetheless, even with advances in MR imaging, the detection of microadenomas, especially < 3 mm in maximum diameter, remains challenging [65]. Additionally, the find- ing of an incidentaloma may confound management [66]. In these situations, Met-PET may offer an additional route to confirming/revealing the tumor, as exemplified by the cases reported in our cohort, and also in other pituitary tumor sub- types [32, 33]. In this way, Met-PET complements routine clinical MRI to improve the accurate localization of small functioning tumours, and thereby enable patients who might otherwise not be considered suitable candidates for surgery or radiotherapy to progress to TSS or SRS. Our findings are also consistent with previous reports that indicate microprolactinomas are particularly 11C-methio- nine-avid [41, 43]. Met-PET may therefore allow more reliable distinction between true microprolactinomas and coincidental small non-secretory adenomas, although for- mal studies would be required to confirm this. It is also likely that some patients with so-called “idiopathic hyper- prolactinemia” harbor microadenomas that are beyond the resolution of current standard clinical MRI, and these may be identified by Met-PET. p g p g In support of this, several groups have reported on the effectiveness and safety of prolactinoma surgery [21–24, 29, 54–62]: after a follow-up of 13.5–102 months, overall remission rates ranged from 26 to 92%, with most estimates around 70%, although not all studies have provided clar- ity on whether patients required ongoing dopamine agonist therapy to achieve postoperative remission. Not surprisingly, most studies have reported higher remission rates for micro- prolactinomas compared to macroprolactinomas, and adeno- mas that are enclosed within the gland may have a more favourable outcome compared with adenomas located at the lateral margins [29, 60]. These findings have been endorsed in several systematic reviews and meta-analyses, which have reported TSS to deliver superior clinical outcomes compared to dopamine agonist therapy [19, 20, 63], with superior cost- effectiveness, although the absence of any randomised trials remains a major limitation [19]. Consent for publication  All authors approved the final manuscript for submission. Consent for publication  All authors approved the final manuscript for submission. Open Access  This article is licensed under a Creative Commons Attri- bution 4.0 International License, which permits use, sharing, adapta- tion, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. In summary, when MRI appearances are indeterminate in a patient with a microprolactinoma, it is logical for surgeons and patients to be apprehensive about surgery, especially for a condition where pharmacological therapy has traditionally been considered as first line treatment. However, the find- ings reported here indicate that Met-PET, a non-invasive technique, can facilitate precise localization of microprol- actinomas, including when MRI findings are inconclusive, thereby enabling the surgeon to represent the benefits and risks of surgery more accurately. Supplementary Information  The online version contains supplemen- tary material available at https://​doi.​org/​10.​1007/​s11102-​022-​01229-9. Acknowledgements  We are grateful to S Hader and L Li, from the Radiopharmacy Unit of the Wolfson Brain Imaging Centre, University of Cambridge, and V Warnes and H Mason from the PET-CT unit, Addenbrooke’s Hospital, Cambridge for their support in performing the 11C-methionine PET-CT scans. 5. Melmed S, Casanueva FF, Hoffman AR, Kleinberg DL, Montori VM, Schlechte JA et al (2011) Diagnosis and treatment of hyper- prolactinemia: an endocrine society clinical practice guideline. J Clin Endocrinol Metab 96:273–288. https://​doi.​org/​10.​1210/​jc.​ 2010-​1692 6. Webster J, Piscitelli G, Polli A, Ferrari CI, Ismail I, Scanlon MF (1995) A comparison of cabergoline and bromocriptine in the treatment of hyperprolactinemic amenorrhea. ACOG Curr J Rev 8:24. https://​doi.​org/​10.​1056/​nejm1​99410​06331​1403 Author contributions  All authors contributed to the article and approved the submitted version. p g j 7. Schade R, Andersohn F, Suissa S, Haverkamp W, Garbe E (2007) Dopamine agonists and the risk of cardiac-valve regurgitation. N Engl J Med 356:29–38. https://​doi.​org/​10.​1056/​nejmo​a0622​22 Funding  W Bashari, J MacFarlane, O Koulouri and M Gurnell are supported by the NIHR Cambridge Biomedical Research Center (BRC-1215–20014). 8. Stiles CE, Tetteh-Wayoe ET, Bestwick JP, Steeds RP, Drake WM (2018) A meta-analysis of the prevalence of cardiac valvulopathy in patients with hyperprolactinemia treated with cabergoline. J Clin Endocrinol Metab 104:523–538. https://​doi.​org/​10.​1210/​jc.​ 2018-​01071 References 1. Karavitaki N (2012) Prevalence and incidence of pituitary adeno- mas. Ann Endocrinol (Paris) 73:79–80. https://​doi.​org/​10.​1016/j.​ ando.​2012.​03.​039 2. Glezer A, Bronstein MD (2015) Prolactinomas. Endocrinol Metab Clin North Am 44:71–78. https://​doi.​org/​10.​1016/j.​ecl.​2014.​11.​ 003 3. Kars M, Dekkers OM, Pereira AM, Romijn JA (2010) Update in prolactinomas. Neth J Med 68:104–112. https://​doi.​org/​10.​7599/​ hmr.​2012.​32.4.​192 4. Andela CD, Scharloo M, Pereira AM, Kaptein AA, Biermasz NR (2015) Quality of life (QoL) impairments in patients with a pituitary adenoma: a systematic review of QoL studies. Pituitary 18:752–776. https://​doi.​org/​10.​1007/​s11102-​015-​0636-7f Supplementary Information  The online version contains supplemen- tary material available at https://​doi.​org/​10.​1007/​s11102-​022-​01229-9. 3 Interestingly, one system- atic review specifically investigated prolactinoma patients i An important limitation of this study is the small sample size. However, the cases reported here represent consecu- tive patients referred to our tertiary center over a four-year period and, importantly, all Met-PET scans demonstrated unequivocal findings. Although outcomes following TSS and SRS are only available for six patients, all demon- strated clinical and biochemical responses that confirm the accuracy of the PET. A further three patients are awaiting surgery (delayed by the pandemic), and the remaining four patients were all offered surgery. Accordingly, there was no selection bias when referring for surgery, and it seems unlikely that these patients would have fared less favora- bly at surgery given the comparable Met-PET findings. 1 3 3 584 Pituitary (2022) 25:573–586 However, it will be important to reproduce our findings in larger cohorts in a mutlicenter study. In addition, T2 MR sequences were not available in our patients, but may have allowed the identification of some occult tumors as previously reported [67, 68]. Accordingly, future studies should also include a comparison of the performance of T2 MRI with Met-PET. Currently, the restricted availability of 11C-methionine (with its short half-life of 20 min) is an important limitation in making this technique more widely available [32, 65], but several other centers in the UK and Europe have recently established molecular imaging for pituitary adenomas, including using related tracers [e.g. 18F-fluoroethyltyrosine (18F-FET)] and the establishment of a small number of centers in each country that develop appropriate expertise would be consistent with the broader Pituitary Tumor Centre Of Excellence (PTCOE) model [69]. Consent to participate  All participants were appropriately consented before any study procedures. Declarations Micko A, Vila G, Höftberger R, Knosp E, Wolfsberger S (2019) Endoscopic transsphenoidal surgery of microprolactinomas: a reappraisal of cure rate based on radiological criteria. 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GenMap: ultra-fast computation of genome mappability
Bioinformatics
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Abstract Motivation: Computing the uniqueness of k-mers for each position of a genome while allowing for up to e mismatches is computationally challenging. However, it is crucial for many biological applications such as the design of guide RNA for CRISPR experiments. More formally, the uniqueness or (k, e)-mappability can be described for every position as the reciprocal value of how often this k-mer occurs approximately in the genome, i.e., with up to e mismatches. Results: We present a fast method GenMap to compute the (k, e)-mappability. We extend the mappability algorithm, such that it can also be computed across multiple genomes where a k-mer occurrence is only counted once per genome. This allows for the computation of marker sequences or finding candidates for probe design by identifying approximate k-mers that are unique to a genome or that are present in all genomes. GenMap supports different formats such as binary output, wig and bed files as well as csv files to export the location of all approximate k-mers for each genomic position. Availability: GenMap can be installed via bioconda. Binaries and C++ source code are available on https://github.com/cpockrandt/genmap. Contact: pockrandt@jhu.edu GenMap: Ultra-fast Computation of Genome Mappability Christopher Pockrandt 1, 2, 3, *, Mai Alzamel 4, 5, Costas S. Iliopoulos 4 and Knut Reinert 2, 3 1Center for Computational Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA 2Department of Computer Science and Mathematics, Freie Universität Berlin, Berlin, Germany, 3Max Planck Institute for Molecular Genetics, Berlin, Germany, 4Department of Informatics, King’s College London, London, UK and 5Department of Computer Science, King Saud University, Riyadh, SA. ∗To whom correspondence should be addressed. Associate Editor: XXXXXXX Received on XXXXX; revised on XXXXX; accepted on XXXXX Received on XXXXX; revised on XXXXX; accepted on XXXXX © The Author(s) 2020. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 2 Algorithm many applications. Sequencing errors and variations such as SNPs require not only the k-mer to be unique or rare enough but also close matches of this k-mer, i.e., all k-mers with a certain number of mismatches have to be considered as well. Since the number of k-mers to be considered grows exponentially in the number of mismatches, k-mer counters are infeasible for this problem. many applications. Sequencing errors and variations such as SNPs require not only the k-mer to be unique or rare enough but also close matches of this k-mer, i.e., all k-mers with a certain number of mismatches have to be considered as well. Since the number of k-mers to be considered grows exponentially in the number of mismatches, k-mer counters are infeasible for this problem. Before we present our algorithm, we give an overview of the approach of Derrien et al. to compute the (k, e)-mappability. For reasons of clarity, we consider computing its inverse, the (k, e)-frequency and neglect searching the reverse strand throughout this paper. To consider the reverse strand, each k-mer has simply to be searched by its reverse complement leading to a doubling of the running time. Furthermore, we consider Hamming distance, if not stated otherwise. It can be applied to other distance metrics such as Edit distance as well. The suite GEM-Tools (Marco-Sola et al. (2012)) includes a program to compute the mappability for arbitrary k-mers and number of mismatches. It is the most common and advanced algorithm to compute the mappability of entire genomes. To improve its performance it offers a heuristic mode leading only to an approximation of the mappability. Nevertheless, it is not feasible to compute many instances of biological relevant k-mer sizes and number of errors. To achieve a feasible running time Derrien et al. implemented a heuristic. First, they initialize the frequency vector with 0s and perform a linear scan over the text (see algorithm 1). Then each k-mer Ti is searched with e errors in an FM index and the number of occurrences is stored in F[i]. If the count value exceeds some user-defined threshold parameter t, the locations of these occurrences are located. Let j be such a location. Since Ti has a high frequency, i.e., F[i] > t and D(Ti, Tj) ≤e, it is likely that Ti and Tj share common approximate matches. Hence, F[j] is assigned the frequency value F[i]. Definition ((k, e)-mappability and (k, e)-frequency). Definition ((k, e)-mappability and (k, e)-frequency). Given a string T of length n, the (k, e)-frequency counts occurrences of every single k-mer in T with up to e errors. We denote the k-mer starting at position i in T as Ti. The values are stored in a frequency vector F of length n −k + 1 such that F[i] = |{j | D(Ti, Tj) ≤e, 1 ≤j ≤n −k + 1}| Algorithm1Inexactalgorithmtocomputethe(k, e)-frequencybyDerrien et al. 1: procedure inexact_frequency(T, k, e, t) 2: F[1..|T| −k + 1] ←{0} 3: for i = 1, ..., |F| do 4: if F[i] = 0 then 5: P ←approximate matches with e errors 6: F[i] ←|P| 7: if |P| > t then 8: for j ∈P do 9: F[j] ←max(F[j], |P|) 10: return F Algorithm1Inexactalgorithmtocomputethe(k, e)-frequencybyDerrien et al. 1: procedure inexact_frequency(T, k, e, t) 2: F[1..|T| −k + 1] ←{0} 3: for i = 1, ..., |F| do 4: if F[i] = 0 then 5: P ←approximate matches with e errors 6: F[i] ←|P| 7: if |P| > t then 8: for j ∈P do 9: F[j] ←max(F[j], |P|) 10: return F Algorithm1Inexactalgorithmtocomputethe(k, e)-frequencybyDerrien et al. 1: procedure inexact_frequency(T, k, e, t) 2: F[1..|T| −k + 1] ←{0} 3: for i = 1, ..., |F| do 4: if F[i] = 0 then 5: P ←approximate matches with e errors 6: F[i] ←|P| 7: if |P| > t then 8: for j ∈P do 9: F[j] ←max(F[j], |P|) 10: return F where D(Ti, Tj) denotes the distance of two k-mers given a metric such as Hamming or Edit distance. Its elementwise multiplicative inverse is called the (k, e)-mappability and stored in a mappability vector M with M[i] = 1/F[i] for 1 ≤i ≤n −k + 1. A mappability value of 1 represents a unique k-mer, a mappability value close to 0 indicates a k-mer occurring in repetitive regions. Figure 1 gives an example for the (4, 0) and (4, 1)-frequency of a given nucleotide sequence considering Hamming distance. Since, for some applications, an exact computation of mappability is favorable, we propose a new algorithm that is not only faster than previous ones but also exact, i.e., does not rely on heuristics. Mappability can not only be used straightforward to retrieve information on the repetitiveness of the underlying data. 1 Introduction process (Fonseca et al. (2012)). Given a set of reads of some fixed length k the process of re-sequencing depends heavily on how mappable a genome is. Thus, for every substring of length k in the sequence, we want to count how many times this substring appears in the sequence while allowing for a small number e of errors. In other terms, mappability is a measure of how unique or repetitive regions in the genome are and is closely related to mapping. Theconceptofmappabilityforsequenceanalysiswasintroduced by Koehler et al. (2010), taken up again and later formalized by Derrien et al. (2012) (see also Antoniou et al. (2009)). Analyzing data derived from massively parallel sequencing experiments often depends on the process of genome assembly via re-sequencing; namely, assembly with the help of a reference sequence. In this process, a large number of reads derived from a DNA donor during these experiments must be mapped back to a reference sequence, comprising a few gigabases to establish the section of the genome from which each read originates. An extensive number of short-read alignment techniques and tools have been introduced to address this challenge emphasizing different aspects of the While k-mer counting became extremely popular in the last years, searching for k-mers with low occurrences does not meet the needs of 1 2 Pockrandt et al. 2 Algorithm To speed up the computation, k- mers that already have frequency values assigned by this heuristic step are skipped during the scan over the text. If a position j is located multiple times as an approximate match of a repetitive k-mer, F[j] is assigned the maximum frequency of all these k-mers to avoid underestimating the frequency value F[j]. In the following paragraph, we give a formal definition of the problem, present our algorithm in the next section and compare it to GEM. Our algorithm does not rely on heuristics and outperforms GEM even in its heuristic mode by far. Definition ((k, e)-mappability and (k, e)-frequency). In this paper, we will also illustrate that it can be used to find marker sequences that allow distinguishing similar strains of the same species, as well as separate strains by groups sharing common k-mers. Theirexperimentsonchromosome19ofthehumangenomewitht = 7 show that almost 90 % of the 50-mers with a frequency of 3 are correct, for 50-mers with frequency values between 8 and 12 only 75 % are correct (similar errors for C. elegans with t = 6). This can be led back to an overestimation of rather unique k-mers. We now present a fast and exact algorithm to compute the (k, e)- frequency. Similar to the algorithm implemented in GEM we scan over the text T while searching and counting the occurrences of each k-mer Ti for 1 ≤i ≤n −k + 1 with up to e errors in an index on T. In contrast to GEM we improve the running time by reducing redundant searches with three major improvements which we introduce in the following. 2.2 Adjacent k-mers Adjacent k-mers in T are highly similar, since they have a large overlap. Hence, we do not search for every k-mer separately. Consider the adjacent k-mers Tj, Tj+1, . . . , Tj+s−1 for some integer s ≤k −e + 1 which all share the common sequence T[j + s −1..j + k −1] of length at least e. Since we already need to allow for up to e errors in their common sequence when searching each k-mer, this infix should only be searched once. Thus, we start searching this infix using optimum search schemes and extend it afterwards to retrieve the occurrences for each k-mer separately using backtracking, allowing for the remaining number of errors not spent in the search of the infix. Since the extension is performed in both directions, a bidirectional index is required. Figure 3a illustrates this approach. Optimum search schemes are based on a framework by Kucherov et al. called search schemes that allows formalizing search strategies in a bidirectional index (Kucherov et al. (2016)). The sequence to be searched is split into p pieces and searched by certain combinations of the pieces in the index while trying to reduce the number of search steps performed in the index. Formally, a search is a triplet S = (π, L, U) of integer strings each of length p. π is a permutation of the numbers {1, 2, ..., p} indicating the order in which the pieces are searched. Starting from an arbitrary piece π[0] the subsequent pieces need to be adjacent to the previously searched pieces. L and U are non-decreasing integer strings indicating the lower and upper bound of errors. After the piece π[i] is searched a total number of errors from L[i] to U[i] must have been spent. A set of searches that covers all possible error distributions with e errors and p pieces forms a search scheme. As a result the number of errors allowed in the first pieces of each search is reduced which speeds up approximate string matching. By performing multiple searches starting with different pieces, it is guaranteed that all possible error distributions among the pieces are covered. i 1 2 3 4 5 6 7 8 9 10 11 12 13 14 . . . T[i] A G C C G T A C A A G T A T . . . T1 A G C C G T A C A A G T2 G C C G T A C A A G T T3 C C G T A C A A G T A T4 C G T A C A A G T A T C G 0 −0 T A 0 −0 C A 1 −2 A G 1 −2 (a) Forward search Sfwd = (1234, 0011, 0022) C G 2 −2 T A 0 −2 C A 0 −1 A G 0 −0 (b) Backward search Sbwd = (4321, 0002, 0122) 1 2 C G 0 −1 T A 0 −1 C A 0 −0 A G 0 −2 (c) Bidirectional search Sbi = (3214, 0000, 0112) T[4, 11] T[2, 11] T1 A T2 T ←− G C T[4, 13] T3 C T4 T −→ T A (b) The same strategy presented as a backtracking tree. It is traversed for all occurrences reported by the search of the infix T[4, 11] using optimum search schemes. Each edge also has to account for remaining errors, i.e., approximate string matching is performed using backtracking. T[4, 11] T[2, 11] T1 A T2 T ←− G C T[4, 13] T3 C T4 T −→ T A T3 2 (b) The same strategy presented as a backtracking tree. It is traversed for all occurrences reported by the search of the infix T[4, 11] using optimum search schemes. Each edge also has to account for remaining errors, i.e., approximate string matching is performed using backtracking. Fig. 3. Searching s overlapping k-mers using optimum search schemes for the infix and extending it using backtracking. Illustrated for k = 11 and s = 4. Fig. 3. Searching s overlapping k-mers using optimum search schemes for the infix and extending it using backtracking. Illustrated for k = 11 and s = 4. Fig. 2. The optimum search scheme for 2 mismatches consists of 3 searches with 4 pieces each. The arrows indicate in which order the pieces are searched. The error bounds below each part are cumulative bounds, i.e., the minimum number of errors that must respectively the maximum number of errors that can be spent until searching the end of the corresponding piece. Illustrated for searching the 8-mer CGTACAAG. The forward search covers the error distributions 0010, 0011, 0020, the backward search covers 2000, 1100, 0200, 1010, 0110, and the bidirectional search 0000, 0001, 0002, 1000, 1001, 0100, 0101. To further reduce the number of redundant computations, the set of overlapping k-mers is recursively divided into two sets of k-mers of roughly equal size that each share a larger common overlap among each other. i 1 2 3 4 5 6 7 8 9 10 11 12 13 14 . . . T[i] A G C C G T A C A A G T A T . . . T1 A G C C G T A C A A G T2 G C C G T A C A A G T T3 C C G T A C A A G T A T4 C G T A C A A G T A T Optimum search schemes are search schemes that are optimal under certain constraints, i.e., the number of backtracking steps in an index over all searches are minimized while still covering all error distributions. Figure 2 illustrates the optimum search scheme for e = 2 errors, p = e+2 pieces and up to 3 searches. (a) First, the common overlap (light gray) is searched using optimum search schemes. Second, the search of T1 and T2 is continued recursively by extending the previously identified approximate matches of the infix in the index by GC to the left (allowing for the remaining number of errors; medium gray). T1 and T2 are then retrieved separately by backtracking in the index by one character to the left and one character to the right (allowing for an error, if any left; dark gray). T3 and T4 are extended analogously in a recursive manner. C G 0 −0 T A 0 −0 C A 1 −2 A G 1 −2 (a) Forward search Sfwd = (1234, 0011, 0022) C G 2 −2 T A 0 −2 C A 0 −1 A G 0 −0 (b) Backward search Sbwd = (4321, 0002, 0122) 1 2 C G 0 −1 T A 0 −1 C A 0 −0 A G 0 −2 (c) Bidirectional search Sbi = (3214, 0000, 0112) Fig. 2. The optimum search scheme for 2 mismatches consists of 3 searches with 4 pi each. The arrows indicate in which order the pieces are searched. The error bounds be each part are cumulative bounds, i.e., the minimum number of errors that must respecti the maximum number of errors that can be spent until searching the end of the correspond piece. Illustrated for searching the 8-mer CGTACAAG. The forward search covers the e distributions 0010, 0011, 0020, the backward search covers 2000, 1100, 0200, 1010, 0 and the bidirectional search 0000, 0001, 0002, 1000, 1001, 0100, 0101. 2.1 Approximate String Matching using Optimum Search Schemes When searching a k-mer in a string index, it is searched character by character. Unidirectional indices only support extending characters into one direction, either to the left or to the right, while bidirectional indices support searching into both directions in any arbitrary order (Lam et al. (2009)). To search for every possible approximate match within the given error bound, backtracking is performed. This leads to exponential running time in the number of errors. Especially allowing for errors at the beginning of the k-mer, i.e., branching at the topmost nodes in the backtracking tree is (b) (4, 1)-frequency Fig. 1. (k, e)-frequency vectors Fe for k = 4 and e ∈{0, 1} on the same sequence. A frequency of 1 indicates that the k-mer starting at that position in the text is unique in the entire sequence without errors respectively with up to one mismatch. GenMap: Ultra-fast Computation of Genome Mappability 3 expensive. Hence, we use optimum search schemes (Kianfar et al. (2018)) when searching each k-mer, a sophisticated search strategy that reduces the number of search steps performed in the index while still searching for all possible approximate matches. 2.2 Adjacent k-mers i 1 2 3 4 5 6 7 8 9 10 11 12 13 14 . . . T[i] A G C C G T A C A A G T A T . . . T1 A G C C G T A C A A G T2 G C C G T A C A A G T T3 C C G T A C A A G T A T4 C G T A C A A G T A T This overlap is then searched using backtracking before the next recursive partitioning of k-mers. The recursion ends when a single k-mer is left and the number of occurrences can be reported and summed up, or no hits are found. The recursive extension is shown in figure 3b. Note, that there are two recursions involved: subdividing the set of k-mers and backtracking in each recursion step. Hence, the same partitioning steps and backtracking steps have to be performed for each set of preliminary matches represented by suffix array ranges in the FM index. Abidirectionalindexisrequiredtoenabletostartasearchwithamiddle piece as illustrated in figure 2c. To improve the overall running time of the index-based search we use a fast implementation of bidirectional FM indices based on EPR dictionaries (Pockrandt et al. (2017)). 4 Pockrandt et al. Tool (36, 0) (24, 1) (36, 2) (50, 2) (75, 3) GEM exact 5h 10m N/A N/A N/A N/A GEM heuristic 23m N/A 7h 11m 5h 50m 4h 26m GenMap 3m 23m 1h 19m 42m 1h 27m (a) Instances are taken from the experiments by Derrien et al. (2012). Tool (101, 0) (101, 1) (101, 2) (101, 3) (101, 4) GEM exact 44m 7h 28m 7h 34m 7h 45m 8h 8m GEM heuristic 28m 2h 40m 3h 17m 3h 31m 3h 49m GenMap 2m 7m 17m 46m 2h 42m (b) Typical Illumina read length with growing number of mismatches. Table 1. Running times for computing the frequency of the human genome (GRCh38) using 16 threads. Timeouts of 1 day are represented as N/A. Tool (36, 0) (24, 1) (36, 2) (50, 2) (75, 3) GEM exact 5h 10m N/A N/A N/A N/A GEM heuristic 23m N/A 7h 11m 5h 50m 4h 26m GenMap 3m 23m 1h 19m 42m 1h 27m (a) Instances are taken from the experiments by Derrien et al. (2012). The question remains on how to combine the improvements of sections 2.1 and 2.2, i.e., how to choose s, the number of adjacent k-mers that are searched together starting with their common sequence using optimum searchschemes. Onone hand, approximate stringmatching usingoptimum search schemes is more efficient than simple backtracking; hence, a longer common infix is favorable. On the other hand, a longer common infix means fewer adjacent k-mers are searched at once which leads to more redundant search steps due to the high similarity of overlapping k-mers. 3 Benchmarks At first, we compare the running times for computing the frequency on the human genome for different lengths and errors based on Hamming distance. We ran GEM in its exact mode as well as in its heuristic mode. Forthelatter, theauthorsrecommendt = 7. Table1acomparestherunning times for shorter k that are of interest for applications such as identifying marker sequences, presented in section 4. Table 1b shows typical instances used for applications in read mapping based on a typical Illumina read length. Even though longer Illumina read lengths are more common these days, we choose a shorter read length, since the frequency is easier to compute for longer k-mers. In conclusion, GenMap is a magnitude faster than GEM in its exact mode, and still faster than GEM using its heuristic, while GenMap is always exact. Even for up to 4 errors GenMap achieves a reasonable running time. This is due to the three techniques described in the previous section. Further improvements can be implemented which might speed up the algorithm even further, such as in-text verification (Pockrandt (2019)), i.e., locating partially searched k-mers and verifying whether their locations in the text match the k-mer with respect to the error bound. A location and verification step in the text is often several times faster than finishing an index-based approximate search. For all computed instances, GenMap is faster than GEM. Compared to the approximate mode, we are almost a magnitude faster for a smaller number of errors, but for 4 errors the heuristic of GEM pays off and is almost as fast as our algorithm. Interestingly, the increase of the running time of GEM in its exact mode gets smaller with more errors. For 101- mers with 1 to 4 errors, the running time is always about 7 to 8 hours, nonetheless GenMap is still faster by a factor from 3 of up to 64 (4 and 1 errors). Even when searching without errors where no backtracking has to be performed, our tool is faster by a factor of 20 to 100 (for 101-mers and 36-mers). The most noticeable improvement is achieved for short k-mers. Derrien et al. point out that their algorithm is not suitable for small k and completely unfeasible for k < 30 without its heuristic which is reflected by our benchmarks, whereas GenMap can handle these instances easily. i 1 2 3 4 5 6 7 8 9 10 11 12 13 14 . . . T[i] A G C C G T A C A A G T A T . . . T1 A G C C G T A C A A G T2 G C C G T A C A A G T T3 C C G T A C A A G T A T4 C G T A C A A G T A T GenMap chooses s according to the following equation derived from optimal values that were determined experimentally on different genomes such as the human and barley genome (see Pockrandt (2019) for details). clamp(v, l, r) returns v if it lies within the range, i.e., l ≤v ≤r, and returns l or r if it is less or greater. Tool (101, 0) (101, 1) (101, 2) (101, 3) (101, 4) GEM exact 44m 7h 28m 7h 34m 7h 45m 8h 8m GEM heuristic 28m 2h 40m 3h 17m 3h 31m 3h 49m GenMap 2m 7m 17m 46m 2h 42m (b) Typical Illumina read length with growing number of mismatches. Table 1. Running times for computing the frequency of the human genome (GRCh38) using 16 threads. Timeouts of 1 day are represented as N/A. s =    ⌊k · 0.7⌋ , e = 0 j k ·  clamp  k 100 , 0.3, 1.0  · 0.7ek , otherwise s =    ⌊k · 0.7⌋ , e = 0 j k ·  clamp  k 100 , 0.3, 1.0  · 0.7ek , otherwise 2.3 Skipping redundant k-mers Finally, we avoid searching the same k-mer multiple times. Especially k-mers from repeat regions may occur many times without errors in the text. Since they all share the same frequency value, it should be avoided to compute it more than once. Hence, after searching and counting the occurrences of a k-mer, we locate the positions of the exact matches and set all their frequency values in F accordingly. index with EPR dictionaries and a suffix array sampling rate of 10), while GEM takes up 4.5 GB (using an unspecified FM index implementation with a suffix array sampling rate of 32). GenMap is also suitable to compute the frequency of larger and more repetitive genomes than the human genome. We computed the (50, 2)- frequency of the barley genome (Mascher et al. (2017)) as it contains large amounts of repetitive DNA (Ranjekar et al. (1976)). Barley has 4.8 billion base pairs while the human genome has 3.2 billion base pairs. As expected the human genome has considerably more unique regions than the barley genome. To be precise 75.4 % of the 50-mers are unique in the human genome, and only 26.4 % in the barley genome. There are 12.0 % (54.4 %), 7.6 % (42.1 %) and 4.8 % (25.6 %) 50-mers in human DNA (resp. barley DNA) with at least 10, 100 and 1,000 occurrences. Computing the (50, 2)-frequency of barley on 16 threads took less than 1h 15m with GenMap and nearly a day with GEM using its heuristic with t = 6 (automatically chosen by GEM). We observed that this strategy leads to longer runs of frequency values forwarded to positions with uncomputed frequency values. When forwarded frequency values of previously counted k-mers are encountered during the scan over the text, they are skipped. 3 Benchmarks GEM takes significantly longer, often does not even terminate within 24 hours on 16 threads. All tests were conducted on Debian GNU/Linux 7.1 with an Intel Xeon E5-2667v2 CPU. To avoid dynamic overclocking effects in the benchmark the CPU frequency was fixed to 3.3 GHz. The data was stored on a virtual file system in the main memory to avoid loading it from disk during the benchmark which might affect the results due to I/O operations. We used the only available version 1.759 beta of the GEM suite that included the mappability algorithm. We did not reach the authors for other versions including their method. Other available and newer versions do not offer this feature anymore. The running times we measured for GEM heuristic differ considerably from the running times for GRCh37 published by the authors. Even when we ran it on a similar CPU with the same number of cores we were 2 to 5 times slower than their published benchmarks. One reason might be that the only available version of GEM with the mappability functionality was published as a beta version, however it was a year after their paper. Nonetheless, GenMap is still faster than the running times published by Derrien et al. For a fair comparison in our GenMap is also faster than GEM when computing the frequency of small genomes like D. melanogaster. Since smaller genomes are generally less challenging, we omit the benchmarks here. For the human genome, the memory consumption of GenMap is about 9 GB (using a bidirectional FM GenMap: Ultra-fast Computation of Genome Mappability 5 benchmark we reduced the genomes to the dna4 alphabet, i.e., replaced Ns by random bases. Based on tests we observed that GEM neither computes the mappability of k-mers that have unknown bases, nor considers them as mismatches in its default mode even when errors are allowed. benchmark we reduced the genomes to the dna4 alphabet, i.e., replaced Ns by random bases. Based on tests we observed that GEM neither computes the mappability of k-mers that have unknown bases, nor considers them as mismatches in its default mode even when errors are allowed. We computed the (30, 2)-mappability on four different strains of group B12. According to the study all strains within B1 share the anonymous DNA fragment TspE4.C2 of 152 base pairs. 4 Experiments Although the main focus of this work lies on presenting a new and fast algorithm for computing the mappability of a genome, we propose an application to identify marker sequences illustrated by a small example on E. coli strains. GenMap has an option to compute the mappability on multiple genomes while at most one approximate occurrence for a k-mer is counted for each genome. This allows us to quickly identify k-mers that are unique to a genome (regardless of the overall number of approximate occurrences in this genome) or k-mers that occur in every genome at least once. Additionally, GenMap not only outputs the mappability or frequency but also outputs the locations where the approximate matches for each k-mer occur into a csv file. This helps to find marker sequences or to select candidates for probe design by identifying k-mers that are unique to a genome or that are present in all genomes while allowing for errors. In table 3, we present the data of a second experiment, where we select strains from more than one group (A and B1); see figure 4b for an illustration. Again, we computed the (30, 2)-mappability, but this time we counted k-mers that match all strains in one group but no strain in the other group. Marker genes or marker sequences are short subsequences of genomes whose presence or absence allows determining the organism, species or even strain when sequencing an unknown sample or helping building phylogenetic trees (Patwardhan et al. (2014)). Depending on the marker length it can span up to dozens of reads. Instead of assembling the strain to search for marker genes or applying experimental methods such as PCR- based AFLP (amplified fragment length polymorphism, see Vos et al. (1995)), we propose using its mappability. all k-mers non-adjacent k-mers Group Strain Unique ∅Dist. Unique ∅Dist. A W3110 109,375 41 ± 731 2,398 1, 867 ± 4, 577 A HS 111,179 39 ± 709 2,414 1, 796 ± 4, 471 B1 IAI1 125,042 37 ± 680 3,063 1, 485 ± 4, 091 B1 SE11 127,302 38 ± 690 3,123 1, 510 ± 4, 148 B1 11128 121,325 42 ± 766 3,275 1, 548 ± 4, 408 B1 11368 131,121 41 ± 814 3,473 1, 537 ± 4, 763 Table 3. (30, 2)-mappability on six strains of E. coli of the groups A and B1. 3 Benchmarks IAI1 171,942 4,992 27 ± 627 1,829 81 2,476 ± 5,560 SE11 305,439 10,365 15 ± 447 2,356 176 1,942 ± 4,708 11128 260,305 40,101 20 ± 953 2,494 685 2,049 ± 9,517 11368 434,033 108,968 13 ± 912 3,142 1,116 1,674 ± 10,592 Table 2. (30, 2)-mappability on four strains of E. coli assigned to the phylogenetic group B1 based on the known marker genes by Clermont et al. We computed the mean distance of the unique marker sequences and their standard deviation. 3 Benchmarks We used GenMap to search for both, unique k-mers among all strains as well as k-mers that occur in each strain at least once, see figure 4a for an illustration. We observed that TspE4.C2 is an exact match in all strains and the 30-mers in this region also have a mappability value of exactly 0.25 when accounting for 2 errors. We further found numerous 30-mers with a mappability of 1, thus allowing to determine a strain among those four, while still accounting for sequencing errors and mutations. Table 2 lists the number of k-mers identified. We counted the number of k-mers matching only one strain, i.e., the strain the k-mer originated from. We refer to this count as unique. Additionally, we counted how many of these k-mers matched multiple times to the strain, referred to as pseudo. GenMap allows to exclude these pseudo marker sequences when computing the mappability on multiple sequence files, i.e., it is only counted in how many sequence files a k-mer is present. To avoid counting highly overlapping k-mers in large unique regions, we break down the numbers for non-adjacent k-mers as well, i.e., for a k-mer to be considered it must have a preceding k-mer with a mappability value smaller than 1. A more recent tool to compute the mappability is Umap (Karimzadeh et al. (2018)). It is limited to computing the (k, 0)-mappability and reporting only unique k-mers, i.e., regions with a mappability value of 1. It uses the read mapper Bowtie to search every single k-mer in the genome and filter non-unique k-mers afterwards. Due to these constraints we excluded it from our benchmarks. From the authors’ benchmarks, we can conclude that GenMap still outperforms Umap as GenMap needs less than one hour without parallelization to compute the (k, 0)-mappability (see table 1), while Umap needs about 200 hours. To verify our tool we compared the results to an exhaustive search with Bowtie1 (Langmead et al. (2009)) by mapping every k-mer to all its possible locations. From the number of mappings of each k-mer the mappability can be computed and written to a bed file. This approach yields identical results. We tested it by computing the (20, 1)-mappability on an E. coli genome1. Locating all mapping positions of each k-mer with a read mapper would be too inefficient on eukaryotic genomes. all k-mers non-adjacent k-mers Strain Unique Pseudo ∅Dist. Unique Pseudo ∅Dist. 2 Strains: IAI1 O8 (GCA_000026265.1), SE11 O152:H28 (GCA_000010385.1), 11128 O111:H- (GCA_000010765.1), 11368 O26:H11 (GCA_000091005.1) 1 https://github.com/cpockrandt/genmap/blob/master/tests/bowtie-test.sh References Antoniou, P., Daykin, J. W., Iliopoulos, C. S., Kourie, D., Mouchard, L., and Pissis, S. P. (2009). Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome. In Information Technology and Applications in Biomedicine, ITAB 2009, pages 1–4. IEEE. Clermont, O., Bonacorsi, S., and Bingen, E. (2000). Rapid and simple determination of theescherichia coli phylogenetic group. Applied and environmental microbiology, 66(10), 4555–4558. B1, Strain 6 B1, Strain 5 B1, Strain 4 B1, Strain 3 A, Strain 2 A, Strain 1 (b) Six sequences belonging to two different phylogenetic groups. Marker sequences are highlighted in light and dark gray. They only occur in one of the groups and are present in all of its strains. Fig. 4. Illustration of the experiments performed on E. coli sequences in tables 2 and 3. Derrien, T., Estellé, J., Sola, S. M., Knowles, D. G., Raineri, E., Guigó, R., and Ribeca, P. (2012). Fast computation and applications of genome mappability. PloS one, 7(1), e30377. Fonseca, N. A., Rung, J., Brazma, A., and Marioni, J. C. (2012). Tools for mapping high-throughput sequencing data. Bioinformatics, 28(24), 3169–3177. Karimzadeh, M., Hoffman, M. M., Ernst, C., and Kundaje, A. (2018). Umap and Karimzadeh, M., Hoffman, M. M., Ernst, C., and Kundaje, A. (2018). Umap and Bismap: quantifyinggenomeandmethylomemappability. NucleicAcidsResearch, 46(20), e120–e120. Kianfar, K., Pockrandt, C., Torkamandi, B., Luo, H., and Reinert, K. (2018). Optimum search schemes for approximate string matching using bidirectional fm-index. bioRxiv, page 301085. Koehler, R., Issac, H., Cloonan, N., and Grimmond, S. M. (2010). The uniqueome: a mappability resource for short-tag sequencing. Bioinformatics, 27(2), 272–274. Kucherov, G., Salikhov, K., and Tsur, D. (2016). Approximate string matching using a bidirectional index. Theoretical Computer Science, 638, 145–158. (b) Six sequences belonging to two different phylogenetic groups. Marker sequences are highlighted in light and dark gray. They only occur in one of the groups and are present in all of its strains. (b) Six sequences belonging to two different phylogenetic groups. Marker sequences are highlighted in light and dark gray. They only occur in one of the groups and are present in all of its strains. Lam, T. W., Li, R., Tam, A., Wong, S., Wu, E., and Yiu, S.-M. (2009). High throughput short read alignment via bi-directional bwt. In Bioinformatics and Biomedicine, 2009. BIBM’09. IEEE International Conference on, pages 31–36. IEEE. Langmead, B., Trapnell, C., Pop, M., and Salzberg, S. L. (2009). References Ultrafast and memory-efficient alignment of short dna sequences to the human genome. Genome biology, 10(3), R25. Fig. 4. Illustration of the experiments performed on E. coli sequences in tables 2 and 3. Fig. 4. Illustration of the experiments performed on E. coli sequences in tables 2 and 3. Marco-Sola, S., Sammeth, M., Guigó, R., and Ribeca, P. (2012). The gem mapper: fast, accurate and versatile alignment by filtration. Nature methods, 9(12), 1185. Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., et al. (2017). A chromosome Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., et al. (2017). A chromosome conformation capture ordered sequence of the barley genome. Nature, 544(7651), 427. Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Acknowledgements The authors acknowledge the support of the de.NBI network for bioinformatics infrastructure, the Intel SeqAn IPCC and the IMPRS for Computational Biology and Scientific Computing. This work was supported in part by US National Institutes of Health grant R35- GM130151. This work has been supported also by the Royal Society, UK under international exchange schema grant IE161405. (a) Four strains belonging to the same phylogenetic group. The sequence in light gray is conserved within this group and a marker sequence. The light gray k-mers belonging to this marker sequence are also all found in the other strains. The k-mers in dark gray are unique among all four strains and allow distinguishing each of the strains. 4 Experiments Only k-mers were counted that perfectly separated the strains in A from B1, i.e., if and only if the k-mer matched all strains of A and no strain of B1 and vice versa. When searching for marker sequences we consider two use cases: on the one hand we want to identify k-mers that match a sequence uniquely to determine the exact strain. On the other hand, we want to search for k-mers shared by many or all strains in the same phylogenetic group. To test this approach we used a data set of E. coli strains. It was shown that E. coli can be grouped into four major phylogenetic groups (A, B1, B2, and D), see Clermont et al. (2000). The authors identified two marker genes (chuA and yjaA) and an anonymous DNA fragment (TspE4.C2) whose combination of presence or absence in the genome can determine the phylogenetic group. This example shows that mappability on multiple species or strains can be used to identify possible marker sequences. Short k-mers could be Pockrandt et al. 6 used to search a data set of reads instead of searching for marker genes that span multiple reads. Since computing the (30, 2)-mappability on a few E. coli strains even takes less than a minute on a consumer laptop, this method is suitable to be run on large sets of similar E. coli strains to identify new marker sequences, even with errors accounting for uncertainty arising from sequencing and mutations such as SNPs. read mapping process itself instead of the post-processing phase. During the index-based search of a read the possible locations of the eventually completely mapped read can be examined beforehand to filter repetitive regions without repeat masking. This allows for new mapping strategies to improve the running time of state-of-the-art read mappers and reduce post-processing overhead (Pockrandt (2019)). Strain 4 Strain 3 Strain 2 Strain 1 (a) Four strains belonging to the same phylogenetic group. The sequence in light gray is conserved within this group and a marker sequence. The light gray k-mers belonging to this marker sequence are also all found in the other strains. The k-mers in dark gray are unique among all four strains and allow distinguishing each of the strains. Strain 4 Strain 3 Strain 2 Strain 1 GenMap: Ultra-fast Computation of Genome Mappability Vos, P., Hogers, R., Bleeker, M., Reijans, M., Lee, T. v. d., Hornes, M., Friters, A., Pot, J., Paleman, J., Kuiper, M., et al. (1995). Aflp: a new technique for dna fingerprinting. Nucleic acids research, 23(21), 4407–4414. 5 Discussion and Outlook We have presented GenMap, a fast and exact algorithm to compute the mappability of genomes up to e errors, which is based on the C++ sequence analysislibrarySeqAn(Reinertetal.(2017)). Itissignificantlyfaster, often by a magnitude than the algorithm from the widely used GEM suite while refraining from heuristics. Patwardhan, A., Ray, S., and Roy, A. (2014). Molecular markers in phylogenetic studies-a review. Journal of Phylogenetics & Evolutionary Biology, 2014. Pockrandt, C. (2019). Approximate String Matching - Improving Data Structures and Algorithms. Ph.D. thesis, Freie Universität Berlin. Pockrandt, C., Ehrhardt, M., and Reinert, K. (2017). Epr-dictionaries: A practical and fast data structure for constant time searches in unidirectional and bidirectional fm indices In International Conference on Research in Computational Molecular Pockrandt, C., Ehrhardt, M., and Reinert, K. (2017). Epr-dictionaries: A practical and fast data structure for constant time searches in unidirectional and bidirectional fm indices. In International Conference on Research in Computational Molecular Biology, pages 190–206. Springer. Mappability has already been used for various purposes (Derrien et al. (2012)). In this paper, we proposed a new application, the computation of mappability on a set of genomes to identify marker sequences for grouping and distinguishing genomes by short k-mers and illustrated it with a small example on closely related E. coli strains. It is also suitable for large scale data as demonstrated by the benchmarks on human and barley genomes in section 3. fm indices. In International Conference on Research in Computational Molecula Biology, pages 190–206. Springer. Ranjekar, P., Pallotta, D., and Lafontaine, J. (1976). Analysis of the genome of plants: Ii. characterization of repetitive dna in barley (hordeum vulgare) and wheat (triticum aestivum). Biochimica et Biophysica Acta (BBA)-Nucleic Acids and Protein Synthesis, 425(1), 30–40. Reinert, K., Dadi, T. H., Ehrhardt, M., Hauswedell, H., Mehringer, S., Rahn, R., Kim, J., Pockrandt, C., Winkler, J., Siragusa, E., et al. (2017). The seqan c++ template library for efficient sequence analysis: a resource for programmers. Journal of biotechnology, 261, 157–168. The ability to compute the mappability efficiently opens up new applications such as incorporating the mappability information into the 7 GenMap: Ultra-fast Computation of Genome Mappability fingerprinting. Nucleic acids research, 23(21), 4407–4414.
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https://sciendo.com/pdf/10.2478/pomr-2022-0006
English
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An Acoustic Sea Glider for Deep-Sea Noise Profiling Using an Acoustic Vector Sensor
Polish Maritime Research
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POLISH MARITIME RESEARCH 1 (113) 2022 Vol. 29; pp. 57-62 10.2478/pomr-2022-0006 Abstract An acoustic sea glider has been developed for ambient sea noise measurement and target detection through the deployment of an acoustic vector sensor (AVS). The glider was designed with three cabins connected in sequence and it can dive to depths exceeding 1200m. The AVS fixed on the glider measure acoustic pressure and particle velocities related to undersea noise, and the inner attitude sensors can effectively eliminate the estimation deviation of the direction of arrival. The inherent self-noises of the acoustic sea glider and AVS are presented respectively in respect to the Knudsen spectra of sea noise. Sea trial results indicate that the AVS could work well for undersea noise measurement when the glider is smooth sliding, and the target azimuth estimated by AVS after correction is remarkably consistent with the values measured by the GPS, and direction-finding errors are less than 10 degrees. The research in this paper shows that the acoustic sea glider is able to undertake tasks such as a wide range of underwater acoustic measurement and detection. Keywords: acoustic sea glider; acoustic vector sensor; ambient sea noise; target detection Keywords: acoustic sea glider; acoustic vector sensor; ambient sea noise; target detection AN ACOUSTIC SEA GLIDER FOR DEEP-SEA NOISE PROFILING USING AN ACOUSTIC VECTOR SENSOR Qindong Sun 1,2 Hongkun Zhou *3,4 1 Naval Submarine Academy, Qingdao , China 2 Pilot National Laboratory for Marine Science and Technology (Qingdao), China 3 China Ship Scientific Research Center, Wuxi, China 4 Taihu Laboratory of Deepsea Technology and Science, Wuxi, China * C di h h hk 02 126 (H Zh ) Qindong Sun 1,2 Hongkun Zhou *3,4 1 Naval Submarine Academy, Qingdao , China 2 Pilot National Laboratory for Marine Science and Technology (Qingdao), China 3 China Ship Scientific Research Center, Wuxi, China 4 Taihu Laboratory of Deepsea Technology and Science, Wuxi, China * Corresponding author: zhouhk702@126.com (H. Zhou) INTRODUCTION data. Low-frequency acoustic signals produced by tsunamis, undersea earthquakes, large mammals and artificial vessels are of increasing concern in the area of natural disaster monitoring and marine ecological protection [3],[4]. Moreover, the detection and identification of surface and underwater objects using acoustic sensors are another aspect of great concern in ship navigation [5],[6]. In order to achieve high-efficiency marine investigation and target detection, the integration of acoustic sensors on underwater moving platforms such as AUVs has become a new research hotspot [7],[8].h The sea glider is a long-range autonomous underwater vehicle (AUV), utilising the buoyancy of sea water as the driving force and converting vertical motion to horizontal in conjunction with wings [1]. It can float upward and dive by only adjusting the density with very low energy consumption. Consequently, the sea glider can be much quieter and more energy-efficient compared to AUVs with propellers, since it is gliding instead of propelling [2]. The acoustic sea glider, a  kind of specially designed glider with low self-noise from machinery and electricity, is appropriate for acoustic sensors with their negligible hydrodynamic noise induced by low-speed motion [9],[10]. As a result, some acoustic sensors have been tentatively employed on the sea glider in the area of natural disaster monitoring and military surveillance [11]-[13]. Inherently, the temperature and salinity of sea water along with depth are the basic parameters of the ocean, and consequently conductivity, temperature and depth (CTD) sensors are the most widely used sensors in surveys of ocean physics. However, further intensive investigation for a better understanding of the ocean needs to be performed and more special sensors are being employed to collect various POLISH MARITIME RESEARCH, No 1/2022 57 Fig. 1. Exploded view of the acoustic sea glider Fig. 1. Exploded view of the acoustic sea glider The head cabin located at the front end of the glider is mainly for installing sensors, including an acoustic module, CTD sensors and buoyancy materials. The acoustic module includes a composite AVS with an acoustic dome and the related signal processor. The acoustic dome is made of polyurethane material to ensure the penetrability of sound waves and alleviate the influence of flow noise, and the AVS is flexibly suspended inside the dome with metal springs. The dome connects the head cabin through an aluminium alloy rod, to keep away from the disturbed stream. INTRODUCTION The acoustic signal processor, situated in the head cabin, is used to collect and store the output signals derived from the AVS. The whole head cabin is exposed to the water and all sensors and parts must be waterproof.h Compared to acoustic pressure sensors or hydrophones, the acoustic glider based on acoustic vector sensors (AVS) shows great superiority in underwater acoustic measurement [14]. A single composite AVS measuring the acoustic pressure and particle velocities (acceleration, displacement or pressure gradient) synchronously can achieve a good signal-to-noise ratio of low-frequency acoustic signals instead of the conventional large-scale hydrophone array [15]. An AVS is insensitive to isotropic noise due to natural cosine directivities and it can be easily integrated on compact and lightweight underwater vehicles [16]. In terms of target detection, the direction of arrival of a target relative to the AVS can be estimated through acoustic intensity processing, and then the absolute bearing angle can be corrected using attitude information of the AVS relative to the geographic coordinate system.h The middle cabin is divided into three separate pressurised compartments. A set of batteries and a drive mechanism are installed in the first compartment, constituting an attitude adjustment module, and hence the desired pitch angle of the glider can be achieved through the movement of batteries. In the second compartment there is a navigation and controller module, and another set of batteries is installed for providing extra electric power. A buoyancy adjustment module is located in the third compartment, and actually it works as an underwater oil pump that changes the buoyancy through filling in and pumping out the oil from the oilcan. A pair of carbon-fibre wings is fixed on the two sides of the third compartment for pitch attitude adjustment.h This paper presents an acoustic sea glider equipped with an inertial-type AVS for deep-sea noise collection. The AVS design integrates one omnidirectional hydrophone, a triaxial accelerometer and the attitude sensors. The acoustic sensitivities and self-noise of the AVS were obtained through laboratory calibrations as well as the glider-radiated noise. Finally, the direction of arrival (DOA) estimation using the AVS on the acoustic sea glider was verified through a sea trial in the South China Sea. SENSOR DESIGN used to achieve orientation correction during signal post- processing. The attitude sensors, including a triaxial MEMS gyroscope, a MEMS accelerometer and a MEMS magnetometer, measure the angular velocity, gravitational acceleration and magnetic flux density respectively. The attitude sensors are located on the circuit board which is supported on the piezoelectric accelerometer. The high-performance single-chip microcomputer based on an ARM-Cortex core on the same circuit board is used to achieve functions such as control, attitude data acquisition and angle calculation.h The miniature and low-power CTD sensors (RBRlegato³) are directly installed on the head of the sea glider with the probe exposed to the seawater, as shown in Fig. 2. Conventionally, the conductivity, temperature and depth data are recorded per second respectively. The composite AVS flexibly suspended inside the acoustic dome mainly consists of a hydrophone, a triaxial piezoelectric accelerometer and attitude sensors. The hydrophone and piezoelectric accelerometer sense the acoustic pressure and particle velocity respectively. The dimensions of the designed AVS are Ø66 × 78 mm with an average density of 1.15 g/cm3. Test results indicate that the sensitivity of the hydrophone is −191.5 dB (0 dB re 1 V/μPa), and the sensitivities of the triaxial piezoelectric accelerometer are 2.85 V/g, with the equivalent pressure sensitivities of −179 dB (0 dB re 1 V/μPa at 1 kHz). The working bandwidth of the AVS can extend from 10 Hz to 3 kHz.h The attitude sensors’ accuracies were tested at the First Metrology and Test Center of National Defense Technology Industry, China. Calibration frequencies were chosen as 0.1 Hz to 2 Hz since the motions induced by sea currents, tides and surges are conventionally below 1 Hz. Test results indicate that the measured heading and roll angle errors are less than 0.5° and the pitch angle error is less than 0.4° when the attitude angles do not exceed 20°. The underwater sea current will change the orientation of an AVS that is mounted on a moving platform, and consequently it is necessary to measure the real-time azimuth and attitude information of the AVS. Conventional countermeasures are directly installed on an electronic compass and an attitude sensor on the platform or vehicle. However, these methods may be less accurate because of the flexible suspension of the AVS and installation deviations of the attitude sensors. Therefore, attitude sensors are integrated into the AVS with acoustic sensors, and then the extended Kalman filter is Fig. GLIDER DESIGN The tail cabin is immersed in the seawater just like the head cabin. An oil bag installed in this cabin is part of the buoyancy adjustment module. An iridium antenna for surface communications and a configurable propeller for providing short-term thrust are deployed outside the tail cabin. The acoustic sea glider is 3.2 m in length and 0.25 m in diameter. It is designed for the maximum diving depth of 1200 m with an endurance of 60 days at the average speed of one knot. The glider structure consists of three independent cabins as presented in Fig. 1. POLISH MARITIME RESEARCH, No 1/2022 58 Fig. 2. CTD sensors and acoustic vector sensor Fig. 2. CTD sensors and acoustic vector sensor Fig. 2. CTD sensors and acoustic vector sensor POLISH MARITIME RESEARCH, No 1/2022 TARGET DETECTION EXPERIMENTS The DOA of a target can be estimated through acoustic intensity processing. Acoustic intensity is generally a complex quantity that describes the propagating power associated with a sound wave in an acoustic medium, and it is mathematically expressed as the cross spectrum between the pressure and particle velocity in the frequency domain. Therefore the active intensity component that describes the transport of acoustic power can be used to determine the bearing of a sound source without ambiguity. During target detection experiments a scientific research ship, 42 m in length and 6 m in width, served as the target. The glider dived twice in total to depths of 579 m and 962 m respectively, and acquisition of the ship’s radiated noise was executed by the AVS on the acoustic sea glider during the first dive. The outputs of the attitude sensors are presented in Fig. 5(a), and it can be observed that the underwater glider adjusts the heading frequently between −10° and 10°, making itself move forward as scheduled. Fig. 5(b) shows the azimuths of the target ship estimated by AVS with no attitude correction and veracious azimuths measured by the GPS from the time of 15:16 to 16:17; obviously, the glider’s movement caused serious deviations. Fig. 5(c) shows the estimated azimuths after attitude correction (extended Kalman filter), which are very close to the values measured by the GPS, and the bearing accuracy achieved was better than 10°. SENSOR DESIGN 3(a) illustrates the self-noise characteristics of the AVS from 20 Hz to 4 kHz, and the Knudsen ambient sea noise levels at sea states 0 to 3 are also presented for comparison. The results show that the self-noise of the hydrophone is 36 dB/√Hz at 1 kHz, which is lower than Knudsen’s ambient noise of zero order sea level, and the self-noises of the vector channels gradually decrease and approach sea state 3 when the frequency is increased to 100 Hz. In addition, the acoustically radiated noise from the acoustic sea glider was tested from 20 Hz to 4 kHz in the anechoic tank Fig. 3. Self-noise of AVS (a) and radiated noise from the acoustic sea glider (b) d i f h i lid (b) Fig. 3. Self-noise of AVS (a) and radiated noise from the acoustic sea glider (b) POLISH MARITIME RESEARCH, No 1/2022 59 Fig. 4. CTD and ambient sea noise data collected through acoustic sea glider in the South China Sea Fig. 4. CTD and ambient sea noise data collected through acoustic sea glider in the South China Sea (pressure sensor), acoustic particle velocity sensors (triaxial accelerometer) are more sensitive to high-frequency structure- borne noise, and hence low-pass filters are essential in the signal post-processing. under different working conditions and the result is provided in Fig. 3(b). It is obvious that radiated noise from the glider under battery sliding is lower than other conditions, although it is almost 20 dB higher than the hydrophone’s self-noise from 400 Hz to 3 kHz. When the oil pump starts up, the radiated noise increases as the noise peaks around 400 Hz and 1 kHz respectively. The propeller, used for emergency manoeuvres, has the most serious influence on the noise, and the peak noise level exceeds 90 dB at 700 Hz when sailing at 3 knots. The measured noise level below 100 Hz may be less accurate due to the size limitation of the anechoic tank. CONCLUSIONS measurements in the coastal zone”, Polish Maritime Research. 2020. Vol. 27(2), 168‒175, doi: 10.2478/pomr-2020-0038. Propeller-less propulsion and stable movement make the sea glider the perfect underwater moving platform for various acoustic measurements. A dedicated acoustic sea glider was developed for underwater wide-range measurements of ambient sea noise and vessel-radiated noise in this paper, through incorporating an inertial-type acoustic vector sensor (AVS). The AVS located at the front end of the glider successfully measured underwater noise relating to sound pressure and particle velocity together with attitude angles. Test results in the anechoic tank show that the AVS has comparatively low self-noise, and the radiated noise is acceptable when the acoustic sea glider is sliding. Sea trial results demonstrated that the AVS worked well when the acoustic sea glider was diving from the surface down to the deep sea. The bearing accuracy of the target through the AVS on the sea glider is better than 10° after attitude correction. This research is of important significance for the application of AVS on acoustic sea gliders, and moreover underwater observation could be more effective in both the military and civilian fields with the employment of a sea glider cluster and various acoustic sensors. 6. Y. Ju, Z. Wei, L. Huangfu, et al., “A new low SNR underwater acoustic signal classification method based on intrinsic modal features maintaining dimensionality reduction”, Polish Maritime Research. 2020. Vol. 27(2), 187‒198, doi: 10.2478/ pomr-2020-0040. 7. M.R. Benjamin, D. Battle, D. Eickstedt, et al., “Autonomous control of an autonomous underwater vehicle towing a vector sensor array”, Proceedings of IEEE International Conference on Robotics and Automation, Rome, Italy, 2007. 4562‒4569, doi: 10.1109/robot.2007.364182. 8. A. Mantouka, P. Felisberto, P. Santos, et al., “Development and testing of a dual accelerometer vector sensor for AUV acoustic surveys”, Sensors. 2017. Vol. 17(6), 1328, doi: 10.3390/s17061328. 9. L. Liu, L. Xiao, S. Lan, et al., “Using Petrel II glider to analyze underwater noise spectrogram in the South China Sea”, Acoustic Australia. 2018. Vol. 46(2), 1–8,10. doi: 10.1007/ s40857-018-0126-y. ACKNOWLEDGEMENTS 10. C. Jiang, J. Li, W. Xu, “The use of underwater gliders as acoustic sensing platforms”, Applied Sciences. 2019. Vol. 9(22), 4839, doi: 10.3390/app9224839. This work was supported by the Programs for National Key R&D Plan (Grant No. 2019YFC0311700), Natural Science Foundation of Jiangsu Province (Grant No. BK20180171), and Wenhai Plan (Grant No. 2017WHZZB0601) of Pilot National Laboratory for Marine Science and Technology in Qingdao of China. 11. S.E. Moore, B.M. Howe, K.M. Stafford, et al., “Including whale call detection in standard ocean measurements: application of acoustic sea gliders”, Marine Technology Society Journal. 2007. Vol. 41(4), 53–57, doi: 10.4031/002533207787442033. AMBIENT SEA NOISE GATHERING Underwater noise measurement experiments were conducted based on the acoustic sea glider in the northern part of the South China Sea in May 2020. During the sea trial, the glider dived from the surface to a depth of 1000 m and the deep-water noise was recorded simultaneously. The conductivity and temperature at the depth from 700 m to 800 m are presented with a 1 Hz sampling rate as shown in Fig. 4, and hence the resulting sound velocity profile could be easily achieved. Acoustic ambient sea noises were faithfully recorded by the AVS under a 20 kHz sampling rate, benefiting from the lower background noise of the acoustic sea glider. The collected noise data related to the four sensors, i.e. the hydrophone and the triaxial piezoelectric accelerometer. Unlike the hydrophone Fig. 5. Outputs of the attitude sensors when the glider is diving (a) and DOA estimation results before attitude correction (b) and after attitude correction (c) attitude sensors when the glider is diving (a) and DOA estimation results before attitude correction (b) and after attitude correction (c) Fig. 5. Outputs of the attitude sensors when the glider is diving (a) and DOA estimation results before attitude correction (b) and af POLISH MARITIME RESEARCH, No 1/2022 POLISH MARITIME RESEARCH, No 1/2022 60 POLISH MARITIME RESEARCH, No 1/2022 REFERENCES 12. H. Matsumoto, S.E. Stalin, R. W. Embley, et al., “Hydroacoustics of a submarine eruption in the Northeast Lau Basin using an acoustic glider”, Oceans 2010 MTS/IEEE Seattle. WA, USA, 2010. 1‒6, doi: 10.1109/oceans.2010.5664494. 1. X. Wu, P. Yu, G. Li, et al., “Numerical study of the effect of wing position on the dynamic motion characteristics of an underwater glider”, Polish Maritime Research. 2021. Vol. 28(2), 4‒17, doi: 10.2478/pomr-2021-0016. 13. L. Uffelen, E.H. Roth, B.M. Howe, et al., “A seaglider integrated digital monitor for bioacoustic sensing”, IEEE Journal of Oceanic Engineering. 2017. Vol. 42(4), 800–807, doi: 10.1109/joe.2016.2637199. 2. R. Zimmerman, G.L. D’Spain and C.D. Chadwell, “Decreasing the radiated acoustic and vibration noise of a mid-size AUV”, IEEE Journal of Oceanic Engineering. 2005. Vol. 30(1), 179‒187, doi: 10.1109/joe.2004.836996. 14. P. Stinco, P. Guerrini, A. Tesei, et al., “Passive acoustic signal processing at low frequency with a 3-D acoustic vector sensor hosted on a buoyancy glider”, IEEE Journal of Oceanic Engineering. 2021. Vol. 46(1), 283‒293, doi: 10.1109/ joe.2020.2968806. 3. K. Buszman, “Analysing the impact on underwater noise of changes to the parameters of a ship’s machinery”, Polish Maritime Research. 2020. Vol. 27(3), 176‒181, doi: 10.2478/ pomr-2020-0059. 4. X. Yan, H. Song, Z. Peng, et al., “Review of research results concerning the modelling of shipping noise”, Polish Maritime Research. 2021. Vol. 28(2), 102‒115, doi: 10.2478/ pomr-2021-0027. 15. K. Kim, T.B. Gabrielson and G.C. Lauchle, “Development of an accelerometer-based underwater acoustic intensity sensor”, Journal of the Acoustical Society of America. 2004. Vol. 116(6), 3384‒3392, doi: 10.1121/1.1804632. 5. K. Buszman and M. Gloza, “Detection of floating objects based on hydroacoustic and hydrodynamic pressure 16. V.A. Gordienko, Vector-Phase Methods in Acoustics, Fizmatlit (in Russian). 2007. POLISH MARITIME RESEARCH, No 1/2022 61 CONTACT WITH THE AUTHORS CONTACT WITH THE AUTHORS Qindong Sun e-mail: sqd2010@163.com Naval Submarine Academy No. 1, Jinshui Road, Licang District 266199 Qingdao Pilot National Laboratory for Marine Science and Technology (Qingdao) No.168 Wenhai Zhong Lu, Jimo District 266237 Qingdao China Hongkun Zhou e-mail: zhouhk702@126.com China Ship Scientific Research Center No. 222 Shanshui East Road Binhu District 214082 Wuxi China Taihu Laboratory of Deepsea Technology and Science No. 222 Shanshui East Road Binhu District 214082 Wuxi China POLISH MARITIME RESEARCH, No 1/2022 62
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https://www.frontiersin.org/articles/10.3389/fped.2022.1052440/pdf
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Ureteropelvic junction obstruction in infants: Open or minimally invasive surgery? A systematic review and meta-analysis
Frontiers in pediatrics
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TYPE Systematic Review PUBLISHED 23 November 2022 DOI 10.3389/fped.2022.1052440 TYPE Systematic Review PUBLISHED 23 November 2022 DOI 10.3389/fped.2022.1052440 Ureteropelvic junction obstruction in infants: Open or minimally invasive surgery? A systematic review and meta-analysis EDITED BY Simone Sforza, University of Florence, Italy REVIEWED BY Gilvydas Verkauskas, Vilnius University, Lithuania Peng Hong, Peking University Third Hospital, China *CORRESPONDENCE Giuseppe Lauriti giuseppe.lauriti@unich.it SPECIALTY SECTION This article was submitted to Pediatric Urology, a section of the journal Frontiers in Pediatrics RECEIVED 23 September 2022 ACCEPTED 31 October 2022 PUBLISHED 23 November 2022 CITATION Cascini V, Lauriti G, Di Renzo D, Miscia M and Lisi G (2022) Ureteropelvic junction obstruction in infants: Open or minimally invasive surgery? A systematic review and meta-analysis. Front. Pediatr. 10:1052440. doi: 10.3389/fped.2022.1052440 COPYRIGHT © 2022 Cascini, Lauriti, Di Renzo, Miscia and Lisi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. EDITED BY Simone Sforza, University of Florence, Italy REVIEWED BY Gilvydas Verkauskas, Vilnius University, Lithuania Peng Hong, Peking University Third Hospital, China *CORRESPONDENCE Giuseppe Lauriti giuseppe.lauriti@unich.it SPECIALTY SECTION This article was submitted to Pediatric Urology, a section of the journal Frontiers in Pediatrics RECEIVED 23 September 2022 ACCEPTED 31 October 2022 PUBLISHED 23 November 2022 CITATION EDITED BY Simone Sforza, University of Florence, Italy REVIEWED BY Gilvydas Verkauskas, Vilnius University, Lithuania Peng Hong, Peking University Third Hospital, China Valentina Cascini 1, Giuseppe Lauriti 2,3*, Dacia Di Renzo 1, Maria Enrica Miscia 2,3 and Gabriele Lisi 2,3 1Pediatric Surgery Unit, “Spirito Santo” Hospital of Pescara, Pescara, Italy, 2Department of Medicine and Aging Science, “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy, 3Pediatric Surgery Unit, “Spirito Santo” Hospital of Pescara, Pescara, Italy Introduction: The historical gold standard treatment for ureteropelvic junction obstruction (UPJO) was the open Anderson–Hynes dismembered pyeloplasty (OP). Minimally invasive surgery (MIS) procedures, including laparoscopic pyeloplasty (LP) and robot-assisted laparoscopic pyeloplasty (RALP), have been reported to achieve better outcomes (i.e., decreased morbidity, reduced postoperative pain, superior esthetic results, and shortened length of hospital stay, LOS), with a success rate similar to OP. The main limitation of the MIS approach is the age and weight of patients, limiting these procedures to children >1 year. This study aims to evaluate the feasibility and benefits of MIS pyeloplasty compared to OP to surgically treat UPJO in children <1 year of age. Materials and methods: A systematic review was independently performed by two authors. Papers comparing both techniques (MIS pyeloplasty vs. OP) in infants were included in the meta-analysis. Data (mean ± DS or percentage) were analyzed using Rev.Man 5.4 A p < 0.05 was considered significant. CITATION Cascini V, Lauriti G, Di Renzo D, Miscia M and Lisi G (2022) Ureteropelvic junction obstruction in infants: Open or minimally invasive surgery? A systematic review and meta-analysis. Front. Pediatr. 10:1052440. doi: 10.3389/fped.2022.1052440 COPYRIGHT © 2022 Cascini, Lauriti, Di Renzo, Miscia and Lisi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Results: Nine studies (eight retrospective and one prospective) meet the inclusion criteria. A total of 3,145 pyeloplasties have been included, with 2,859 (90.9%) OP and 286 (9.1%) MIS. Age at operation was 4.9 ± 1.4 months in OP vs. 5.8 ± 2.2 months in MIS, p = ns. Weight at surgery was 6.4 ± 1.4 kg in OP vs. 6.9 ± 1.4 kg in MIS, p = ns. Operative time was 129.4 ± 24.1 min for OP vs. 144.0 ± 32.3 min for MIS, p < 0.001. LOS was 3.2 ± 1.9 days for OP vs. 2.2 ± 0.9 days for MIS, p < 0.01. Postoperative complications were present in 10.0 ± 12.9% of OP vs. 10.9 ± 11.6% in MIS, p = ns. Failure of surgery was 5.2 ± 3.5% for OP vs. 4.2 ± 3.3% for MIS, p = ns. Conclusion: The development of miniaturized instruments and technical modifications has made MIS feasible and safe in infants and small children. MIS presented a longer operative time than OP. However, MIS seemed effective for treating UPJO in infants, showing shortened LOS compared to OP. No differences have been reported with regard to the incidence of postoperative complications and failure of pyeloplasty. Given the low quality of evidence of the meta-analysis according to the GRADE methodology, we would suggest limiting MIS procedures in infants to only those high-volume centers with experienced surgeons. Frontiers in Pediatrics frontiersin.org 01 Cascini et al. 10.3389/fped.2022.1052440 KEYWORDS ureteropelvic junction obstruction, Anderson–Hynes dismembered pyeloplasty, minimally invasive surgery, infants, systematic review, meta-analysis ureteropelvic junction obstruction, Anderson–Hynes dismembered pyeloplasty, minimally invasive surgery, infants, systematic review, meta-analysis Introduction present study, we aimed to compare the outcomes of OP vs. MIS (both LAP and RALP) in infants affected by UPJO. The historical gold standard for the treatment of pediatric ureteropelvic junction obstruction (UPJO) was the open Anderson–Hynes dismembered pyeloplasty (OP), with a reported success rate of 90%–100% (1). Materials and methods Over the last decades, minimally invasive surgery (MIS) procedures, i.e., conventional laparoscopic pyeloplasty (LAP) and robot-assisted laparoscopic pyeloplasty (RALP), have been reported to be a possible replacement for OP (2). Few reports and a recent meta-analysis have confirmed that both LAP and RALP seemed safe and effective (3–7). Moreover, a multicenter study comparing both approaches in pediatrics has confirmed how both procedures were safe and as successful as OP, with an incidence of failure of <5% (2). Moreover, LAP and RALP have been reported to correlate with several advantages, such as decreased morbidity, reduced postoperative pain, superior esthetic results, and shortened length of hospital stay (LOS). The main limit to the MIS approach has been reported to depend on the age and weight of the patients, limiting these procedures to children >1 year (1, 8). Since the publication of Tan’s work in 1999 (9), where LAP was not recommended in small children, there has been a doubt about performing LAP in small children. The main concerns were related to the operative field offered by a pneumoperitoneum in infants, the limited space for port placement, the small working space, and the small ureteral diameter. However, following studies have established that LAP was safe and feasible in infants (10, 11). frontiersin.org Data sources and study selection The present study was registered on PROSPERO (registration # CRD42022358981), an international database of prospectively registered systematic reviews (National Institute for Health Research) (14). The systematic review was drafted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement (15). Using a stated search strategy (Table 1), two investigators (VC, GLa) individually screened the main databases (PubMed/Medline, Scopus, Web of Science, and Cochrane) with combined keywords. MeSH headings and terms used were “Pyeloplasty” AND “Infants” (Supplementary material S1). Studies published from 1984 to August 2022 in English language were included. The list of references was screened as well to detect possible pertinent cross references. Case reports, opinion articles, and reviews were excluded. All comparative studies reporting the outcomes of OP compared to those of MIS (i.e., LAP and/or RALP) to treat UPJO in infants or patients <15 kg were included. The full text of theoretically suitable papers was retrieved and individually assessed for eligibility by the same two authors. Any divergence over the entitlement of papers was solved through a further debate with a third author (GLi). fants (10, 11). More recently, RALP seemed to have advantages of maneuverability, improved vision, comfort in suturing, and improved ergonomics compared to LAP (4, 6). The main issues in RALP are the absence of correct-sized trocars for infants and the shortage of robots in most pediatric units because of their cost (2, 8). It has been reported how MIS pyeloplasty was extremely uncommon in infants, even if the incidence of RALP procedures has boosted over the last years (12). Following an increased knowledge of MIS pyeloplasty, there have been few publications on LAP and RALP in infants over the last few years. However, most of them have reported outcomes in a reduced number of cases. RALP has been reported to simplify the MIS approach in children,, with results comparable to OP (13). However, to the best of our knowledge, only a few studies were focused on infants. Those comparing the results of the different approaches (OP vs. MIS) were extremely scarce. In the TABLE 1 Inclusion criteria of the systematic review. Publication Language English Time period January 1984–August 2022 Subject Human studies Study type Retrospective Prospective Case–control Cohort Excluded Case report Case series (<10 patients) Editorials Letters Gray literature Keywords Pyeloplasty Infants 2 frontiersin.org TABLE 1 Inclusion criteria of the systematic review. Publication Language English Time period January 1984–August 2022 Subject Human studies Study type Retrospective Prospective Case–control Cohort Excluded Case report Case series (<10 patients) Editorials Letters Gray literature Keywords Pyeloplasty Infants frontiersin.org TABLE 1 Inclusion criteria of the systematic review. Publication Language English Time period January 1984–August 2022 Subject Human studies Study type Retrospective Prospective Case–control Cohort Excluded Case report Case series (<10 patients) Editorials Letters Gray literature Keywords Pyeloplasty Infants TABLE 1 Inclusion criteria of the systematic review. Publication Language English Time period January 1984–August 2022 Subject Human studies Study type Retrospective Prospective Case–control Cohort Excluded Case report Case series (<10 patients) Editorials Letters Gray literature Keywords Pyeloplasty Infants frontiersin.org TABLE 1 Inclusion criteria of the systematic review. Frontiers in Pediatrics frontiersin.org 02 10.3389/fped.2022.1052440 Cascini et al. median and range were reported, mean ± SD were valued (16). The studies comparing OP vs. MIS for the Anderson–Hynes pyeloplasty in infants were included in the meta-analysis. The exclusion criteria are as follows: The meta-analysis was managed with RevMan 5.4 (17). The random effects model was selected. The risk ratio (RR) was assessed for categorical variables. fants (10, 11). Differently, mean differences (MD) were preferred in the case of continuous variables. Both results were reported with 95% confidence intervals (CIs). Data were expressed as mean ± SD. I2 values were used to judge homogeneity and quantify the dispersion of effect sizes. Biases among the papers included were evaluated with the funnel plot. Quantitative and demographic data were compared using Fisher’s exact test and expressed as number, percentage, or mean ± SD using the RR and 95% CI. A p < 0.05 was considered significant. • treatment other than Anderson–Hynes pyeloplasty, retroperitoneoscopy, OTAP, recurrent UPJO, secondary UPJO, patients >1 year; and • studies without valid data about the comparison of these two techniques. Systematic review The initial review retrieved 811 studies from databases using keywords “Pyeloplasty” AND “Infants.” Thanks to the screening of all these titles and abstracts, we selected 70 papers focusing on infants or children <15 kg of weight with UPJO. Among these, only 13 publications were comparative studies between OP vs. MIS (1, 13, 22–32) (Figure 1). Six studies (1, 22, 24, 25, 27, 31) described OP vs. LAP, and one was excluded (31) due to incomplete data. Three papers treating OP vs. RALP (26, 30, 32) were included. Two studies compared OP vs. LAP + RALP (13, 28); one was excluded (28) due to incomplete information. Two papers (23, 29) treating RALP vs. LAP were excluded. TABLE 2 Demographic data of papers included in the meta-analysis. TABLE 2 Demographic data of papers included in the meta-analysis. OP MIS p-Value M (%) 2,092/2,859 (73.2) 209/286 (73.1) ns* F (%) 767/2,859 (26.8) 77/286 (26.9) Left kidney (%) 162/279 (58.1) 101/183 (55.2) ns* Right kidney (%) 117/279 (41.9) 82/183 (44.8) Age (months) 4.9 ± 1.4 5.8 ± 2.2 ns Weight (kg) 6.4 ± 1.4 6.9 ± 1.4 ns Follow-up (months) 21.5 ± 8.1 13.9 ± 4.7 ns OP, open pyeloplasty; MIS, minimally invasive surgery. *Fisher’s exact test. Data analysis Categorical variable rates were compared with Pearson’s χ2 test or two-tailed Fisher’s exact probability test. When FIGURE 1 Diagram of workflow in the systematic review and meta-analysis. Diagram of workflow in the systematic review and meta-analysis. frontiersin.org 03 Frontiers in Pediatrics Cascini et al. 10.3389/fped.2022.1052440 Quality assessment 75%–100%, respectively (20). If a score overlapped two groups, we inserted a mixed inconsistency (e.g., low/ moderate) in our GRADE table. Finally, imprecision was evaluated with optimal information size (OIS) based on 25% relative risk reduction, 0.05 a-error, and 0.20 b-error (21). Two authors (DDR and MEM) assessed the risk of bias for individual studies. This assessment was achieved with a methodological index for nonrandomized studies (MINORS) (18). Dissimilarities between the two authors (DDR and MEM) were solved through a discussion with a third author (GLi). The score for this index ranges between 0 and 24 points. The “gold standard” cutoff was 19.8 points. With regard to the quality of each outcome, we graded the quality of evidence, thanks to the Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology (19). The quality of evidence was graded as high, moderate, low, and very low in all results. Observational studies were assessed as low quality of evidence. The quality of evidence was further reduced in the case of risk of bias, inconsistency, indirectness imprecision, and publication bias. MINORS was adopted to judge the risk of bias in observational papers. Inconsistency was determined according to heterogeneity, and I2 value was used to evaluate heterogeneity. As established in Cochrane guidelines, heterogeneity was assessed as low, moderate, substantial, and considerable when I2 values were 0–40, 30–60, 50–90, and Meta-analysis Nine articles were included in the meta-analysis, eight retrospective studies (1, 22, 24–27, 30, 32) and one prospective study (13). The total number of pyeloplasties performed in infants and patients <15 kg of weight was 3,145, with 2,859 (90.9%) OP and 286 (9.1%) MIS, comprising 145 (50.7%) LAP and 141 (49.3%) RALP. The M/F ratio was 3:1, with 2,301M (73.2%) and 844F (26.8%). Of 2,859 OP patients, 2,092 were males (73.2%) and 767 were females (26.8%); of 286 in the MIS group, 209 were males (73.1%) and 77 were females (26.9%), with no FIGURE 2 Forest plot comparison of age at procedure between OP and MIS in infants. Frontiers in Pediatrics frontiersin.org 04 frontiersin.org Cascini et al. 10.3389/fped.2022.1052440 differences between OP and MIS groups [p = ns, RR: 1.001, 95% CI: (0.93–1.08), Table 2]. The side of the kidney affected by UPJO has been reported in seven papers (1, 22, 24–26, 30, 32), with 462 patients (279 OP and 183 MIS). Of 279 OP patients, 162 had left kidneys affected (58.1%) and 117 had right kidneys affected (41.9%). Of 183 in the MIS group, 101 had left kidneys affected (55.2%) and 82 had right renal units affected (45%), with no differences between the two groups [p = ns, RR: 1.052, 95% CI (0.89–1.24), Table 2]. differences between OP and MIS groups [p = ns, RR: 1.001, 95% CI: (0.93–1.08), Table 2]. The mean age at procedure has been reported in nine papers (1, 13, 22, 24–27, 30, 32), with no difference between OP infants (4.9 ± 1.4 months) and MIS patients [5.8 ± 2.2 months; p = ns, MD −0.9, 95% CI: (−2.21–0.22), Table 2 and Figure 2]. The side of the kidney affected by UPJO has been reported in seven papers (1, 22, 24–26, 30, 32), with 462 patients (279 OP and 183 MIS). Of 279 OP patients, 162 had left kidneys affected (58.1%) and 117 had right kidneys affected (41.9%). Of 183 in the MIS group, 101 had left kidneys affected (55.2%) and 82 had right renal units affected (45%), with no differences between the two groups [p = ns, RR: 1.052, 95% CI (0.89–1.24), Table 2]. The weight at surgery has been reported in six of the included papers (1, 22, 24, 26, 30, 32). Weight was not significantly different among the two groups: 6.4 ± 1.4 kg in OP vs. Meta-analysis 6.9 ± 1.4 in MIS [p = ns, MD −0.71, 95% CI (−1.47– 0.06), Table 2 and Figure 3]. affected (58.1%) and 117 had right kidneys affected (41.9%). Of 183 in the MIS group, 101 had left kidneys affected (55.2%) and 82 had right renal units affected (45%), with no differences between the two groups [p = ns, RR: 1.052, 95% CI (0.89–1.24), Table 2]. The weight at surgery has been reported in six of the included papers (1, 22, 24, 26, 30, 32). Weight was not significantly different among the two groups: 6.4 ± 1.4 kg in OP vs. 6.9 ± 1.4 in MIS [p = ns, MD −0.71, 95% CI (−1.47– 0.06), Table 2 and Figure 3]. FIGURE 4 Forest plot comparison of operative time at procedure between OP and MIS in infants. FIGURE 5 Forest plot comparison of the length of hospital stay between OP and MIS in infants. FIGURE 3 Forest plot comparison of weight at procedure between OP and MIS in infants. FIGURE 3 Forest plot comparison of weight at procedure between OP and MIS in infants. FIGURE 4 Forest plot comparison of operative time at procedure between OP and MIS in infants. FIGURE 5 Forest plot comparison of the length of hospital stay between OP and MIS in infants. 05 05 Frontiers in Pediatrics frontiersin.org frontiersin.org Cascini et al. 10.3389/fped.2022.1052440 FIGURE 6 Forest plot comparison of the incidence of postoperative complications between OP and MIS in infants. FIGURE 6 Forest plot comparison of the incidence of postoperative complications between OP and MIS in infants. FIGURE 7 Forest plot comparison of the length of follow-up between OP and MIS in infants. FIGURE 8 Forest plot comparison of the incidence of failure between OP and MIS in infants. FIGURE 6 Forest plot comparison of the incidence of postoperative complications between OP and MIS in infants. FIGURE 7 Forest plot comparison of the length of follow-up between OP and MIS in infants. FIGURE 7 Forest plot comparison of the length of follow-up between OP and MIS in infants. FIGURE 8 Forest plot comparison of the incidence of failure between OP and MIS in infants. leakage, urinary infection, and bleeding. The incidence of complications was comparable between the two groups: 10.0 ± 12.9% in OP (32/319 patients) vs. 10.9 ± 11.6% in MIS procedures [27/248 patients; p = ns, RR: 0.95, 95% CI (0.45– 2.01), Figure 6]. Meta-analysis Operative time (OT) has been reported in seven studies (1, 24, 26, 32, 25, 13, 32). OT was significantly lower in OP than that in MIS [129.4 ± 24.1 vs. 144.0 ± 32.3 min, respectively; p = 0.0004, MD: −18.19, 95% CI: (−28.35, −8.04), Figure 4]. Nine papers (1, 13, 22, 24–27, 30, 32) have shown an increased LOS in OP compared to that in MIS [3.2 ± 1.9 vs. 2.2 ± 0.9 days, respectively; p = 0.01, MD: 0.76, 95% CI: (0.16–1.36), Figure 5]. The length of postoperative follow-up has been reported in five papers (13, 25, 26, 30, 32). OP presented a longer but not significant follow-up than MIS [21.5 ± 8.1 months vs. 13.9 ± 4.7 months, respectively; p = ns; MD: 7.03, 95% CI: (−2.23– 16.29), Table 2 and Figure 7]. Eight studies have been reported on postoperative complications (1, 13, 22, 24–26, 30, 32), such as urinary Frontiers in Pediatrics frontiersin.org 06 Cascini et al. 10.3389/fped.2022.1052440 TABLE 3 Risk of bias assessment for individual studies using the methodological index for nonrandomized studies (MINORS) (18). Item Masieri (1) Andolfi (13) Neheman (22) Garcìa- Aparicio (24) Tong (25) Bansal (26) Tanaka (27) Rague (30) Dangle (11) 1. A clearly stated aim 2 2 2 2 2 2 2 2 2 2. Inclusion of consecutive patients 2 2 2 2 2 2 2 2 2 3. Prospective collection of data 0 2 0 0 0 0 0 0 0 4. Endpoints appropriate to the aim of the study 2 2 2 2 2 2 2 2 2 5. Unbiased assessment of the study endpoint 0 0 0 0 0 0 0 0 0 6. Follow-up period appropriate to the aim of the study 1 1 1 0 1 1 1 1 1 7. Loss to follow-up less than 5% 0 0 0 0 2 0 0 0 0 8. Prospective calculation of the study size 0 0 0 0 0 0 0 0 0 9. An adequate control group 2 2 2 2 2 2 2 2 2 10. Contemporary groups 2 2 2 2 2 2 2 2 2 11. Baseline equivalence of groups 1 1 2 2 2 1 2 1 1 12. Meta-analysis Adequate statistical analyses 2 2 2 2 2 2 2 2 2 Total score 14 16 15 14 17 14 15 14 14 0 = not reported; 1 = reported but inadequate; 2 = reported and adequate. Validated “gold standard” cut-off: 19.8. 0 = not reported; 1 = reported but inadequate; 2 = reported and adequate. Validated “gold standard” cut-off: 19.8. hydronephrosis causing a mass effect, recurrent urinary tract infection (UTI), worsening of hydronephrosis with thinning of renal parenchyma, or UPJO in a solitary kidney (8, 30, 33). The gold standard procedure to treat UPJO is the Anderson–Hynes dismembered pyeloplasty, commonly performed through an open miniflank approach in infants (13, 33–36). MIS procedures have progressively been adopted over the last years, although these procedures are technically challenging with the need for a long learning curve, especially for LAP. However, these procedures seemed safe and effective, as an increasing number of studies have reported similar outcomes compared to OP in pediatric patients. Several meta- analyses comparing OP and MIS showed that children in the MIS group were older than those in OP, with the same success rate and complications for both techniques (3, 5, 6). MIS procedures have shown benefits in terms of shortened LOS, decreased postoperative pain, and enhanced esthetic outcomes in older pediatric cases, gaining increased popularity as an alternative to OP (2, 37). The failure rate has been mentioned in seven papers (1, 13, 22, 24–26, 30). In most of the studies included, success has been defined as resolutions of symptoms and improved ultrasonographic or renographic parameters at the follow-up. The failure rate was not different in OP (5.2 ± 3.5%, 16/308 patients) and MIS [4.2 ± 3.3%, 10/238 patients; p = ns; RR: 1.28, 95% CI: (0.58–2.82), Figure 8]. hydronephrosis causing a mass effect, recurrent urinary tract infection (UTI), worsening of hydronephrosis with thinning of renal parenchyma, or UPJO in a solitary kidney (8, 30, 33). Only the paper by Andolfiet al. (13) further compared LAP vs. RALP. No conversion was reported in both groups. Furthermore, the incidence of complications and the success rates were similar for both procedures. We further screened these nine papers included in the meta- analysis with regard to the outcomes between left surgery and right surgery. Meta-analysis However, no data were reported on operative time, the length of hospital stay, the incidence of complications, and the failure rate regarding the side of the procedure. Discussion A cohort study including a nationwide inpatient sample data (time period 2008–2010) has reported that the distribution of OP and MIS approaches for pyeloplasty in infants was about 78% and 0.7%, respectively (28). The limits of the utilization of MIS pyeloplasties in infants or smaller children depend on the technical aspects unique to this population. First, the increase of intra-abdominal pressure and the peritoneal absorption of CO2 due to the pneumoperitoneum could bring physiological and time- depending respiratory issues, such as displacement of the diaphragm and acidosis (23, 41). A pressure of 10 mmHg or greater may cause a reduction in venous return, right ventricular output, left cardiac output, and bradycardia due to vagal reflex. When greater than 8 mmHg, the pneumoperitoneum could cause renal issues because of the stimulation of the renin–angiotensin–aldosterone system, with consequent emission of the antidiuretic hormone, leading to salt and water retention with oliguria (41). The further concern in this population is the limited space for port placement and the restricted working space, making the procedure challenging (11, 42). The incidence of complications such as bleeding, UTI, or urinary leakage was similar between OP (10.0%) and MIS (10.9%). Looking specifically at MIS procedures, Bansal et al. (26) reported a higher complication rate in RALP (33.3%) than OP (6.6%), whereas Chandrakhaseram et al. in their meta-analysis focusing on infants (7) reported more complications in RALP (16.2%) than LAP (9.3%). In a recent meta-analysis, the success of LAP and RALP in infants was found to be similar, with RALP having more OT duration and complications than LAP (21). Analyzing the KID database, Liu et al. evidenced that the use of MIS in children has gradually boosted from 0.3% in 2000 to 11.7% in 2009, with RALP representing 82% of these cases (40). Nevertheless, studies have reported outcomes on a small number of infants (13). In fact, in the present systematic review and meta-analysis, the included studies comparing OP and MIS techniques were relatively scarce: all papers were published between 2008 and 2022. Among 3,145 pyeloplasties, only 9.1% were performed with MIS, with an equal distribution between LAP (50.7%) and RALP (49.3%). Finally, different from the previous report, where the follow- up was longer for the traditional OP (25, 26, 32), this meta- analysis presented no statistically significant differences between OP and MIS in terms of length of postoperative follow-up. Discussion However, MIS was preferred in older children, with infants still receiving OP (6, 38, 39). Liu et al. indicated in the Kid’s Inpatient Database (KID) that age is the only characteristic that augmented the odds of having MIS (40). In infants, the The indications to surgically treat UPJO in infants are specific, including impaired renal function, severe Frontiers in Pediatrics frontiersin.org 07 Cascini et al. 10.3389/fped.2022.1052440 TABLE 4 GRADE evidence profile (19) for the present meta-analysis. Quality assessment No. of patients Effect Quality No. of studies Study design Risk of bias Inconsistency Indirectness Imprecision Other considera-tions Cases Controls Relative (95% CI) Absolute (95% CI) Operative time between MIS and OP in infants MIS OP 7 OS Moderatea Substantial Not serious Seriousb None 225 332 — MD 18.19 lower (from 28.35 to 8.04 lower) ⊗OOO VERY LOW Length of hospital stay between MIS and OP in infants MIS OP 9 OS Moderatea Substantial Not serious Seriousb None 286 2,898 — MD 0.76 higher (from 0.16 to 1.36 higher) ⊗⊗OO LOW Incidence of complications between MIS and OP in infants MIS OP 8 OS Moderatea Moderate Not serious Seriousb None 27/248 (10.9%) 32/319 (10.0%) RR 0.95 (0.45, 2.01) 9 more per 1,000 (from 99 less to 182 more) ⊗⊗OO LOW Incidence of failure between MIS and OP in infants MIS OP 7 OS Moderatea Low Not serious Seriousb None 10/238 (4.2%) 116/308 (5.2%) RR 1.28 (0.58, 2.82) 10 fewer per 1,000 (from 15 fewer to 65 more) ⊗⊗OO LOW MIS, minimally invasive surgery; OP, open pyeloplasty. GRADE Working Group grades of evidence. High quality: Further research is very unlikely to change our confidence in the estimate of effect. Moderate quality: Further research is likely to have an important impact on our confidence in the estimate of effect and may change the estimate. Low quality: Further research is very likely to have an important impact on our confidence in the estimate of effect and is likely to change the estimate. Very low quality: We are very uncertain about the estimate. aBias due to possible confounding. Frontiers in Pediatrics frontiersin.org 08 Cascini et al. 10.3389/fped.2022.1052440 miniflank lumbotomy is preferred for several reasons. First, it avoids muscle splitting, thus decreasing postoperative pain and allowing a fast recovery. Second, it allows for a direct approach to the posterior side of both the renal pelvis and the ureter (8). Discussion This result highlights that MIS has already been used for a sufficient time to compare the outcome of both techniques. While LAP showed a lengthier learning curve and known technical difficulties, RALP has become more accepted because of instruments with 7 degrees of motion, a 3D screen with magnification, and hand-tremor reduction. Moreover, it has been reported that the learning curve for RALP seemed to be comparable to the one for OP (4, 8). The current availability of miniaturized instruments has improved the use of MIS. In LAP, a 5-mm camera and 3-mm instruments enhance the ability to perform the anastomosis, reporting similar results to OP (10, 24). Regarding RALP, the Si system allowed an option for pediatric cases with an 8.5-mm camera and 5-mm instruments, which decreased in comparison with a 12-mm camera and 8-mm instruments of the standard option (8). Moreover, it is necessary to consider that the robot system is not available in all centers, and it presents higher costs than OP. Limitation of the study There are several limitations of the present study. As reported above, all but one studies were retrospective, which may lead to select bias. None of the papers provided sample size calculations. As expected, a blinded evaluation of objective endpoints was not possible. Moreover, the outcomes of MIS were strictly dependent on procedural volume. High- volume centers presented perioperative outcomes that were equivalent to or better than those of OP, different from low- volume centers (28). Furthermore, none of the studies have reported with regard to the loss of follow-up. As a consequence, in our meta-analysis, none of the studies reached the gold standard cutoff on MINORS of 19.8 out of 24 (Table 3). From 2003 to 2015, the rate of RALP augmented by 29% annually. However, most of these cases were children and adolescents. RALP was 40% among these patients in 2015. Differently, 85% of infants were still treated with OP (8). Many authors still prefer to perform an OP in infants. In these cases, the surgical procedure may be done by a mini- incision, avoiding muscle splitting, with reduced postoperative pain, fast patient recovery, and good aesthetic result. Therefore, the role of MIS in infants is still controversial: Tanaka et al. have reported that the benefits of LAP were evident only in older children (27). Data availability statement The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fped. 2022.1052440/full#supplementary-material. The raw data supporting the conclusions of this article will be made available by the authors without undue reservation. g 24 (Table 3). According to the GRADE methodology, the quality of evidence of the meta-analysis was low regarding the length of hospital stay, the incidence of postoperative complications, and the failure of the surgical procedure (Table 4). Both the reduced number of MIS infants and the considerable heterogeneity of the data could generate possible bias. However, when assessed in duplicate by two authors (DDR and MEM) using A Measurement Tool to Assess Systematic Frontiers in Pediatrics frontiersin.org 09 Cascini et al. 10.3389/fped.2022.1052440 Publisher’s note However, more high-quality data from well-designed randomized control trials and sufficient adjustment for volume outcome are necessary to indicate the feasibility and safety of MIS in infants compared with OP. Until then, in our opinion, only experienced surgeons should perform MIS procedures in infants, with appropriate counseling with the family to evaluate the benefits and limitations of each technique. All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher. Conflict of interest The present systematic review and meta-analysis showed that MIS seemed a safe and effective procedure for surgically treating UPJO in infants. MIS procedures present similar outcomes in terms of success rate and postoperative complications to OP, in front of a shortened length of hospital stay. In the current practice, LAP and RALP may be used as an alternative to the traditional open technique, but their several limitations must be recognized. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. 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Shea BJ, Grimshaw JM, Wells GA, Boers M, Andersson N, Hamel C, et al. Development of AMSTAR: a measurement tool to assess the methodological quality of systematic reviews. BMC Med Res Methodol. (2007) 7:10. doi: https:// doi.org/10.1186/1471-2288-7-10 References Anderson-Hynes pyeloplasty in patients less than 12 months old. Is the laparoscopic approach safe and feasible? J Endourol. (2014) 28(8):906–8. doi: 1089/end.2013.0704 39. Vemulakonda VM, Cowan CA, Lendvay TS, Joyner BD, Grady RW. Surgical management of congenital ureteropelvic junction obstruction: a pediatric health information system database study. J Urol. (2008) 180:1689–92. doi: 10.1016.j. juro.2008.03.096 25. Tong Q, Zheng L, Tang S, Zeng F, Du Z, Mei H, et al. Comparison of laparoscopic assisted versus open dismembered pyelolasty for uretropelvic junction obstruction in infants: intermediate results. Urol. (2009) 74(4):889–93. doi: 10.10167j.urology.2009.03.053 40. Liu DB, Ellimoottil C, Flum AS, Casey JT, Gong EM. 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J Pediatr Urol. (2015) 11(5):272. doi: 10.1016/j.jpurol.2015.05.013 43. Shea BJ, Grimshaw JM, Wells GA, Boers M, Andersson N, Hamel C, et al. Development of AMSTAR: a measurement tool to assess the methodological quality of systematic reviews. BMC Med Res Methodol. (2007) 7:10. doi: https:// doi.org/10.1186/1471-2288-7-10 28. Sukumar S, Djhangirian O, Sood A, Sammon JD, Varda B, Janosek-Albright K, et al. Minimally invasive vs open pyeloplasty in children: the differential effect Frontiers in Pediatrics frontiersin.org 11
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Investigating the magnetospheric accretion process in the young pre-transitional disk system DoAr 44 (V2062~Oph). A multiwavelength interferometric, spectropolarimetric, and photometric observing campaign
arXiv (Cornell University)
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ABSTRACT Context. Young stars interact with their accretion disk through their strong magnetosphere. Context. Young stars interact with their accretion disk through their strong magnetosphere. Aims. We aim to investigate the magnetospheric accretion/ejection process in the young stellar system DoAr 44 (V2062 Oph). Methods. We monitored the system over several rotational cycles, combining high-resolution spectropolarimetry at both optical and near-IR wavelengths with long-baseline near-IR inteferometry and multicolor photometry. Aims. We aim to investigate the magnetospheric accretion/ejection process in the young stellar system DoAr 44 (V2062 Oph). Methods We monitored the system over several rotational cycles combining high-resolution spectropolarimetry at both optical and Aims. We aim to investigate the magnetospheric accretion/ejection process in the young stellar system DoAr 44 (V2062 Oph). Methods. We monitored the system over several rotational cycles, combining high-resolution spectropolarimetry at both optical and near IR wavelengths with long baseline near IR inteferometry and multicolor photometry Results. We derive a rotational period of 2.96 d from the system’s light curve, which is dominated by stellar spots. We fully char- acterize the central star’s properties from the high signal-to-noise, high-resolution optical spectra we obtained during the campaign. DoAr 44 is a young 1.2 M⊙star, moderately accreting from its disk ( ˙Macc = 6.5 10−9 M⊙yr−1), and seen at a low inclination (i ≃30◦). Several optical and near-IR line profiles probing the accretion funnel flows (Hα, Hβ, HeI 1083 nm, Paβ) and the accretion shock (HeI 587.6 nm) are modulated at the stellar rotation period. The most variable line profile is HeI 1083 nm, which exhibits modulated redshifted wings that are a signature of accretion funnel flows, as well as deep blueshifted absorptions indicative of transient outflows. The Zeeman-Doppler analysis suggests the star hosts a mainly dipolar magnetic field, inclined by about 20◦onto the spin axis, with an intensity reaching about 800 G at the photosphere, and up to 2 ± 0.8 kG close to the accretion shock. The magnetic field appears strong enough to disrupt the inner disk close to the corotation radius, at a distance of about 4.6 R⋆(0.043 au), which is consistent with the 5 R⋆(0.047 au) upper limit we derived for the size of the magnetosphere in our Paper I from long baseline interferometry. Conclusions. DoAr 44 is a pre-transitional disk system, exhibiting a 25–30 au gap in its circumstellar disk, with the inner and outer disks being misaligned. J. Bouvier1, E. Alecian1, S. H. P. Alencar2, A. Sousa1, J.-F. Donati3, K. Perraut1, A. Bayo4,5, L. M. Rebull6, C. Dougados1, G. Duvert1, J.-P. Berger1, M. Benisty1,7, K. Pouilly1, C. Folsom3, C. Moutou3, and the SPIRou consortium 1 Univ. Grenoble Alpes, CNRS, IPAG, 38000 Grenoble, France e-mail: jerome.bouvier@univ-grenoble-alpes.fr 2 Departamento de Fisica – ICEx – UFMG, Av. Antonio Carlos 6627, 30270-901 Belo Horizonte, MG, Brazil 3 Univ de Toulouse CNRS IRAP 14 avenue Belin 31400 Toulouse France 2 Departamento de Fisica – ICEx – UFMG, Av. Antonio Carlos 6627, 30270-901 B 3 3 Univ. de Toulouse, CNRS, IRAP, 14 avenue Belin, 31400 Toulouse, France , , , , , 4 Instituto de Física y Astronomía, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile 5 l il i d i l i i id d d l l hil 4 Instituto de Física y Astronomía, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile 5 4 Instituto de Física y Astronomía, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 5 Instituto de Física y Astronomía, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chi 5 Núcleo Milenio de Formación Planetaria – NPF, Universidad de Valparaíso, Valparaíso, Chile 5 Núcleo Milenio de Formación Planetaria – NPF, Universidad de Valparaíso, Valparaíso, Chile 6 p p 6 Infrared Science Archive (IRSA), IPAC, 1200 E. California Blvd., California Institute of Tech 7 6 Infrared Science Archive (IRSA), IPAC, 1200 E. California Blvd., California Institute of Technology, Pasadena, Infrared Science Archive (IRSA), IPAC, 1200 E. California Blvd., California Institute of Technology, Pasadena, CA 91125, USA 7 Unidad Mixta Internacional Franco-Chilena de Astronomía (CNRS, UMI 3386), Departamento de Astronomía, Universidad de Chile, Camino El Observatorio 1515, Las Condes, Santiago, Chile 7 Unidad Mixta Internacional Franco-Chilena de Astronomía (CNRS, UMI 3386), Departamento de Astronomía, Universidad de Chile, Camino El Observatorio 1515, Las Condes, Santiago, Chile 7 Unidad Mixta Internacional Franco-Chilena de Astronomía (CNRS, UMI 3386), Departamento de Astronomía, Universidad de Chile, Camino El Observatorio 1515, Las Condes, Santiago, Chile Received 10 July 2020 / Accepted 10 September 2020 Received 10 July 2020 / Accepted 10 September 2020 ABSTRACT On a scale of 0.1 au or less, our results indicate that the system is steadily accreting from its inner disk through its tilted dipolar magnetosphere. We conclude that in spite of a highly structured disk on the large scale, perhaps the signature of ongoing planetary formation, the magnetospheric accretion process proceeds unimpeded at the star-disk interaction level. pp g p p g y Conclusions. DoAr 44 is a pre-transitional disk system, exhibiting a 25–30 au gap in its circumstellar disk, with the inner and outer disks being misaligned. On a scale of 0.1 au or less, our results indicate that the system is steadily accreting from its inner disk through its tilted dipolar magnetosphere. We conclude that in spite of a highly structured disk on the large scale, perhaps the signature of ongoing planetary formation, the magnetospheric accretion process proceeds unimpeded at the star-disk interaction level. Key words. stars: pre-main sequence – stars: variables: T Tauri, Herbig Ae/Be – stars: magnetic field – stars: formation – accretion, accretion disks Open Access article, published by EDP Sciences, under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Astronomy & Astrophysics Astronomy & Astrophysics Astronomy & Astrophysics A&A 643, A99 (2020) https://doi.org/10.1051/0004-6361/202038892 c⃝J. Bouvier et al. 2020 ⋆Full Table 1 is only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc. u-strasbg.fr/viz-bin/cat/J/A+A/643/A99 ⋆Full Table 1 is only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc. u-strasbg.fr/viz-bin/cat/J/A+A/643/A99 ⋆⋆Based on observations obtained at the Canada-France-Hawaii Telescope (CFHT), at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programme 0103.C- 0097, and at the Las Cumbres Observatory global telescope network (LCOGT). ey words. stars: pre-main sequence – stars: variables: T Tauri, Herbig Ae/Be – stars: magnetic field – stars: formatio ccretion, accretion disks Investigating the magnetospheric accretion process in the young pre-transitional disk system DoAr 44 (V2062 Oph) A multiwavelength interferometric, spectropolarimetric, and photometric observing campaign⋆,⋆⋆ J. Bouvier1, E. Alecian1, S. H. P. Alencar2, A. Sousa1, J.-F. Donati3, K. Perraut1, A. Bayo4,5, L. M. Rebull6, C. Dougados1, G. Duvert1, J.-P. Berger1, M. Benisty1,7, K. Pouilly1, C. Folsom3, C. Moutou3, and the SPIRou consortium J. Bouvier1, E. Alecian1, S. H. P. Alencar2, A. Sousa1, J.-F. Donati3, K. Perraut1, A. Bayo4,5, L. M. Rebull6, C. Dougados1, G. Duvert1, J.-P. Berger1, M. Benisty1,7, K. Pouilly1, C. Folsom3, C. Moutou3, and the SPIRou consortium 1. Introduction The rotational modulation over a timescale of weeks of emission line profiles, veiling, and Zeeman signatures allows one to draw magnetic maps of the stellar surface and to recon- struct the structure of the magnetospheric accretion region and investigate its dynamics. Previous monitoring campaigns have been quite successful in interpreting the observed properties and variability of young stellar objects in the framework of the magnetospheric accretion model (e.g., Bouvier et al. 2007b; Alencar et al. 2012, 2018; Donati et al. 2019). These provided new insights into the physics of the interaction region between the inner disk edge and the stellar surface, which impacts both early stellar evolution, and, potentially, planet formation and/or migration at the inner disk edge. addition, below we derive a photometric period of 2.96 d from a publicly available ASAS-SN light curve (see Sect. 3.2), which we ascribe to the stellar rotation period. These properties made it a suitable target for a dedicated large-scale monitoring cam- paign, with the additional interest of probing the magnetospheric accretion process in a pre-transitional disk system. This sys- tem featured a large dust-depleted cavity in its circumstellar disk, extending up to a distance of 30 au from the central star (Andrews et al. 2011). The goal of this campaign was to con- strain the structure and dynamics of the magnetospheric accre- tion region between the inner edge of the compact inner disk and the central star by measuring the magnetic field strength at the stellar surface, reconstructing the geometry of the magne- tospheric funnel flows and accretion shocks from the analysis of line profile variability and photometric variations, and, ulti- mately, attempting to resolve the interaction region over scales of a few stellar radii above the stellar surface using long-baseline interferometry. The VLTI/GRAVITY interferometric results are reported in an accompanying paper (Bouvier et al. 2020, here- after Paper I). Section 2 describes the observations and data reduction, Sect. 3 features our results, and Sect. 4 offers a con- sistent interpretation of the observed variability of the system in the framework of the magnetospheric accretion model. We present here the results of a new campaign target- ing the young star DoAr 44 (also known as V2062 Oph, Haro 1–16, ROXs 44, HBC 268) located at a distance of 146 ± 1 pc (Gaia Collaboration 2016, 2018) in the L1688 cloud of the Rho Ophiuchi molecular complex. 1. Introduction material from their circumstellar disks, a remnant of the pro- tostellar collapse and the birthplace of planetary systems. The so-called classical T Tauri stars (cTTSs) have specific proper- ties, such as a rich emission-line spectrum, large photometric variability, and a strong continuum excess flux superimposed onto a late-type photospheric spectrum (Herbig 1962). The unique properties of this class of objects eventually vanish as the disk dissipates on a timescale of a few million years, and the young stellar object transitions to a weak-line T Tauri star (wTTS, Ménard et al. 1999). Indeed, many of the spe- cific properties of cTTSs are thought to derive from the accre- tion process (Kenyon & Hartmann 1987; Bertout et al. 1988; T Tauri stars are low-mass pre-main sequence stars at an early stage of their evolution. For a few million years, they accrete ⋆Full Table 1 is only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc. u-strasbg.fr/viz-bin/cat/J/A+A/643/A99 ⋆⋆Based on observations obtained at the Canada-France-Hawaii Telescope (CFHT), at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programme 0103.C- 0097, and at the Las Cumbres Observatory global telescope network (LCOGT). A99, page 1 of 18 A99, page 1 of 18 A&A 643, A99 (2020) E E E E E S S S S S S S S G G 8640 8645 8650 8655 8660 HJD-2,450,000.0 0.9 1.0 1.1 g' (mag) June 2019 Fig. 1. Visual summary of observations obtained in June 2019, as part of the DoAr 44 coordinated campaign. The differential g′-band light curve (see Sect. 3.2) is shown as colored circles, with the color scale reflecting the Julian Date, while the epochs of CFHT/ESPaDOnS, CFHT/SPIRou, and ESO VLTI/Gravity observations are indicated by triangles labeled with “E”, “S”, and “G”, respectively. Note that the March 2019 ESPaDOnS run, which is part of the campaign reported here, is not shown in this figure. The average g-band magnitude of the system during the campaign was g = 13.35 according to the publicly available Zwicky Transient Facility light curve (Masci et al. 2019). Basri & Bertout 1989) and, more specifically, to arise from the interaction region between the inner disk and the star. 1. Introduction E E E E E S S S S S S S S G G 8640 8645 8650 8655 8660 HJD-2,450,000.0 0.9 1.0 1.1 g' (mag) June 2019 g The currently accepted paradigm that describes this interac- tion is the magnetospheric accretion scenario where the strong stellar magnetic field controls, at least partly, the accretion flow from the inner disk edge to the stellar surface (Camenzind 1990; Koenigl 1991, see reviews by Bouvier et al. 2007a; Hartmann et al. 2016). With large-scale surface magnetic fields of a few hundred to a few kG (e.g., Donati 2020; Sokal et al. 2020), the stellar magnetosphere truncates the inner gaseous disk at a distance of a few stellar radii (typically 3–8 R⋆) above the photosphere. From there, the accreted material is channeled along magnetic funnel flows, and hits the stellar surface almost at free-fall velocity to create a localized accretion shock where the kinetic energy of the flow is dissipated. In this scenario, the emission line spectrum of cTTSs is partly formed in the accre- tion funnel flows (Hartmann et al. 1994), and the accretion shock is responsible for the continuum excess flux from the X-ray range to the optical wavelengths, which is referred to as veiling (Calvet & Gullbring 1998). Fig. 1. Visual summary of observations obtained in June 2019, as part of the DoAr 44 coordinated campaign. The differential g′-band light curve (see Sect. 3.2) is shown as colored circles, with the color scale reflecting the Julian Date, while the epochs of CFHT/ESPaDOnS, CFHT/SPIRou, and ESO VLTI/Gravity observations are indicated by triangles labeled with “E”, “S”, and “G”, respectively. Note that the March 2019 ESPaDOnS run, which is part of the campaign reported here, is not shown in this figure. The average g-band magnitude of the system during the campaign was g = 13.35 according to the publicly available Zwicky Transient Facility light curve (Masci et al. 2019). g The magnetospheric process extends over a scale less than 0.1 au from the star, which corresponds to ≤1 mas angular sepa- ration on the sky at the distance of nearby star forming regions. Therefore, most constraints on the physics of magnetospheric accretion come from observational campaigns monitoring the spectral variability of selected cTTSs over successive rotation periods. 2. Observations In this section, we describe the acquisition and data-reduction processes of photometric and spectropolarimetric datasets obtained during the large-scale campaign performed on the cTTS DoAr 44, which also included long-baseline near-IR interferom- etry. A summary plot of the main part of the DoAr 44 observing campaign is provided in Fig. 1. The dedicated monitoring campaign of this source we present here combines, for the first time, high angular resolu- tion (≃1 mas) long-baseline interferometry, optical and near-IR high-resolution spectropolarimetry, and multicolor photometry. DoAr 44 was selected for this campaign based on its brightness (V = 12.6, K = 7.6), which is amenable to both long-baseline interferometry and spectropolarimetry; the presence of a Brγ line in emission in its near-IR spectrum, with EW(Brγ) ≃4 Å mea- sured on an archival ESO/XSHOOTER spectrum; and the recent report of its high surface magnetic field (Lavail et al. 2017). In 1. Introduction This moderately bright source of spectral type K3 exhibits strong Hα emis- sion with EW(Hα) ≃50 Å (Bouvier & Appenzeller 1992) and accretes at a substantial rate from its circumstellar disk, ˙Macc = 6.0–9.3 10−9 M⊙yr−1 (Espaillat et al. 2010; Manara et al. 2014). From the measurement of the Zeeman broadening of near-IR FeI lines, Lavail et al. (2017) derived a mean surface magnetic field strength amounting to 1.8 ± 0.4 kG, and possibly up to 3.6 kG. These authors further derived a projected rotational velocity of v sin i = 17.5 ± 1.0 km s−1, and estimated a mass of 1.25 M⊙for this source. A99, page 2 of 18 2.1. LCOGT photomery 2), the PSF photometry includes the target DoAr 44, the nearby W Uma eclipsing binary V2394 Oph, the T Tauri stars ROX 42B, ROX 43, ROX 47B, and DoAr 43, as well as four potential comparison and check stars: [JDH94]Oph 587, TYC 6795-600-1, TYC 6795-516-1, and an anonymous star (RA, Dec: 247.8519d, −24.3306d), referred to as C5 in the following. We verified that Oph 587 and C5, located within 10 arcmin of DoAr 44, were stable at a few 0.01 mag level in all filters. While the two TYC stars are brighter than Oph 587 and C5, and also appear to be photometrically stable at similar levels, they are located in a corner of the image, and are therefore more prone to systematics (e.g. flat-field correction). Table 2. Journal of ESPaDOnS observations of DoAr 44. Date UT HJD Φrot S/N (2019) (hh:mm:ss) (2 450 000.+) (731 nm) Mar 15 14:31:32 8558.10852 0.48 137 Mar 16 15:32:19 8559.15082 0.83 141 Mar 18 15:11:40 8561.13665 1.50 133 Mar 19 14:47:48 8562.12015 1.83 124 Mar 20 14:13:53 8563.09667 2.16 131 Mar 21 14:50:36 8564.12225 2.51 132 Mar 22 13:32:39 8565.06818 2.83 143 Jun 08 09:16:27 8642.89230 29.12 139 Jun 09 09:21:13 8643.89558 29.46 135 Jun 10 09:19:12 8644.89415 29.80 135 Jun 11 10:15:19 8645.93308 30.15 134 Jun 12 10:07:45 8646.92779 30.48 130 Notes. All observations consist of sequences of four subexposures, each lasting 950 s. Columns respectively list, for each observation, the UT date, time, heliocentric Julian date (HJD), rotational phase, and signal- to-noise ratio (S/N) at 731 nm (per 2.6 km s−1 velocity bin). Table 2. Journal of ESPaDOnS observations of DoAr 44. p y g We therefore used Oph 587 as a reference star and C5 as a check star to derive the differential light curves for DoAr 44. Stars Oph 587 and C5 are within one magnitude of difference from the target’s brightness in all filters. The rms error of the photometric measurement in each filter amounts to about 0.02 mag. DoAr 44 is found to be variable in all four filters: the rms dispersion of the u′g′r′i′ differential light curves (DoAr 44 – Oph 587) is 0.17, 0.09, 0.07, and 0.09 mag, respectively, while the corresponding values for the comparison and check stars (Oph 587 – C5) are 0.03, 0.03, 0.04, and 0.04 mag. 2.1. LCOGT photomery Photometric observations were obtained at the Las Cumbres Observatory Global Network (LCOGT, Brown et al. 2013) with the 1m Sinistro telescopes from June 4 to June 24, 2019. We used SDSS/PanSTARRS u′g′r′i′ filters with exposure times of A99, page 2 of 18 J. Bouvier et al.: DoAr 44 Table 1. LCOGT u′g′r′i′ differential photometry (first 10 of 229 mea- surements). Table 1. LCOGT u′g′r′i′ differential photometry (first 10 of 229 mea- surements). Fig. 2. Field of view of LCOGT images, with the target, as well as comparison and check stars identified. North is up, east is left. The FOV is 27 arcmin on the side. Table 1. LCOGT u′g′r′i′ differential photometry (first 10 of 229 mea surements). Julian date Target Check Filt. Airmass Moon (2 450 000.+) (mag) (mag) dist. (◦) 8638.9847732 1.03 0.39 gp 1.14 163 8638.9858978 0.09 0.28 ip 1.13 163 8638.9867561 0.5 0.43 rp 1.13 163 8638.9876614 0.95 0.02 up 1.13 163 8639.7314887 0.99 0.43 gp 1.04 152 8639.7326015 0.09 0.3 ip 1.04 152 8639.7334362 0.46 0.43 rp 1.04 152 8639.7343175 0.97 0 up 1.04 152 8639.9927617 0.94 0.4 gp 1.1 149 8639.9939326 0.06 0.3 ip 1.1 149 . . . Notes. The columns list: Julian date, differential magnitude (see text) between DoAr 44 and the comparison star, between the comparison star and the check star, filter, airmass, and Moon distance from the tar- get. We note that the results are given for different filters on each row. In any given filter, the comparison-check star values listed in the third column are constant within errors (see text). The full table is available electronically at CDS, Strasbourg. Fig. 2. Field of view of LCOGT images, with the target, as well as comparison and check stars identified. North is up, east is left. The FOV is 27 arcmin on the side. 60, 30, 10, and 5s, respectively. A total of 219 images centered on DoAr 44 were obtained over 20 days with a cadence of nearly three photometric sequences per 24 hours. Point-spread function (PSF) photometry was performed using IRAF/DAOPHOT on the pipe-line reduced images provided by LCOGT. Over the field of view (FOV) of 27 arcmin (see Fig. 2.1. LCOGT photomery The nearby bright Moon toward the middle of the photometric campaign (June 16, 2019; JD 2458650.5) strongly increased the sky background, especially in the u′-band, leading to poorer quality photometry around this date. DoAr 44’s differential photometry is provided in Table 1. Notes. All observations consist of sequences of four subexposures, each lasting 950 s. Columns respectively list, for each observation, the UT date, time, heliocentric Julian date (HJD), rotational phase, and signal- to-noise ratio (S/N) at 731 nm (per 2.6 km s−1 velocity bin). of 65 000 covering 370–1000 nm (Donati 2003). During the first run, seven circularly polarized spectra were collected, and five additional spectra were obtained during the second run. Raw frames were reduced with the standard ESPaDOnS reduction package, and a least-squares deconvolution (LSD, Donati et al. 1997) was applied to all spectra, using a line list appropriate to DoAr 44. The journal of observations is presented in Table 2. Near-IR spectropolarimetric observations of DoAr 44 were com- pleted from June 14 to 21, 2019 with the SPIRou spectropo- larimeter at the CFHT, covering from 0.95 to 2.50 microns, at a spectral resolution of 70 000 (Donati et al. 2020) at a rate of one visit per night. Raw data were processed by the SPIRou pipe- line at CFHT and the reduced data provided by the Canadian Astronomy Data Center. The journal of observations is presented in Table 3. 2.2. CFHT spectropolarimetry Optical spectropolarimetric observations of DoAr 44 were com- pleted during two runs, from March 15 to 22 and from June 8 to 12, 2019, with the ESPaDOnS spectropolarimeter at the Canada-France-Hawaii Telescope (CFHT), at a resolving power A99, page 3 of 18 A99, page 3 of 18 A&A 643, A99 (2020) Table 3. Journal of SPIRou observations of DoAr 44. (Gustafsson et al. 2008) and VALD line lists (Ryabchikova et al. 2015). Assuming log g = 4.0, we derived the following param- eters: v sin i = 17.0 ± 1.1 km s−1, Vr = −5.70 ± 0.24 km s−1, Teff= 4600 ± 120 K, and Vmic = 0.27 ± 0.27 km s−1. The veiling, that is to say, the ratio of the continuum excess flux to the stellar pho- tospheric flux, is measured as constant over time and amounts to r ≃0.18 ± 0.05 over the wavelength range 610–670 nm. Date UT HJD Φrot S/N (2019) (hh:mm:ss) (2 450 000.+) (2135 nm) Jun 14 08:43:03 8648.8680960 31.14 223 Jun 15 08:54:21 8649.8759002 31.48 227 Jun 16 09:17:09 8650.8916925 31.82 227 Jun 17 09:39:18 8651.9070323 32.16 137 Jun 18 08:28:37 8652.8579025 32.49 216 Jun 19 09:27:16 8653.8985925 32.84 237 Jun 20 08:07:01 8654.8428144 33.16 237 Jun 21 10:17:10 8655.9331438 33.52 211 Notes. All observations consist of sequences of four subexposures, each lasting 300 s. Columns respectively list, for each observation, the UT date, time, HJD, and S/N at 2135 nm per 2.3 km s−1 velocity bin. g g Using the optical photometry of Bouvier et al. (1988) and 2MASS J-band, and adopting a K2–K3 spectral type with intrinsic colors listed in Pecaut & Mamajek (2013), we derived color excesses in the (V−Ic) and (V–J) col- ors that correspond to a visual extinction AV = 2.0 ± 0.2 mag. From the J-band magnitude, bolometric corrections from Pecaut & Mamajek (2013) for K2–K3 young stars, and a dis- tance of 146 ± 1 pc (Gaia Collaboration 2016, 2018), we thus obtained L⋆= 1.6 ± 0.2 L⊙. Combined with Teff= 4600 K derived above, this yields R⋆= 2.0 ± 0.15 R⊙. From its position in the HR diagram, we derived M⋆= 1.23 ± 0.15 M⊙using the CESAM evolutionary models (Marques et al. 3.2. Photometric variability Notes. The V-band and 2MASS J-band magnitudes, and the Gaia DR2 distance are taken from the literature (see text). All other values are derived in this study. The LCOGT observations yielded 20 day-long differential light curves for DoAr 44 in the u′g′r′i′ filters. We searched for a periodicity in the photometric variations, excluding about five measurements per filter taken when the bright moon was under 15 degrees away from the target. We used both the CLEAN periodogram analysis (Roberts et al. 1987) and the string-length method (Dworetsky 1983). The former yields a period of 3.09 d in the r′ filter only, while the latter returns a most proba- ble period in all filters in the range from 2.97 d to 3.07 d. In order to confirm the period, we downloaded ASAS-SN pho- tometry (Shappee et al. 2014), which contains 288 single fil- ter measurements over a single season extending from MJD 57780 to MJD 58030 (February-September 2017). Using the same period-search algorithms, we found a clear periodicity of 2.960 ± 0.018 d in this much richer dataset, with a peak-to-peak amplitude of about 0.1 mag. The LCOGT g′r′i′ light curves folded in phase with this period are shown in Fig. 3 and suggest a low-level modulation by surface spots, of the order of a 0.08 mag peak to peak in the g′r′i′ filters. While a period is found in the u′- band light curve as well, the phased light curve exhibits a scat- ter of the same order as the photometric amplitude. We there- fore adopted the more accurate 2.960 d period derived from the ASAS-SN dataset and ascribed it to the rotational period of the star. We thus define an ephemeris such that the origin of phase corresponds to the epoch of maximum brightness at the time of our observations, so 2.3. ESO/VLTI interferometry DoAr 44 was observed on June 22 and 23, 2019 in the K-band with the GRAVITY instrument (Gravity Collaboration 2017) combining the four unit telescopes of the ESO/VLTI (ESO run 60.A-9256). At 2.2 µm, with a maximum baseline of 130 m, we thus reach an angular resolution of λ/2Bmax = 1.7 mas, corresponding to 0.25 au at 146 pc. We used the instru- ment in its high spectral-resolution mode (R ∼4000), thus partly resolving the Brγ line profile. The observations, data reduction, and interferometric results are described in full in Paper I. 2.2. CFHT spectropolarimetry 2013), and the star appears to have a modest radiative core, with Mrad/M⋆= 0.22 ± 0.20 and Rrad/R⋆= 0.35 ± 0.2, where Mrad and Rrad are the mass and radius of the radiative core, respectively. We note, however, that the lat- ter values are strongly model dependent, as, using Siess et al. (2000) models, we would derive M⋆= 1.4 M⊙, Mrad/M⋆= 0.73 and Rrad/R⋆= 0.50. Notes. All observations consist of sequences of four subexposures, each lasting 300 s. Columns respectively list, for each observation, the UT date, time, HJD, and S/N at 2135 nm per 2.3 km s−1 velocity bin. Table 4. Stellar properties of the DoAr 44 system. Table 4. Stellar properties of the DoAr 44 system. V, J 12.6, 9.1 SpT K2–K3 AV 2.0 ± 0.2 mag Teff 4600 ± 120 K L⋆/L⊙ 1.6 ± 0.2 R⋆/R⊙ 2.0 ± 0.15 M⋆/M⊙ 1.2 ± 0.15 EW(LiI) 430 mÅ v sin i 17.0 ± 1.1 km s−1 Prot 2.960 ± 0.018 d i 30 ± 5◦ ˙Macc 7 ± 3 10−9 M⊙yr−1 d 146 ± 1 pc rcor 0.043 au (4.63 R⋆) rsub 0.044 au (4.74 R⋆) Notes. The V-band and 2MASS J-band magnitudes, and the Gaia DR2 distance are taken from the literature (see text). All other values are derived in this study. Finally, we used the above estimate of the stellar radius to derive the inclination of the stellar rotational axis on the line of sight (LoS). Using v sin i = 17 km s−1 and Prot = 2.96 d (see below), and propagating the uncertainties, yields sin i = 0.50 ± 0.05, which translates to i = 30 ± 5◦, meaning the system is seen at low inclination. Table 4 summarizes the properties of the stel- lar system with their uncertainties. HJD(d) = 2, 458, 556.7 + 2.960 × E. 3.1. Stellar properties The g′r′i′ light curves (green, blue, and red, respectively) are shown folded in phase with a period of 2.960 days derived from periodogram analysis (see text). A sine curve was eye fit to the light curves and is shown for illustration with a peak- to-peak amplitude of 0.08 mag in the g′r′i′ bands. qualitatively accounted for by dipolar magnetospheric accretion models considering moderate to low inclinations, i ≃30−45◦ (Muzerolle et al. 1998, 2001). Both the Hα and Hβ profiles exhibit significant variance in the blue and red wings up to velocities of a few hundred km s−1, and comparatively less vari- ability in the line center. As is often observed in T Tauri stars (Beristain et al. 2001), the HeI line profile is composite, con- sisting of a centrally peaked broad component, extending up to velocities of ±200 km s−1, and a narrow component located close to the line center with a FWHM of about 40 km s−1. The profile’s variability seems to be predominantly associated with the narrow component. According to Beristain et al. (2001), the properties of this type of HeI profile suggest the narrow component arises in the post-shock region close to the stellar surface, while the broad component is formed in the main accretion column above the accretion shock. Fig. 4. From left to right: mean (black) and variance (red) residual pro- files for Hα, Hβ, and HeI 587.6 nm. Hα and Hβ appear on overlapping spectral orders, which are both shown here. For HeI, the variance has been multiplied by 10. The increased scatter over the blue wing of the HeI line profile is due to spectral order overlap. Fig. 4. From left to right: mean (black) and variance (red) residual pro- files for Hα, Hβ, and HeI 587.6 nm. Hα and Hβ appear on overlapping spectral orders, which are both shown here. For HeI, the variance has been multiplied by 10. The increased scatter over the blue wing of the HeI line profile is due to spectral order overlap. Figure 5 shows the superimposed Hα and Hβ line profiles recorded for DoAr 44 during the CFHT/ESPaDOnS runs of March and June 2019. Figure 6 is another representation of the same dataset, ordered by Julian date and by rotational phase. Similar plots are shown for the HeI 587.6 nm line in Fig. 7. 3.1. Stellar properties We derived estimates of the system’s properties based on the newly acquired high-resolution spectra. We followed the same procedure as we used in Pouilly et al. (2020) to which the reader is referred for details. We selected 16 spectral windows between 600 and 800 nm where the mean ESPaDOnS spectrum of DoAr 44 is fit with a synthetic spectrum generated from the ZEEMAN code (Folsom et al. 2012) based on MARCS stellar atmosphere grids (1) HJD(d) = 2, 458, 556.7 + 2.960 × E. A99, page 4 of 18 J. Bouvier et al.: DoAr 44 Fig. 3. DoAr 44 photometric variations. The g′r′i′ light curves (green, blue, and red, respectively) are shown folded in phase with a period of 2.960 days derived from periodogram analysis (see text). A sine curve was eye fit to the light curves and is shown for illustration with a peak- to-peak amplitude of 0.08 mag in the g′r′i′ bands. Fig. 5. Superimposed residual line profiles: Hα (left) and Hβ (right). The color code corresponds to different rotational cycles. Each line is covered by two spectral orders and both are shown. qualitatively accounted for by dipolar magnetospheric accretion models considering moderate to low inclinations, i ≃30−45◦ (Muzerolle et al. 1998, 2001). Both the Hα and Hβ profiles exhibit significant variance in the blue and red wings up to velocities of a few hundred km s−1, and comparatively less vari- ability in the line center. As is often observed in T Tauri stars (Beristain et al. 2001), the HeI line profile is composite, con- Fig. 5. Superimposed residual line profiles: Hα (left) and Hβ (right). The color code corresponds to different rotational cycles. Each line is covered by two spectral orders and both are shown. Fig. 5. Superimposed residual line profiles: Hα (left) and Hβ (right). The color code corresponds to different rotational cycles. Each line is covered by two spectral orders and both are shown. Fig. 5. Superimposed residual line profiles: Hα (left) and Hβ (right). The color code corresponds to different rotational cycles. Each line is covered by two spectral orders and both are shown. Fig. 5. Superimposed residual line profiles: Hα (left) and Hβ (right). The color code corresponds to different rotational cycles. Each line is covered by two spectral orders and both are shown. Fig. 3. DoAr 44 photometric variations. 3.1. Stellar properties We note that the Balmer line profiles appear more symmetric in June than in March, while the HeI line profile has remained the same, and it exhibits a broad component and a narrow component at both epochs. Remarkably, the Hα and Hβ profiles do no exhibit high-velocity redshifted absorptions below the continuum at any rotational phase, contrary to what is often seen in other accreting sources as the funnel flow intercepts the LoS (e.g., Bouvier et al. 2007b; Alencar et al. 2012, 2018). The lack of inverse P Cygni profile signatures provides further support for a low inclination of the system (Muzerolle et al. 2001), as independently derived for the stellar rotational axis and for the outer disk that both sug- gest i ≃20−35◦(see above and Paper I). Finally, we note that the uncertainty on the derived period, δP = 0.018 d, could induce a phase shift between the March and June ESPaDOnS runs up to δΦ = 0.16 rms. 3.3. Optical line profiles Deciphering the shape and variability of the emission line pro- files seen in the spectra of cTTSs offers a window to the physical processes occurring close to the star, particularly the structure and dynamics of accretion and outflows (e.g., Alencar & Basri 2000; Edwards et al. 2006; Lima et al. 2010; Esau et al. 2014). In the optical range, DoAr 44’s spectrum shows line emission primarily the HI Balmer and Paschen series, in the CaII H&K doublet and near-IR triplet, as well as in the HeI 587.6 nm, 667.8 nm, and 706.6 nm, [OI] 630.0 nm, and OI 777.3 nm lines. Residual emission line profiles were computed by subtracting the broadened photospheric spectrum of the Hyades cluster member Melotte 25–151, a K2-type star with Vr = 37.98 km s−1, v sin i = 4.83 km s−1, and Teff= 4920 K (Folsom et al. 2018), also observed with ESPaDOnS. g ( p ) Equivalent width measurements for Hα, Hβ, and HeI emis- sion lines are reported in Table 5. As the continuum is well defined around these lines, the equivalent width measurement is accurate to within a few percent. The median equivalent widths over the two epochs amount to 44, 6.8, and 0.8 Å, for Hα, Hβ, and HeI lines, respectively. The lines have slightly larger median equivalent widths in June than in March. Their variation as a function of rotational phase is shown in Fig. 8. There is a hint of rotational modulation in the equivalent width variations of the three line profiles during the June run, with minimum val- ues close to a rotational phase of 0.5, while no such modula- tion is seen in the March run. We estimate the mass accretion rate onto the star from the flux measured in the Hα and Hβ lines, using relationships between accretion and line luminosity from Alcalá et al. (2014). From the Hα line we thus derive Lacc/L⊙= 0.06–0.13, taking into account EW(Hα) variations, 3.3.1. Line profile variability The spectral series we obtained on DoAr 44 with CFHT/ ESPaDOnS allows us to investigate the spectral variability of the source on timescales ranging from days to months. Figure 4 shows the mean and variance profile for the main emission lines. The Balmer line profiles are double peaked with a slightly depressed red peak, corresponding to the Type II(R) profiles in the classification of Reipurth et al. (1996). This profile shape is A99, page 5 of 18 A&A 643, A99 (2020) 500 0 500 v (km/s) phase 29.12 30.15 2.16 29.46 0.48 30.48 1.5 2.51 29.8 2.83 0.83 1.83 500 0 500 v (km/s) phase 29.12 30.15 2.16 29.46 0.48 30.48 1.5 2.51 29.8 2.83 0.83 1.83 500 0 500 v (km/s) day 8558.11 8559.15 8561.14 8562.12 8563.1 8564.12 8565.07 8642.89 8643.9 8644.89 8645.93 8646.93 500 0 500 v (km/s) phase 29.12 30.15 2.16 29.46 0.48 30.48 1.5 2.51 29.8 2.83 0.83 1.83 500 0 500 v (km/s) day 8558.11 8559.15 8561.14 8562.12 8563.1 8564.12 8565.07 8642.89 8643.9 8644.89 8645.93 8646.93 Fig. 6. Hα (top) and Hβ (bottom) residual line profile variability as a function of date and phase. The color code corresponds to different rotational cycles. We note that both profiles appear less asymmetric in June than in March 2019, with a more depressed red wing at the earlier epoch. 250 0 250 v (km/s) phase 29.12 30.15 2.16 29.46 0.48 30.48 1.5 2.51 29.8 2.83 0.83 1.83 250 0 250 v (km/s) day 8558.11 8559.15 8561.14 8562.12 8563.1 8564.12 8565.07 8642.89 8643.9 8644.89 8645.93 8646.93 Fig. 7. Same as Fig. 6 for HeI 587.6 nm residual line profile. We note the presence of a narrow component superimposed on a broad pedestal. Similar line profiles are observed in March and June 2019. Table 5. Photospheric radial velocity, Vr, and equivalent width, W, of Hα, Hβ, and HeI emission lines from ESPaDOnS spectra. 3.3.1. Line profile variability HJD Vr (†) W(Hα) W(Hβ) W(HeI) (−2 450 000) km s−1 (Å) (Å) (Å) 8558.10852 −5.59 41.6 8.2 1.13 8559.15082 −5.78 38.2 5.8 0.62 8561.13665 −5.60 31.8 4.3 0.60 8562.12015 −5.80 48.1 7.7 0.85 8563.09667 −6.00 41.0 5.8 0.46 8564.12225 −5.63 44.1 6.8 0.76 8565.06818 −5.76 45.5 7.2 0.80 8642.89230 −6.10 60.5 12.5 1.06 8643.89558 −5.55 44.8 6.6 0.66 8644.89415 −5.66 53.3 10.0 1.04 8645.93308 −6.02 43.9 7.7 0.99 8646.92779 −5.58 39.6 6.1 0.77 500 0 500 v (km/s) day 8558.11 8559.15 8561.14 8562.12 8563.1 8564.12 8565.07 8642.89 8643.9 8644.89 8645.93 8646.93 250 0 250 v (km/s) phase 29.12 30.15 2.16 29.46 0.48 30.48 1.5 2.51 29.8 2.83 0.83 1.83 250 0 250 v (km/s) day 8558.11 8559.15 8561.14 8562.12 8563.1 8564.12 8565.07 8642.89 8643.9 8644.89 8645.93 8646.93 500 0 500 v (km/s) day 8558.11 8559.15 8561.14 8562.12 8563.1 8564.12 8565.07 8642.89 8643.9 8644.89 8645.93 8646.93 500 0 500 v (km/s) phase 29.12 30.15 2.16 29.46 0.48 30.48 1.5 2.51 29.8 2.83 0.83 1.83 v (km/s) v (km/s) Fig. 7. Same as Fig. 6 for HeI 587.6 nm residual line profile. We note the presence of a narrow component superimposed on a broad pedestal. Similar line profiles are observed in March and June 2019. Table 5. Photospheric radial velocity, Vr, and equivalent width, W, of Hα, Hβ, and HeI emission lines from ESPaDOnS spectra. HJD Vr (†) W(Hα) W(Hβ) W(HeI) (−2 450 000) km s−1 (Å) (Å) (Å) 8558.10852 −5.59 41.6 8.2 1.13 8559.15082 −5.78 38.2 5.8 0.62 8561.13665 −5.60 31.8 4.3 0.60 8562.12015 −5.80 48.1 7.7 0.85 8563.09667 −6.00 41.0 5.8 0.46 8564.12225 −5.63 44.1 6.8 0.76 8565.06818 −5.76 45.5 7.2 0.80 8642.89230 −6.10 60.5 12.5 1.06 8643.89558 −5.55 44.8 6.6 0.66 8644.89415 −5.66 53.3 10.0 1.04 8645.93308 −6.02 43.9 7.7 0.99 8646.92779 −5.58 39.6 6.1 0.77 Notes. (†)The rms uncertainty on Vr amounts to 0.05 km s−1. Fig. 6. Hα (top) and Hβ (bottom) residual line profile variability as a function of date and phase. The color code corresponds to different rotational cycles. We note that both profiles appear less asymmetric in June than in March 2019, with a more depressed red wing at the earlier epoch. Notes. (†)The rms uncertainty on Vr amounts to 0.05 km s−1. which yields ˙Macc = 4.0–8.5 10−9 M⊙yr−1 assuming a magneto- spheric truncation radius of 5 R⋆. 3.3.1. Line profile variability Similarly, from the Hβ line, we obtain Lacc/L⊙= 0.05–0.17 and ˙Macc = 3–10 10−9 M⊙yr−1. These estimates are consistent with those reported by Manara et al. (2014), who obtained ˙Macc = 6.3 10−9 M⊙yr−1 from slab models applied to XSHOOTER spectra. low number of spectra obtained during each run. Nevertheless, the examination of the shape of the line profiles plotted as a func- tion of rotational phase in Fig. A.1 tends to support rotational modulation at both epochs, with a systematically depressed line flux in the red part of the profile around phase 0.5 for Balmer lines, as expected from accretion funnel flows as they cross the LoS (e.g., Symington et al. 2005). low number of spectra obtained during each run. Nevertheless, the examination of the shape of the line profiles plotted as a func- tion of rotational phase in Fig. A.1 tends to support rotational modulation at both epochs, with a systematically depressed line flux in the red part of the profile around phase 0.5 for Balmer lines, as expected from accretion funnel flows as they cross the LoS (e.g., Symington et al. 2005). A periodogram analysis of the line profiles is detailed in Appendix A. The analysis does not reveal any significant period- icity in the intensity variations of the velocity channels across the Hα, Hβ, and HeI line profiles when the full dataset is analyzed. This presumably results from the large temporal gap between the March and June ESPaDOnS runs. As described in Appendix A, when each run is analyzed independently, we do find some evi- dence for the rotational modulation of the Hα and Hβ line pro- files at the stellar rotation period. More specifically, the intensity of the red wing (from about +50 to +150 km s−1) of the Hα and Hβ profiles appears to be modulated at the stellar rotation period during the March run. Since the veiling is nearly constant at these dates, we ascribe these variations to changes in the intrinsic line flux, as opposed to continuum variations. This result is of limited significance, due to the poor rotational phase sampling and the 3.3.2. Line profile decomposition We further analyzed the line profiles attempting to reproduce their shape as a combination of Gaussian components. Details on the line profile decomposition are given in Appendix B, and a few examples are illustrated in Fig. B.1. The Balmer line pro- files are well fit with three Gaussian components, consisting of a broad central emission peak and two absorption components, one blueshifted, and the other redshifted, relative to the line center. The HeI line profile can be reproduced using only two emission components, a broad and a narrow one. The results are A99, page 6 of 18 J. Bouvier et al.: DoAr 44 Fig. 8. Equivalent width (Å) as a function of rotational phase. Left panel: Hα (top) and Hβ (bottom); right panel: HeI. The color code cor- responds to Julian date, mostly March (bright) and June (dark) 2019. broad components, and the fact that the radial velocities of both components appear to be modulated but reach a maximum value at different rotational phases (see Fig. 9), suggest the two com- ponents probe different regions along the funnel flow. Considering the two absorption components in the Hα pro- file, one being blueshifted, the other redshifted, we find that their FWHMs are rotationally modulated and strongly anti-correlated (see Table B.1). The equivalent width and peak absorption inten- sity of the blueshifted component are the largest around phase 0, while the equivalent width of the redshifted absorption compo- nent is the largest around phase 0.5. As the former is probably related to an outflow, while the latter probes accretion, this sug- gests that both flows are physically related and occur at oppo- site rotational phases. We also notice a hint of a correlation between the radial velocity variations of these two absorption components in the Hα line profile, as reported earlier for AA Tau (Bouvier et al. 2003) and LkCa 15 (Alencar et al. 2018). Fig. 8. Equivalent width (Å) as a function of rotational phase. Left panel: Hα (top) and Hβ (bottom); right panel: HeI. The color code cor- responds to Julian date, mostly March (bright) and June (dark) 2019. Fig. 9. Radial velocity (left) and FWHM (right) variations of the narrow (top) and broad (bottom) components of the HeI line profile in the stellar rest frame as a function of rotational phase. The color code reflects the Julian date for the March (bright) and June (dark) ESPaDOnS runs. 3.3.3. Correlation matrices The observed emission lines of DoAr 44 are highly variable, with emission and absorption components superposed, as can be seen in Fig 5. The different components may come from various circumstellar regions, like the chromosphere, the accretion fun- nel, and the wind, which can vary over different timescales. To investigate how the variations across a line or between different lines are related, we calculated correlation matrices consisting of 2D plots of the linear correlation coefficients of the line profile intensity variations at different velocity bins. A good correlation between two components indicates a common origin of the com- ponents, for example. given in Table B.1, which lists the equivalent width, peak inten- sity, radial velocity, and FWHM of each component. The narrow component of the HeI line profile shows signif- icant radial velocity variations between +4.4 and +11.4 km s−1 in the stellar rest frame, while its FWHM varies over the range 38–47 km s−1. We find these variations to be modulated by stel- lar rotation with a strong phase coherence between the March and June ESPaDOnS runs (see Fig. 9). Assuming that the HeI line narrow component arises from the accretion post-shock (Beristain et al. 2001), as suggested by its slightly redshifted velocity, and covers a small area on the stellar surface, one can relate the radial velocity amplitude δVr to the hot spot latitude θ, with δVr = 2 · v sin i · cos θ (Bouvier et al. 2007b). We deduce a latitude of 78 ±2 ◦for the accretion shock at the stellar surface, assuming an uncertainty of 0.5 km s−1 on δVr. The Hα and Hβ lines are similar, and their correlation matri- ces also show the same characteristics (Fig. 10). There is little correlation between the blue and red part of the profile, which suggests different physical processes at the origin of their vari- ability. The red wing of the profile varies coherently beyond +200 km s−1 and is strongly anti-correlated with the red emis- sion peak around 100 km s−1. This red emission peak is strongly variable, as can be clearly seen in Figs. 5 and 6. As the velocity channels corresponding to the peak appear to be modulated at the stellar rotation period, we interpret its anti-correlation with the profile’s far red wing as the signature of periodic redshifted absorptions due to the funnel flow crossing the LoS. 3.3.2. Line profile decomposition As illustrated in Fig. B.1, the decomposition of the CaII 854.2 nm emission line reveals the presence of a highly red- shifted absorption component during the March run, around Vr ≃+120 km s−1. It is observed at phases 0.83 (JD 8559.15) and 2.83 (JD 8565.07), but, surprisingly enough, not at phase 1.83 (JD 8562.12). Similar high-velocity redshifted absorptions are also seen in the NaI D line profiles at the same phases. This suggests transient accretion episodes onto the stellar surface or, at least, mass accretion rate variations occur within the funnel flow. No redshifted absorption components are seen in this line profile during the June run. Fig. 9. Radial velocity (left) and FWHM (right) variations of the narrow (top) and broad (bottom) components of the HeI line profile in the stellar rest frame as a function of rotational phase. The color code reflects the Julian date for the March (bright) and June (dark) ESPaDOnS runs. 3.3.3. Correlation matrices HJD EW(HeI) EW(Brγ) EW(Paβ) (−2 450 000) (Å) (Å) (Å) 8648.86809 4.0 2.7 6.9 8649.87590 4.7 3.0 8.6 8650.89169 5.5 3.2 8.4 8651.90703 4.0 3.4 8.1 8652.85790 5.1 2.8 8.6 8653.89859 6.8 3.3 8.5 8654.84281 6.7 3.8 8.9 8655.93314 8.3 4.0 9.3 Notes. The uncertainty on EW is of the order of 0.1–0.2 Å depending on the S/N. Notes. The uncertainty on EW is of the order of 0.1–0.2 Å depending on the S/N. 2008) predict such a rotationally modulated intensity of the high velocity redshifted wing of the Paβ profile, as funnel flows peri- odically cross the LoS. A strong signal is also seen in the 2D periodogram from the line center up to +100 km s−1 at frequen- cies around 0.9 d−1, with its alias at 0.1 d−1. The former fre- quency is close to the sampling rate, and the latter is beyond the observation time span. The signal at these frequencies is there- fore probably spurious, being induced by the observing window. Nevertheless, the variability seen in this part of the Paβ profile is real, and is also seen in the Brγ line profile over the same veloc- ity channels, where the line intensity seems to first increase then decrease smoothly over the time span of the observations (see Fig. 11). Fig. 10. Top: auto-correlation matrices of Hα (left) and Hβ (right) line profile variation for ESPaDOnS March run. Bottom: auto-correlation matrices of HeI (left) and cross-correlation matrices of HeI vs. Hα (right). the HeI line profile becomes stronger, which is consistent with both the redshifted Hα absorption and the HeI BC emission orig- inating from an accretion funnel flow crossing the LoS. The 2D periodogram of the HeI line profile displays the strongest signal at a frequency corresponding to the stellar rota- tion period, extending over redshifted velocity channels from +30 to +100 km s−1 (see Fig. 13). This periodic variability of the red part of the line profile is most likely induced by the rotational modulation of accretion funnel flow as the star rotates (e.g., Fischer et al. 2008). The other parts of the HeI profile are extremely variable, especially around the line cen- ter and throughout the blueshifted wing down to velocities of −350 km s−1. The blue wing exhibits a rapidly changing blueshifted absorption component sometimes reaching below the continuum. Yet, this outflow component shows no sign of modulation. 3.3.3. Correlation matrices g y r Interestingly, the radial velocity of the wide component of the HeI line profile seems to be rotationally modulated as well, albeit with increased scatter. If this component arises from a hot wind close to the star, the modulation may result from the geometric projection of the wind velocity pattern onto the LoS. However, its slightly redshifted velocity relative to the star instead suggests it arises from the accretion funnel flow, located above the post-shock region probed by the narrow component (Beristain et al. 2001). The FWHM of the narrow and wide com- ponents appears to be rotationally modulated as well. They reach a maximum at phase 0.5 of 259 km s−1 for the broad compo- nent and 47 km s−1 for the narrow one, and both vary by about 15% along the rotational cycle. This variation could conceivably be related to the projection on the LoS of the velocity gradi- ents of the emitting regions responsible for the narrow and broad HeI components. The vastly different FWHM of the narrow and The HeI line is composed of a broad and a narrow compo- nent. The correlation matrix is shown in Fig. 10. It indicates that the BC varies coherently and independently of the NC compo- nent. The Hα vs. HeI cross correlation matrix reveals that the HeI BC component is correlated with the high velocity wings of the Balmer profile beyond 200 km s−1. The red wing of the HeI BC is, however, strongly anti-correlated with the red emission peak seen in the Hα profile around 100 km s−1. This suggests that redshifted absorption in the Hα profile occurs as the BC of A99, page 7 of 18 A99, page 7 of 18 A&A 643, A99 (2020) Table 6. Equivalent width (EW) of HeI 1083.3 nm, Brγ, and Paβ emis- sion lines from SPIRou spectra. Table 6. Equivalent width (EW) of HeI 1083.3 nm, Brγ, and Paβ emis- sion lines from SPIRou spectra. Fig. 10. Top: auto-correlation matrices of Hα (left) and Hβ (right) line profile variation for ESPaDOnS March run. Bottom: auto-correlation matrices of HeI (left) and cross-correlation matrices of HeI vs. Hα (right). 3.3.3. Correlation matrices Instead, we observe significant change in HeI line profiles taken at the same rotational phase over succes- sive cycles, for example, at φ = 31.14, 32.16, 33.16, and at φ = 31.48, 32.49 (see Fig. 12), which suggests intrinsic varia- tions of the outflow component over a timescale of days. The velocity of the peak of the blueshifted absorption component appears to be the most extreme at the beginning of the obser- vations (vblue ≃−200 km s−1), shifting toward the line center up to vblue ≃−60 km s−1 within three days, then returning to much bluer channels (vblue ≃−130 km s−1) over the same timescale. Its width changes as well, the most blueshifted absorption hav- ing the largest FWHM. 3.4. Infrared line profiles 500 0 500 v (km/s) phase 31.14 33.16 32.16 31.48 32.49 33.52 31.82 32.84 500 0 500 v (km/s) day 8648.87 8649.88 8650.89 8651.91 8652.86 8653.9 8654.84 8655.93 200 0 200 v (km/s) phase 31.14 33.16 32.16 31.48 32.49 33.52 31.82 32.84 500 0 500 v (km/s) phase 31.14 33.16 32.16 31.48 32.49 33.52 31.82 32.84 500 /s) 500 0 500 v (km/s) phase 31.14 33.16 32.16 31.48 32.49 33.52 31.82 32.84 200 0 200 v (km/s) phase 31.14 33.16 32.16 31.48 32.49 33.52 31.82 32.84 200 0 200 v (km/s) day 8648.87 8649.88 8650.89 8651.91 8652.86 8653.9 8654.84 8655.93 200 0 200 v (km/s) day 8648.87 8649.88 8650.89 8651.91 8652.86 8653.9 8654.84 8655.93 200 0 200 v (km/s) 200 0 200 v (km/s) 200 0 200 v (km/s) Fig. 12. HeI 1083.3 nm (left), Paβ (middle), and Brγ (right) residual line profile variability as a function of date and phase. The narrow, slightly blueshifted absorption component close to the center of the Paβ line profile is due to imperfect telluric line correction. The color code corresponds to different rotational cycles Fig. 12. HeI 1083.3 nm (left), Paβ (middle), and Brγ (right) residual line profile variability as a function of date and phase. The narrow, slightly blueshifted absorption component close to the center of the Paβ line profile is due to imperfect telluric line correction. The color code corresponds to different rotational cycles. 400 200 0 200 400 v (km/s) 0.2 0.4 0.6 0.8 1.0 Frequency (1/days) hei profile 2D-periodogram 0.2 0.4 0.6 0.8 Power 300 200 100 0 100 200 300 v (km/s) 0.2 0.4 0.6 0.8 1.0 Frequency (1/days) pab profile 2D-periodogram 0.2 0.4 0.6 0.8 Power Fig. 13. 2D periodogram of the HeI 1083.3 nm (left) and Paβ (right) line profiles computed from the eight SPIRou spectra obtained on con- secutive nights. The color code represents the periodogram power, and the superimposed white curve is the average line profile. We note the symmetry of the periodogram around the frequency 0.5 d−1 due to the one-day alias resulting from the night-to- night sampling. Fig. 14. Auto-correlation matrices for the HeI, Paβ, and Brγ line profiles (left), and cross-correlation matrices for the three line profiles (right). 3.4. Infrared line profiles The wide spectral range covered by SPIRou includes a num- ber of circumstellar diagnostics, such as HeI 1083.3 nm, Paβ 1282.2 nm, and Brγ 2166.1 nm. These lines are seen in emis- sion in all the spectra acquired during the SPIRou observ- ing run, and their equivalent widths are listed in Table 6. From the equivalent widths of the Paβ and Brγ line profiles measured on the mean spectrum, EW(Paβ) = 8.75 ± 0.15 Å and EW(Brγ) = 3.5 ± 0.2 Å, and using Alcalá et al. (2014) relation- ship between line and accretion luminosities, we derived a mass accretion rate ˙Macc = 6.5 ± 0.5 10−9 M⊙yr−1, which is consistent with the estimate obtained above from the luminosity of the opti- cal emission lines. Residual line profiles were computed following the same procedure as described above for optical spectra, using the weak- line T Tauri star V819 Tau (SpT K4) as a template, also observed with SPIRou. Line profiles are shown in Fig. 11. The HeI profile exhibits a strongly asymmetric shape, with significant blueshifted absorption components reaching down to velocities of −350 km −1 with a depth that varies on a timescale of days, while the red wing appears in emission and also exhibits signif- icant variability. In contrast, the Paβ and Brγ profiles are much more symmetric, with only low-level variability in intensity over the course of the observations. The profiles are plotted as a func- tion of date and rotational phase in Fig. 12. Radiative transfer models assign the presence of moderately blueshifted, narrow absorption components in the profile of the HeI 1083.3 nm line to a disk wind (e.g., Kurosawa et al. 2011), while broader absorptions extending to large blueshifted veloci- ties are usually considered as the signature of accretion powered, hot inner winds originating close to the star (e.g., Edwards et al. 2003, 2006). We are apparently witnessing here a mix of disk and “stellar” winds, with a predominance of the former except We performed a 2D periodogram analysis across the line pro- files. The 2D periodogram of the Paβ line profile is shown in Fig. 13. A strong signal appears at the star’s rotational period in the redshifted wing of the profile over a velocity range extending from +100 to +200 km s−1. Radiative transfer models of magne- tospheric accretion onto an inclined dipole (e.g., Kurosawa et al. 3.4. Infrared line profiles A99, page 8 of 18 J. Bouvier et al.: DoAr 44 J. Bouvier et al.: DoAr 44 400 200 0 200 400 v (km/s) 0.4 0.2 0.0 0.2 0.4 0.6 0.8 1.0 1.2 Residual flux 300 200 100 0 100 200 300 v (km/s) 0.2 0.0 0.2 0.4 0.6 0.8 1.0 1.2 Residual flux 300 200 100 0 100 200 300 v (km/s) 0.0 0.1 0.2 0.3 Residual flux Fig. 11. HeI 1083.3 nm (left), Paβ (middle), and Brγ (right) residual line profiles. The narrow, slightly blueshifted absorption component close the center of the Paβ line profile is due to imperfect telluric line correction. The color code corresponds to successive rotational cycles. 300 200 100 0 100 200 300 v (km/s) 0.2 0.0 0.2 0.4 0.6 0.8 1.0 1.2 Residual flux 300 200 100 0 100 200 300 v (km/s) 0.0 0.1 0.2 0.3 Residual flux 400 200 0 200 400 v (km/s) 0.4 0.2 0.0 0.2 0.4 0.6 0.8 1.0 1.2 Residual flux Fig. 11. HeI 1083.3 nm (left), Paβ (middle), and Brγ (right) residual line profiles. The narrow, slightly blueshifted absorption component close the center of the Paβ line profile is due to imperfect telluric line correction. The color code corresponds to successive rotational cycles. 500 0 500 v (km/s) phase 31.14 33.16 32.16 31.48 32.49 33.52 31.82 32.84 500 0 500 v (km/s) day 8648.87 8649.88 8650.89 8651.91 8652.86 8653.9 8654.84 8655.93 200 0 200 v (km/s) phase 31.14 33.16 32.16 31.48 32.49 33.52 31.82 32.84 200 0 200 v (km/s) day 8648.87 8649.88 8650.89 8651.91 8652.86 8653.9 8654.84 8655.93 200 0 200 v (km/s) phase 31.14 33.16 32.16 31.48 32.49 33.52 31.82 32.84 200 0 200 v (km/s) day 8648.87 8649.88 8650.89 8651.91 8652.86 8653.9 8654.84 8655.93 Fig. 12. HeI 1083.3 nm (left), Paβ (middle), and Brγ (right) residual line profile variability as a function of date and phase. The narrow, slightly blueshifted absorption component close to the center of the Paβ line profile is due to imperfect telluric line correction. The color code corresponds to different rotational cycles. 3.4. Infrared line profiles Middle: Stokes I and Stokes V LSD profiles ordered as a function of rotational phase. Right: Stokes I and Stokes V profiles of the HeI 587.6 nm line’s narrow component ordered as a function of rotational phase. The broad component of the HeI line profile has been fitted by a Gaussian and subtracted. The color code corresponds to successive rotational cycles. A&A 643, A99 (2020) A&A 643, A99 (2020) , ( ) Fig. 15. Left: Stokes I and Stokes V LSD profiles ordered as a function of Julian date. Middle: Stokes I and Stokes V LSD profiles ordered as a function of rotational phase. Right: Stokes I and Stokes V profiles of the HeI 587.6 nm line’s narrow component ordered as a function of rotational phase. The broad component of the HeI line profile has been fitted by a Gaussian and subtracted. The color code corresponds to successive rotational cycles. component of the large scale magnetic field, Bl, derived from the Stokes I and V signatures (Donati et al. 1997; Wade et al. 2000), are shown in Fig. 17. It varies between −14 and −136 Gauss (see Table 5) and appears to be modulated by stellar rotation. Remarkably, the magnetic field intensity does not exhibit sig- nificant change between the March and June runs, nor does the phase of its modulation. This suggests a fairly stable magnetic configuration between the two epochs. low-velocity and high-velocity redshifted channels, and the latter also varies independently. The cross-correlation matrix between Paβ and Brγ reveals the same three components: the blue wing, the low-velocity red channels, and the high-velocity red channels. While each of these components varies independently of the other, they are well correlated between the Paβ and Brγ line profiles. A more complex behavior is seen in the cross-correlation matrices of HeI with Paβ and Brγ. The high-velocity blue wing of the HeI line is clearly correlated with that of the hydrogen lines. More surprisingly perhaps, there is a hint of a correlation, albeit relatively weak, between the high-velocity redshifted wing of HeI and the blueshifted wing of the Paβ profile. Another fea- ture is the apparent anti-correlation between the low-velocity redshifted HeI channels and the high-velocity redshifted hydro- gen wings. This occurs over the interval of velocities where both profiles are rotationally modulated, namely around 30– 100 km s−1 for HeI and beyond 100 km s−1 for Paβ. 3.4. Infrared line profiles 300 200 100 0 100 200 300 v (km/s) 0.2 0.4 0.6 0.8 1.0 Frequency (1/days) pab profile 2D-periodogram 0.2 0.4 0.6 0.8 Power 400 200 0 200 400 v (km/s) 0.2 0.4 0.6 0.8 1.0 Frequency (1/days) hei profile 2D-periodogram 0 0 0 0 Fig. 13. 2D periodogram of the HeI 1083.3 nm (left) and Paβ (right) line profiles computed from the eight SPIRou spectra obtained on con- secutive nights. The color code represents the periodogram power, and the superimposed white curve is the average line profile. We note the symmetry of the periodogram around the frequency 0.5 d−1 due to the one-day alias resulting from the night-to- night sampling. for the first spectrum of the series, whose relative strength varies on a timescale of days. Indeed, the gallery of emission line profiles gathered from the quasi-simultaneous optical and near-IR high-resolution spec- tra obtained for DoAr 44 during this campaign, including HeI 587.6 nm, HeI 1083.3 nm, Hα, Hβ, Paβ, and Brγ, bears strong resemblance with synthetic line profiles derived from the com- bined magnetospheric accretion and disk wind, low-inclination (i = 20◦) model presented in Fig. 7 of Kurosawa et al. (2011). It is therefore likely that most of the emission seen in these profiles comes from magnetospheric funnel flows controlled by a misaligned dipole, with additional wind components best seen in the HeI near-IR line profile. The qualitative agree- ment between observations and models supports this interpre- tation. The low inclination of the system is further supported by the maximum edge velocity at which the blueshifted HeI absorption component meets the continuum, which amounts to −350 km s−1. According to the edge velocity versus the sys- Fig. 14. Auto-correlation matrices for the HeI, Paβ, and Brγ line profiles (left), and cross-correlation matrices for the three line profiles (right). tem’s inclination relationship reported for this component by Appenzeller & Bertout (2013), here the system’s inclination should lie in the range 20–35◦. The auto-correlation matrices of the three profiles are shown in Fig. 14 and share the same behavior: different parts of the line profile vary independently of each other. In the Paβ line for instance, the blue wing varies independently of both the A99, page 9 of 18 A&A 643, A99 (2020) Fig. 15. Left: Stokes I and Stokes V LSD profiles ordered as a function of Julian date. 3.4. Infrared line profiles If real, this anti-correlation is somewhat surprising as the redshifted absorp- tions in both profiles, though appearing at different velocities, are expected to occur simultaneously at the time the funnel flow crosses the LoS. This feature is also present in the autocorre- lation matrices of HeI and Paβ. In fact, the HeI vs. Paβ matrix closely mimics the structures seen in the HeI auto-correlation matrix. While these features are intriguing, the value of the cor- relation coefficient remains of the order of 0.5 or less, and would therefore have to be confirmed from a longer time series. A similar analysis has been performed in the CaII near-IR triplet. The three lines of the CaII triplet exhibit consistent mag- netic signatures in their Stokes V profiles as shown in Fig. 16. The longitudinal component of the magnetic field projected onto the LoS is still modulated at the stellar rotation period (see Fig. 17) and now reaches a maximum value of 800 G, which is about four times larger than the intensity deduced from the LSD profiles, as is often the case for young accreting stars (e.g., Donati et al. 2019). It is worth mentioning here that the inten- sity of Bl, as well as its sign, are widely different when using LSD (photospheric) profiles and the CaII IRT (chromospheric) lines. Indeed, these spectral features probe different regions at the stellar surface. The Stokes V signal in the optical HeI line was also analyzed, as it provides the most direct estimate of the magnetic field strength at the base of the funnel flow, close to the accretion shock. Unfortunately, the Stokes V profile in the narrow component of the line is weak (see Fig. 15), which trans- lates into large uncertainties in the derivation of the longitudinal field strength. Figure 17 shows the absence of modulation within error bars, with an average field strength of 2 ± 0.8 kG. The lack of significant modulation may result from the low inclination of the system, where the high latitude accretion shock remains in view during the whole rotational cycle. 3.5. Zeeman-Doppler analysis The polarimetric capabilities of CFHT/ESPaDOnS allow us to investigate the large-scale structure of the magnetic field at the surface of the star. Figure 15 shows the least-square deconvolu- tion ((LSD) Donati et al. 1997) Stokes I and Stokes V profiles over the two ESPaDOnS runs, computed using a mean Landé factor of 1.2 and a central wavelength of 500 nm. We did not use the spectrum obtained on JD 8559.15 (φ = 0.83) for the ZDI analysis as the LSD profiles show contamination by the morn- ing twilight. A clear and relatively stable magnetic signature is present in all Stokes V profiles. The variation of the longitudinal We used the Doppler imaging (DI) and Zeeman-Doppler imaging (ZDI) implementation of Folsom et al. (2018) to respec- tively map the surface brightness and magnetic field of DoAr 44. A full description of the code can be found in Folsom et al. (2018). Briefly, the code uses a time series of Stokes I and V LSD profiles to construct a surface brightness map and the large- scale vector magnetic field. The local line models are calculated using a Voigt profile, with a Gaussian width of 1.2 km s−1 and a Lorentzian width of 1.9 km s−1. The local line models for Stokes A99, page 10 of 18 J. Bouvier et al.: DoAr 44 Fig. 16. Stokes I (left panels) and V (right panels) profiles ordered as a function of Julian date for the three emission components of the CaII IR triplet: 849 nm (left), 854 nm (middle), 866 nm (right). The phase of the corresponding rotational cycles is indicated on the left of the profiles. The color code corresponds to successive rotational cycles. J. Bouvier et al.: DoAr 44 Fig. 16. Stokes I (left panels) and V (right panels) profiles ordered as a function of Julian date for the three emission components of the CaII IR triplet: 849 nm (left), 854 nm (middle), 866 nm (right). The phase of the corresponding rotational cycles is indicated on the left of the profiles. The color code corresponds to successive rotational cycles. Table 7. Longitudinal magnetic field strength (Bl) expressed in Gauss and computed from photospheric Stokes LSD profiles, from each line of the CaII IR triplet (CaII1,2,3), and from the HeI 587.6 nm line appearing on two successive spectral orders (HeI1,2). 3.5. Zeeman-Doppler analysis Longitudinal magnetic field strength Bl (G) HJD LSD σ CaII1 σ CaII2 σ CaII3 σ HeI1 σ HeI2 σ 8558.10852 −119 14 270 80 290 70 310 90 890 640 280 620 8559.15082 – – 540 60 650 70 750 80 3020 470 4070 450 8561.13665 −122 14 310 60 300 70 370 90 2340 720 1210 630 8562.12015 −14 15 460 70 690 90 390 110 1780 880 420 910 8563.09667 −85 14 310 70 490 90 410 100 920 860 2700 770 8564.12225 −136 15 170 80 300 90 330 110 1380 640 2720 620 8565.06818 −50 14 480 60 550 60 520 70 2450 390 2480 370 8642.8923 −58 15 350 70 550 80 690 90 2110 380 1830 340 8643.89558 −123 14 60 70 140 90 140 110 400 520 2190 580 8644.89415 −43 14 490 70 790 80 730 90 2150 360 1860 350 8645.93308 −62 14 510 70 440 70 630 80 2280 470 1430 420 8646.92779 −116 14 340 80 310 80 320 120 1510 570 2500 610 V are calculated from the local I line profile, using the weak-field approximation (Landi Degl’Innocenti & Landolfi2004), and the LSD mean Landé factor and central wavelength. The magnetic field is expressed as a combination of spherical harmonics as in Donati et al. (2006). The integration over the surface of the star is done using a linear limb-darkening coefficient of 0.8 (Claret & Bloemen 2011), adapted to the temperature and grav- ity of DoAr 44. The fit to the data is performed by both minimiz- ing χ2 and maximizing the entropy, using the maximum entropy fitting routine of Skilling & Bryan (1984). We have adopted the photometric ephemeris defined above, and fixed the inclination of the rotation axis at 35◦, which is consistent with the inclina- tion of the inner disk seen in interferometry on a scale of 0.14 au (see Paper I). ZDI and reconstruct the magnetic map. We fixed the maximum value of the Legendre polynomial degree l–15 in the spherical harmonics decomposition. The resulting distribution of the mag- netic vectors over the stellar surface is shown in Fig. 18. It indi- cates a dominant dipolar component, encompassing 75% of the total flux, while only 8% and 4% of the flux is contained in the quadrupolar and octupolar components, respectively. 3.5. Zeeman-Doppler analysis The neg- ative pole of the dipole is facing us at the phase 0.5, which is consistent with the maximum absolute value of the longitudinal field. It is located at the latitude of 70◦, and thus inclined by 20◦ onto the rotational axis. ZDI and reconstruct the magnetic map. We fixed the maximum value of the Legendre polynomial degree l–15 in the spherical harmonics decomposition. The resulting distribution of the mag- netic vectors over the stellar surface is shown in Fig. 18. It indi- cates a dominant dipolar component, encompassing 75% of the total flux, while only 8% and 4% of the flux is contained in the quadrupolar and octupolar components, respectively. The neg- ative pole of the dipole is facing us at the phase 0.5, which is consistent with the maximum absolute value of the longitudinal field. It is located at the latitude of 70◦, and thus inclined by 20◦ onto the rotational axis. A99, page 11 of 18 4. Discussion 18. Top: brightness map derived from the variation of the LSD Stokes I profiles. The color code is 1 for the photospheric temperature, increases for hot spots, and decreases for cold ones. Bottom: the large- scale total, radial, longitudinal, and latitudinal surface magnetic field components, as derived from the variations of the LSD Stokes V pro- files. The color code indicates the strength of the surface magnetic field in Gauss. A&A 643, A99 (2020) A99 (2020) Fig. 17. Rotational modulation of the longitudinal component of the large-scale magnetic field, derived from the LSD profiles (top), from the CaII IR triplet (middle), and from the narrow component of the HeI 587.6 nm lines profile (bottom). The color code corresponds to succes- sive rotational cycles. We emphasize the phase consistency between the March and June datasets, as well as the apparently constant amplitude of the field between the two epochs. In the top panel, the sine curve has been fit with the period and origin of phase of the photometric ephemeris. It shows that the maximum intensity of the photospheric field occurs at phase 0.5, that is, at the time of minimum brightness (see Fig. 3). In the middle panel, the three measurements at each phase are obtained for each line of the CaII IR triplet. In the lower panel, there are two measurements per spectrum, as the HeI line appears on successive spectral orders. The three plots are not on the same scale. Fig. 17. Rotational modulation of the longitudinal component of the large-scale magnetic field, derived from the LSD profiles (top), from the CaII IR triplet (middle), and from the narrow component of the HeI 587.6 nm lines profile (bottom). The color code corresponds to succes- sive rotational cycles. We emphasize the phase consistency between the March and June datasets, as well as the apparently constant amplitude of the field between the two epochs. In the top panel, the sine curve has been fit with the period and origin of phase of the photometric ephemeris. It shows that the maximum intensity of the photospheric field occurs at phase 0.5, that is, at the time of minimum brightness (see Fig. 3). In the middle panel, the three measurements at each phase are obtained for each line of the CaII IR triplet. In the lower panel, there are two measurements per spectrum, as the HeI line appears on successive spectral orders. 4. Discussion The resulting brightness and magnetic maps are shown in Fig. 18. One large cool spot is observed on the brightness map, located close to the rotational axis and facing the observer around phase 0.83. Two bright spots are present at lower lati- tudes, facing the observer around phases 0.30 and 0.70. Due to the low inclination of the system, little is known of the southern hemisphere of the star. We used this brightness map to perform The variability analysis of the DoAr 44 system is complicated by its nearly integer rotational period of 2.96 d. While we observed the system over several rotational periods, the resulting phase coverage remains limited, with essentially the same three phases being sampled over the observations, at every third of the rotational cycle. This prevents us from having a complete picture A99, page 11 of 18 A99, page 11 of 18 A&A 643, A99 (2020) Fig. 17. Rotational modulation of the longitudinal component of the large-scale magnetic field, derived from the LSD profiles (top), from the CaII IR triplet (middle), and from the narrow component of the HeI 587.6 nm lines profile (bottom). The color code corresponds to succes- sive rotational cycles. We emphasize the phase consistency between the March and June datasets, as well as the apparently constant amplitude of the field between the two epochs. In the top panel, the sine curve has been fit with the period and origin of phase of the photometric ephemeris. It shows that the maximum intensity of the photospheric field occurs at phase 0.5, that is, at the time of minimum brightness (see Fig. 3). In the middle panel, the three measurements at each phase are obtained for each line of the CaII IR triplet. In the lower panel, there are two measurements per spectrum, as the HeI line appears on successive spectral orders. The three plots are not on the same scale. of the circumstellar environment of this young stellar object, and Fig. 18. Top: brightness map derived from the variation of the LSD Stokes I profiles. The color code is 1 for the photospheric temperature increases for hot spots, and decreases for cold ones. Bottom: the large- scale total, radial, longitudinal, and latitudinal surface magnetic field components, as derived from the variations of the LSD Stokes V pro- files. The color code indicates the strength of the surface magnetic field in Gauss. A99 (2020) Fig. 4. Discussion In Paper I, we measured the size of the Brγ line emitting region, thought to reflect the extent of the magnetospheric cavity, from long baseline near-IR interferometry, and we found it to be less than 0.047 au, that is, 5 R⋆. All the results summarized above suggest that DoAr 44 was observed during a phase of stable magnetospheric accre- tion with a magnetic topology that shares some similarities with other young accreting systems that we previously studied, such as V2129 Oph (Alencar et al. 2012). Some of these systems exhibit dipper light curves at times, with deep periodic eclipses of the central object being produced by circumstellar dust: for example, AA Tau (Bouvier et al. 2003, 2007b) and LkCa 15 (Alencar et al. 2018), as well as periodic redshifted absorptions reaching below the continuum appearing in the wings of emis- sion lines formed in the funnel flow. These specific properties are not shared by DoAr 44 in spite of a qualitatively similar magne- tospheric structure. We estimate that the dust sublimation radius lies at a distance of Rsub = 4.7 R⋆= 0.044 au, as derived from Eq. (1) of Monnier & Millan-Gabet (2002) for Tsub = 1500 K and Qr = 1. Dust might thus to be present at the disk trunca- tion radius, even though the half-flux radius of the inner dusty disk we report in Paper I is of the order of 0.14 au. While a pho- tometric modulation is observed, the light curve is spot domi- nated, with no evidence for significant dips. Similarly, while the red wing of Balmer line profiles appear modulated at the stel- lar rotation period, there is no sign of high-velocity redshifted absorptions reaching below the continuum, even at phases where the magnetic pole is facing the observer. Fig. 19. Photospheric radial velocity variations are plotted as a function of rotational phase. The color code reflects the Julian date for the March (bright) and June (dark) ESPaDOnS runs. the Doppler image, the high-latitude spot faces the observer at phase 0.83, which yields symmetric LSD profiles (see Fig. 15). Indeed, the photospheric radial velocity lies midway from the extrema of the Vr curve at this phase, as expected when the spot is on the LoS (see Fig. 19). 4. Discussion The three plots are not on the same scale. Fig. 18. Top: brightness map derived from the variation of the LSD Stokes I profiles. The color code is 1 for the photospheric temperature, increases for hot spots, and decreases for cold ones. Bottom: the large- scale total, radial, longitudinal, and latitudinal surface magnetic field components, as derived from the variations of the LSD Stokes V pro- files. The color code indicates the strength of the surface magnetic field in Gauss. of the circumstellar environment of this young stellar object, and also severely limits the longitudinal resolution we have on the stellar surface for image reconstruction. With the data at hand we are nevertheless able to derive the main physical and geo- metrical properties of the system in the region where the stellar magnetic field interacts with the inner disk. baseline near-IR interferometry. That the inner system seen at low inclination is further supported by the lack of strong photo- metric modulation. While we do recover a photometric period of 2.96 d, assigned to the stellar rotational period, the photometric amplitude of ≤0.1 mag in the V-band is significantly lower than that of most accreting T Tauri stars (e.g., Grankin et al. 2007). The photospheric radial velocity is modulated over the same 2.96 d period (see Fig. 19), which confirms the presence of a long-lived, large, dark spot at the stellar surface. According to The combination of the rotational period derived above and the v sin i we measure suggests that the star is seen at a low incli- nation of 30 ± 5◦. In Paper I, we derived a similar inclination of 34 ± 2◦for the inner edge of the circumstellar disk from long A99, page 12 of 18 J. Bouvier et al.: DoAr 44 Fig. 19. Photospheric radial velocity variations are plotted as a function of rotational phase. The color code reflects the Julian date for the March (bright) and June (dark) ESPaDOnS runs. would derive a truncation radius that is about twice the coro- tation radius. However, the large error bars associated with the field strength and derived from the HeI NC component are not inconsistent with the disk being truncated close to the corotation radius. 4. Discussion These concordant results confirm that the 2.96 d period is the rotational period of the star whose surface, seen at a low inclination, is covered by a high-latitude, large, cold spot. In contrast, the photometric minimum appears to occur at phase 0.5, which suggests a more complex distri- bution of bright and dark spots at the stellar surface drives the photometric modulation. In spite of the low inclination, clear modulation signals are also detected in several accretion diagnostics. This is the case of the redshifted wings of emission lines formed in the funnel flow (e.g., Hβ, Hα, Paβ, HeI 1083.3 nm) that smoothly vary along the rotational cycle, even though they do not exhibit inverse P Cygni components, that is, absorptions reaching below the continuum, which are the hallmark of accretion funnel flow passing onto the LoS in high-inclination systems. The radial velocity and the intensity of the narrow component of the HeI 587.6 nm line pro- file are also modulated at the stellar rotational period and indi- cate a high-latitude hot spot at the stellar surface, presumably the location of the accretion shock close to the magnetic pole. Indeed, the magnetic surface map reconstructed from the ZDI analysis features a dominant dipolar field whose axis is moder- ately inclined onto the rotational axis, thus producing an accre- tion shock at high latitudes. These results suggest that the inner disk is truncated at some distance above the stellar surface and that the accretion onto the star proceeds along magnetospheric funnel flows. Indeed, dipper characteristics and conspicuous inverse P Cygni profiles are expected to occur primarily in systems seen at a moderate to high inclination (e.g., McGinnis et al. 2015; Sousa et al. 2016; Fonseca et al. 2014). This is clearly not the case in DoAr 44, and the low inclination of this sys- tem accounts for the low-amplitude, smooth light curve; the mildly varying red wings of the emission line profiles; and more generally, the global shape of the emission line profiles as suggested by radiative transfer models of magnetospheric accretion onto a misaligned dipole. This clearly highlights the importance of taking into account inclination when investi- gating the variability of young stellar systems. Systems with otherwise similar properties, notably regarding the magneto- spheric accretion process, might exhibit quite different charac- teristics depending on the viewing angle under which they are seen. 4. Discussion If we assume that the disk’s truncation radius lies close to the disk’s corotation radius, we get DoAr 44 is a pre-transitional disk system. On the large scale, from mm observations, Andrews et al. (2009, 2011) and van der Marel et al. (2016) reported the existence of a large cav- ity extending from the central star up to 25–30 au in the circum- stellar disk. They showed that cold dust emission arises from an outer, relatively narrow ring (25 to 35 au wide), inclined by 20–35◦on the LoS. On much smaller scales, the existence of a compact, inner disk close to the star is supported by the near- infrared excess flux measured in the spectral energy distribution of the system (Espaillat et al. 2010) and significant CO emis- sion arising from the inner disk edge (Salyk et al. 2009, 2011). Furthermore, a misalignment between the inner and outer disk was assumed to be responsible for shadows seen in the outer dusty ring (Casassus et al. 2018). In Paper I, we reported the direct detection of the inner disk from long baseline near-IR interferometry. The half-flux radius is 0.14 au, and the compact rtr ≃rco = (GM⋆)1/3(Prot/2π)2/3 = 0.043 au = 9.2 R⊙= 4.6 R⋆, and according to Bessolaz et al. (2008), the truncation radius occurs at rtr ≃rco = (GM⋆)1/3(Prot/2π)2/3 = 0.043 au = 9.2 R⊙= 4.6 R⋆, and according to Bessolaz et al. (2008), the truncation radius occurs at rtr/R⋆= 2 · B4/7 ⋆ ˙M−2/7 acc M−1/7 ⋆ R5/7 ⋆, where the stellar field at the equator B⋆is normalized to 140 G, the mass accretion rate ˙Macc to 10−8 M⊙yr−1, the stellar mass M⋆to 0.8 M⊙, and the stellar radius R⋆to 2 R⊙. Thus, the condition rtr ≃rco requires a dipolar magnetic field of the order of 537 G at the equator, which translates into 1.1 kG at the pole. The average value of the longitudinal com- ponent of the magnetic field we measure in the narrow compo- nent of the HeI 587.6 nm line amounts to 2 ± 0.8 kG. Assuming this is the large scale component that interacts with the disk, we A99, page 13 of 18 A99, page 13 of 18 A&A 643, A99 (2020) disk is indeed found to be inclined relative to the outer ring, as predicted by the Casassus et al. (2018) model to account for the outer shadows. Acknowledgements. We gratefully acknowledge the help from Tim Brown at LCOGT for obtaining test images and from LCOGT support service for schedul- ing and data reduction. We thank the very efficient QSO team at CFHT. This 4. Discussion This publication is based in part on data obtained under CNTAC program CLN2019B-004. This publication is based in part on observations col- lected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programme 0103.C-0097. This work has made use of data from the European Space Agency (ESA) mission Gaia (https://www. cosmos.esa.int/gaia), processed by the Gaia Data Processing and Anal- ysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/ consortium). Funding for the DPAC has been provided by national institu- tions, in particular the institutions participating in the Gaia Multilateral Agree- ment. SHPA acknowledges financial support from CNPq, CAPES, Fapemig, and Cofecub. A. B. acknowledges support from FONDECYT Grant 1190748 and from ICM (Iniciativa Científica Milenio) via the Núcleo Milenio de Formación Planetaria grant. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innova- tion programme (grant agreement No 742095; SPIDI: Star-Planets-Inner Disk- Interactions, http://www.spidi-eu.org, and Grant agreement No. 740651 NewWorlds). References Alcalá, J. M., Natta, A., Manara, C. F., et al. 2014, A&A, 561, A2 Alencar, S. H. P., & Basri, G. 2000, AJ, 119, 1881 Alencar, S. H. P., & Basri, G. 2000, AJ, 119, 1881 Alencar, S. H. P., Bouvier, J., Walter, F. M., et al. 2012, A&A, 541, A11 Alencar, S. H. P., Bouvier, J., Donati, J. F., et al. 2018, A&A, 620, A195 Andrews, S. M., Wilner, D. J., Hughes, A. M., Qi, C., & Dullemond, C. P. 2009, ApJ, 700, 1502 Andrews, S. M., Wilner, D. J., Espaillat, C., et al. 2011, ApJ, 732, 42 Andrews, S. M., Wilner, D. J., Espaillat, C., et al. 201 Appenzeller, I., & Bertout, C. 2013, A&A, 558, A83 Basri, G., & Bertout, C. 1989, ApJ, 341, 340 p y In an attempt to link the outer scales, best studied with mid- IR and radio interferometry, to the inner scales, we focused here on the characterization of the DoAr 44 system at the star- disk interaction level, meaning on a scale extending from the stellar surface up to a few 0.1 au, combining photometric and spectropolarimetric monitoring with long baseline interferome- try. The accretion diagnostics studied here and the direct inter- ferometric measurements we reported in Paper I (Bouvier et al. 2020) suggest the existence of an inner magnetospheric cavity extending from a distance of about 4.6 stellar radii (0.043 au) down to the stellar surface. A large-scale, mainly dipolar stellar magnetic field of a few hundred Gauss over the photosphere, but reaching up to 2 ± 0.8 kG close to the accretion shock, is suf- ficient to disrupt the inner-disk region at the corotation radius or beyond in this moderately accreting system. The reported line profile variability is consistent with the expected behavior of fun- nel flows rotating at the stellar period. Yet, due to the low incli- nation of the inner system, of the order of 30◦, the modulation signatures are not as pronounced as in other, more inclined sys- tems. Importantly, the combination of contemporaneous optical and near-IR high-resolution spectroscopic monitoring provides us with a unique means to investigate diagnostics that simulta- neously probe accretion funnel flows and stellar or disk winds. 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If the pre-transitional nature of disks is the signature of ongoing planet formation in the disk, does this process affect accretion on any scale? 4. Discussion The pre-transitional status of DoAr 44’s disk was a strong motivation to include this specific target in our long- term monitoring program of T Tauri stars. The goal here was to investigate whether the highly structured disk, including a large cavity and inner-outer disk misalignment, both possibly betray- ing ongoing planetary formation, may impact the accretion pro- cess on the central star. All the results obtained here suggest that, at the star-disk interaction scale of less than 0.1 au, this pre- transitional disk system is not qualitatively different from other young stellar objects surrounded by smoother protoplanetary disks. study is based in part on observations obtained at the Canada-France-Hawaii Telescope (CFHT) which is operated by the National Research Council of Canada, the Institut National des Sciences de l’Univers of the Centre National de la Recherche Scientifique of France, and the University of Hawaii. The observations at the Canada-France-Hawaii Telescope were performed with care and respect from the summit of Maunakea, which is a significant cultural and historic site. This publication is based in part on data obtained under CNTAC program CLN2019B-004. This publication is based in part on observations col- lected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programme 0103.C-0097. This work has made use of data from the European Space Agency (ESA) mission Gaia (https://www. cosmos.esa.int/gaia), processed by the Gaia Data Processing and Anal- ysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/ consortium). Funding for the DPAC has been provided by national institu- tions, in particular the institutions participating in the Gaia Multilateral Agree- ment. SHPA acknowledges financial support from CNPq, CAPES, Fapemig, and Cofecub. A. B. acknowledges support from FONDECYT Grant 1190748 and from ICM (Iniciativa Científica Milenio) via the Núcleo Milenio de Formación Planetaria grant. 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Appendix A: Line profile variability 250 0 250 v (km/s) phase 29.12 30.15 29.46 30.48 29.8 250 0 250 v (km/s) phase 29.12 30.15 29.46 30.48 29.8 250 0 250 v (km/s) day 8642.89 8643.9 8644.89 8645.93 8646.93 25 phase 29.12 30.15 29.46 30.48 29.8 250 0 250 v (km/s) day 8642.89 8643.9 8644.89 8645.93 8646.93 250 0 250 v (km/s) day 8558.11 8559.15 8561.14 8562.12 8563.1 8564.12 8565.07 250 0 250 v (km/s) day 8642.89 8643.9 8644.89 8645.93 8646.93 250 0 250 v (km/s) phase 2.16 0.48 1.5 2.51 2.83 0.83 1.83 Fig. A.3. 2D periodogram of Hα, Hβ, and HeI line profiles from the five spectra obtained during the ESPaDOnS June run. The color code repre- sents the periodogram power, and the superimposed white curve is the average line profile. We note the symmetry of the periodogram around the frequency 0.5 d−1 due to the 1 d alias resulting from the night-to- night sampling. Fig. A.1. Hα, Hβ, and HeI line profiles from the seven spectra obtained during the ESPaDOnS March run (left panels) and the five spectra obtained during the June run (right panels). In each panel, the profiles are plotted in order of increasing date (left) and phase (right). Each color corresponds to a specific rotational cycle. Since the shape of the emisson line profiles has varied between the ESPaDOnS March and June 2019, runs, we present in Fig. A.1 their variability over timescales of days, independently for each run. The periodogram analysis of line profiles over the two ESPaDOnS runs is inconclusive. We therefore proceed to ana- lyzing the March and June 2019 runs independently. Figures A.2 and A.3 show the periodogram analysis of the Hα, Hβ, and HeI line profiles for the two epochs, respectively. During the March run, seven spectra were obtained over eight nights, while during the June run, five spectra were obtained over five nights. More- over, since the stellar period of 2.96 d is close to an integer, the same rotational phase repeats every third night. The short duration of each run combined with the poor phase sampling makes the periodogram analysis fragile. Nevertheless, we find marginal evidence for the rotational frequency of 0.34 d−1 in the red wing of the Hα and Hβ line profiles around +100 km s−1 during the March run, and in the narrow central component of the HeI line during the June run. Appendix A: Line profile variability 500 0 500 v (km/s) phase 2.16 0.48 1.5 2.51 2.83 0.83 1.83 500 0 500 v (km/s) day 8558.11 8559.15 8561.14 8562.12 8563.1 8564.12 8565.07 500 0 500 v (km/s) phase 29.12 30.15 29.46 30.48 29.8 500 0 500 v (km/s) day 8642.89 8643.9 8644.89 8645.93 8646.93 500 0 500 v (km/s) phase 2.16 0.48 1.5 2.51 2.83 0.83 1.83 500 0 500 v (km/s) day 8558.11 8559.15 8561.14 8562.12 8563.1 8564.12 8565.07 500 0 500 v (km/s) phase 29.12 30.15 29.46 30.48 29.8 500 0 500 v (km/s) day 8642.89 8643.9 8644.89 8645.93 8646.93 250 0 250 v (km/s) phase 2.16 0.48 1.5 2.51 2.83 0.83 1.83 250 0 250 v (km/s) day 8558.11 8559.15 8561.14 8562.12 8563.1 8564.12 8565.07 250 0 250 v (km/s) phase 29.12 30.15 29.46 30.48 29.8 250 0 250 v (km/s) day 8642.89 8643.9 8644.89 8645.93 8646.93 Fig. A.1. Hα, Hβ, and HeI line profiles from the seven spectra obtained during the ESPaDOnS March run (left panels) and the five spectra obtained during the June run (right panels). In each panel, the profiles are plotted in order of increasing date (left) and phase (right). Each color corresponds to a specific rotational cycle. 500 0 500 v (km/s) phase 2.16 0.48 1.5 2.51 2.83 0.83 1.83 500 0 500 v (km/s) day 8642.89 8643.9 8644.89 8645.93 8646.93 500 0 500 v (km/s) day 8642.89 8643.9 8644.89 8645.93 8646.93 500 0 500 v (km/s) phase 29.12 30.15 29.46 30.48 29.8 500 0 500 v (km/s) day 8558.11 8559.15 8561.14 8562.12 8563.1 8564.12 8565.07 500 0 500 v (km/s) phase 2.16 0.48 1.5 2.51 2.83 0.83 1.83 Fig. A.2. 2D periodogram of Hα, Hβ, and HeI line profiles from the seven spectra obtained during the ESPaDOnS March run. The color code represents the periodogram power, and the superimposed white curve is the average line profile. We note the symmetry of the peri- odogram around the frequency 0.5 d−1 due to the 1 d alias resulting from the night-to-night sampling. A11 van der Marel, N., van Dishoeck, E. F., Bruderer, S., et al. 2016, A&A, 585, A58 Ménard, F., & Bertout, C. 1999, in NATO Advanced Science Institutes (ASI) Series C, eds. C. J. Lada, & N. D. Kylafis, NATO ASI Ser. C, 540, 341 Wade, G. A., Donati, J. F., Landstreet, J. D., & Shorlin, S. L. S. 2000, MNRAS, 313, 851 , , y , Monnier, J. D., & Millan-Gabet, R. 2002, ApJ, 579, 694 A99, page 15 of 18 A&A 643, A99 (2020) Fig. A.2. 2D periodogram of Hα, Hβ, and HeI line profiles from the seven spectra obtained during the ESPaDOnS March run. The color code represents the periodogram power, and the superimposed white curve is the average line profile. We note the symmetry of the peri- odogram around the frequency 0.5 d−1 due to the 1 d alias resulting from the night-to-night sampling. Appendix A: Line profile variability Appendix A: Line profile variability Appendix B: Line profile decomposition absorption components are superimposed. The HeI line is well fit by the combination of two Gaussian components in emis- sion: a broad one and a narrow one, respectively. This is also the case for the CaII line profile except for two occurrences, on JD 8559.15 and JD 8565.07, where an additional redshifted absorption component is required to reproduce the observed line profile. Here, we illustrate examples of line profile decomposition by multiple Gaussian fits for the Hα, Hβ, HeI, and CaII emission line profiles observed on JD 8565.07 and JD8644.89. The Hα and Hβ line profiles are well reproduced with a central Gaus- sian emission peak onto which a blueshifted and a redshifted Table B.1. Gaussian components of optical emission line profiles. . Gaussian components of optical emission line profiles. Notes. The table lists the Julian date, the equivalent width, the peak intensity, radial velocity, and FWHM of the G Notes. The table lists the Julian date, the equivalent width, the peak intensity, radial velocity, and FWHM of the Gaussian fit for each component. Appendix A: Line profile variability While of limited signifi- cance, the similar shapes exhibited by the various line profiles Fig. A.3. 2D periodogram of Hα, Hβ, and HeI line profiles from the five spectra obtained during the ESPaDOnS June run. The color code repre- sents the periodogram power, and the superimposed white curve is the average line profile. We note the symmetry of the periodogram around the frequency 0.5 d−1 due to the 1 d alias resulting from the night-to- night sampling. at specific rotational phases (see Fig. A.1) lends credit to this result. For instance, the Balmer line profiles appear much more symmetric around phases 0.12–0.16 and 0.83–0.93 than around phases 0.46–0.51, where the red wing is consistently depressed. This suggests additional redshifted absorption occurs at phases around 0.5. A99, page 16 of 18 J. Bouvier et al.: DoAr 44 Appendix B: Line profile decomposition HJD EW1 EW2 EW3 Int1 Vr1 FWHM1 Int2 Vr2 FWHM2 Int3 Vr3 FWHM3 (−2 450 000) (Å) (Å) (Å) km s−1 Å km s−1 Å km s−1 Å Hα 8558.10852 59.7 −1 −16.4 10 13.1 255.7 −0.8 −39.7 53.1 −4.9 50.3 142.4 8559.15082 50.3 −5.8 −5.5 9 11.9 239.2 −2.7 −7.6 92.8 −3.4 47 67.7 8561.13665 46 −1.1 −12.2 8.7 6.9 226.3 −0.9 −42.8 51.7 −4.8 41.1 107.6 8562.12015 60.9 −8.7 −5.4 10.7 5 242.3 −3.1 −4.2 119.1 −2.7 50.4 84.1 8563.09667 52.2 −5.9 −3.8 9.5 −0.6 235.5 −2.9 −25.1 87.7 −2.3 41.3 69.3 8564.12225 61.2 −2.6 −14 10.5 8.5 249.8 −2 −41.9 55.9 −5.2 39.1 114.9 8565.06818 64 −4.1 −14.5 12.3 4.3 222.1 −2.7 −39.5 63.5 −6.5 29 94.7 8642.8923 86.3 −10.7 −13.8 15 4.9 246.5 −5.4 −34.5 85.1 −6.9 40.2 85.3 8643.89558 60.7 −1.4 −14.6 10.5 14.1 247.9 −1.1 −49.3 54.3 −5 30.6 125.3 8644.89415 69 −2.6 −12.1 11.3 6.5 261.6 −1.9 −41.2 59.2 −4.4 28.4 116.1 8645.93308 60.6 −7.1 −9.9 11.2 16.6 230.3 −3.5 −18.1 86.0 −5.1 49.8 83.4 8646.92779 58.2 −2.1 −16.7 11 12.7 226.5 −1.5 −33.7 57.3 −5.9 33.2 120.8 Hβ 8558.10852 13.9 −0.48 −4.4 3.3 18.9 241.3 −0.5 −41.8 55.2 −2.1 56.4 119.1 8559.15082 7.9 −0.27 −0.9 2 3.6 225.8 −0.31 −41 49.8 −0.8 45 58.3 8561.13665 7.9 −0.13 −1.6 2 1.5 223.3 −0.24 −37.5 31.0 −1.1 48.9 88.1 8562.12015 11.4 −0.33 −1.3 2.9 3.5 227.2 −0.41 −32.9 45.6 −1 41.2 69.6 8563.09667 8.9 −0.55 −0.6 2.4 −5 214.8 −0.59 −34.7 53.8 −0.5 42.5 66.3 8564.12225 15 −0.77 −5.5 3.9 15.5 222.3 −0.78 −39.4 57.3 −2.6 45.8 117.7 8565.06818 10.2 −0.26 −0.8 2.5 −3.9 229.4 −0.34 −32.8 43.5 −0.8 41.7 60.6 8642.8923 18.6 −1.94 −2.3 4.5 4.8 239.0 −1.68 −33.5 67.0 −1.8 39.9 74.0 8643.89558 13.4 −0.45 −4.2 3.3 19.1 231.9 −0.57 −43.7 45.4 −1.8 41.1 128.5 8644.89415 16.3 −1.06 −3 3.9 5.6 238.8 −0.98 −39.6 62.5 −1.5 39.9 113.7 8645.93308 12.9 −0.92 −2.1 3.2 14.5 232.2 −0.9 −34.7 58.8 −1.5 44.2 79.9 8646.92779 13.9 −0.5 −5.2 3.8 18.2 212.4 −0.62 −33.7 47.2 −2.4 39.5 122.2 HeI 587.6 nm 8558.10852 1.63 0.21 0.31 17.5 248.6 0.22 5.8 47.0 8559.15082 0.81 0.28 0.16 −4.1 238.8 0.31 7.1 43.0 8561.13665 0.99 0.17 0.18 11.1 259.0 0.2 5.6 41.4 8562.12015 1.12 0.19 0.25 −10.4 215.5 0.21 5.9 43.0 8563.09667 0.76 0.17 0.16 −8.5 229.1 0.21 10.9 38.5 8564.12225 1.15 0.23 0.21 5.3 256.6 0.24 5.6 46.8 8565.06818 1.02 0.31 0.21 −10.3 228.0 0.34 7 43.5 8642.8923 1.3 0.32 0.28 −0 221.6 0.4 11.4 38.8 8643.89558 1.1 0.20 0.2 14.1 264.1 0.23 6.1 41.8 8644.89415 1.27 0.33 0.27 0.4 222.8 0.38 4.4 40.9 8645.93308 1.3 0.28 0.27 4.7 228.9 0.35 11.2 38.3 8646.92779 1.12 0.24 0.22 12.7 236.4 0.25 6 46.3 CaII 854.2 nm 8558.10852 6.9 0.62 1.26 19.7 180.5 0.74 0.2 27.3 8559.15082 4.0 0.75 −0.25 0.87 16.7 149.9 0.83 2.1 29.6 −0.1 122.4 84.4 8561.13665 3.3 0.68 0.73 11.7 147.1 0.72 1 31.0 8562.12015 5.1 0.81 1.21 10.3 138.9 0.8 1.4 33.4 8563.09667 4.2 0.62 1 6.6 136.8 0.68 1.8 29.6 8564.12225 5.8 0.69 1.21 14.1 157.0 0.68 −0.2 33.6 8565.06818 4.6 0.92 −0.25 1.01 7.7 149.7 0.94 −0 32.2 −0.1 123.3 83.4 8642.8923 7.4 0.69 1.5 1.6 162.2 0.79 1.7 28.7 8643.89558 4.6 0.60 0.99 13.4 152.0 0.64 1.9 30.8 8644.89415 6.0 0.64 1.22 −6.3 161.2 0.69 −0.5 30.1 8645.93308 5.3 0.77 1.1 13.7 157.5 0.8 2.7 31.3 8646.92779 6.0 0.65 1.28 12.7 151.8 0.65 −0.7 32.9 e table lists the Julian date, the equivalent width, the peak intensity, radial velocity, and FWHM of the Gaussian fit for each com A99, page 17 of 18 A&A 643, A99 (2020) −600 −400 −200 0 200 400 600 −5 0 5 10 Hα − JD=8565.06 −600 −400 −200 0 200 400 600 v (km/s) −5 0 5 10 normalized profile −600 −400 −200 0 200 400 600 −2 0 2 4 6 8 10 12 Hα − JD=8644.89 −600 −400 −200 0 200 400 600 v (km/s) −2 0 2 4 6 8 10 12 normalized profile −600 −400 −200 0 200 400 600 0.5 1.0 1.5 2.0 2.5 3.0 3.5 Hβ − JD=8565.06 −600 −400 −200 0 200 400 600 v (km/s) 0.5 1.0 1.5 2.0 2.5 3.0 3.5 normalized profile −600 −400 −200 0 200 400 600 0 1 2 3 4 Hβ − JD=8644.89 −600 −400 −200 0 200 400 600 v (km/s) 0 1 2 3 4 normalized profile −400 −200 0 200 400 1.0 1.1 1.2 1.3 1.4 1.5 HeI − 5876A − JD=8565.06 −400 −200 0 200 400 v (km/s) 1.0 1.1 1.2 1.3 1.4 1.5 normalized profile −400 −200 0 200 400 1.0 1.2 1.4 1.6 HeI − 5876A − JD=8644.89 −400 −200 0 200 400 v (km/s) 1.0 1.2 1.4 1.6 normalized profile −400 −200 0 200 400 1.0 1.5 2.0 2.5 CaII − 8542A − JD=8565.06 −400 −200 0 200 400 v (km/s) 1.0 1.5 2.0 2.5 normalized profile −400 −200 0 200 400 1.0 1.5 2.0 2.5 CaII − 8542A − JD=8644.89 −400 −200 0 200 400 v (km/s) 1.0 1.5 2.0 2.5 normalized profile Fig. Appendix B: Line profile decomposition B.1. Line profile decomposition in Gaussian components. The Gaussian components are shown as blue curves, and the resulting modeled profile in red, while the observed profile is in black. From top to bottom: Hα, Hβ, HeI, and Ca II 854.2 nm. −600 −400 −200 0 200 400 600 −2 0 2 4 6 8 10 12 Hα − JD=8644.89 −600 −400 −200 0 200 400 600 v (km/s) −2 0 2 4 6 8 10 12 normalized profile −600 −400 −200 0 200 400 600 −5 0 5 10 Hα − JD=8565.06 −600 −400 −200 0 200 400 600 v (km/s) −5 0 5 10 normalized profile −600 −400 −200 0 200 400 600 0 1 2 3 4 Hβ − JD=8644.89 −600 −400 −200 0 200 400 600 v (km/s) 0 1 2 3 4 normalized profile −600 −400 −200 0 200 400 600 0.5 1.0 1.5 2.0 2.5 3.0 3.5 Hβ − JD=8565.06 −600 −400 −200 0 200 400 600 v (km/s) 0.5 1.0 1.5 2.0 2.5 3.0 3.5 normalized profile −400 −200 0 200 400 1.0 1.1 1.2 1.3 1.4 1.5 HeI − 5876A − JD=8565.06 −400 −200 0 200 400 v (km/s) 1.0 1.1 1.2 1.3 1.4 1.5 normalized profile −400 −200 0 200 400 1.0 1.2 1.4 1.6 HeI − 5876A − JD=8644.89 −400 −200 0 200 400 v (km/s) 1.0 1.2 1.4 1.6 normalized profile −400 −200 0 200 400 1.0 1.5 2.0 2.5 CaII − 8542A − JD=8644.89 −400 −200 0 200 400 v (km/s) 1.0 1.5 2.0 2.5 normalized profile −400 −200 0 200 400 1.0 1.5 2.0 2.5 CaII − 8542A − JD=8565.06 −400 −200 0 200 400 v (km/s) 1.0 1.5 2.0 2.5 normalized profile Fig. B.1. Line profile decomposition in Gaussian components. The Gaussian components are shown as blue curves, and the resulting modeled profile in red, while the observed profile is in black. From top to bottom: Hα, Hβ, HeI, and Ca II 854.2 nm. A99, page 18 of 18
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283 283 1) Monatshefte f. Cheniie 13: 539 (1893). Zur elektrolytischen Bestimmung des Bleis; von (2. Voytmann. (Eingelaufen beim Redactions-Cornit6 der Lieben-Festschrift am 5. Juni 1906.) Die elektrolytische Abscheidung des Bleis als Superoxyd gehort ohne Zweifel zu den fur die Laboratoriurnspraxis wich- tigsten Methoden ; sie gestattet die FBllung in kurzester Zeit. auszufihren und das Blei von vielen anderen Metallen zu trennen. Die gunstigsten Fgllungsbedingungen sind durch die Arbeiten von Luckow, v. Xlobukow, Classen, Neumann, Nissen- son, Smith, Medicus u. A. zur Genuge festgestellt worden. Welchen Einfluss andere Karper auf die Filllung ausiiben, hat namentlich Neumann ermittelt. Nach den bisher veroffent- lichten Vorschriften mijchte man meinen, dass die Bleibestimmnng durch Elektrolyse in den meisten Fallen gute Resultate g&be und nur ausnahmsweise (hei Anwesenlieit von Arsen, Selen, Mangan, Wisrnuth) nicht vortheilliaft auszufuhren wLre. Die Bleibestiinmung durch Elektrolyse wird vielfach aur Analpse des Bleiglanzes empfolilen (Classen, Nissenson), welclier zu- ngchst durch Oxydation in Bleisulfat ubergefiihrt und dann am salpetersaurer Losung als Bleisuperoxyd gefillt werden soll. Die in Folgendein veroffentlichten Versuche habe ich znm Die in Folgendein veroffentlichten Versuche habe ich znm grossen Theil schon vor zeltn Jahren begonnen, doch war es mir Mangels an Zeit nicht moglich dieselben zu Ende zu fuhren; schon damals fand icli, dass die elektrolytische Bleibestimmnng Voi’tmanii, Zw elektrolytiscken Bestimmung des Bleis. 284 durcliaus niclit so gut ausfgllt als allgemein angenominen wurde, und die inzwischen erschieneneii Arbeiten bestBtigen die von iiiir gemachten Erfahrungen. Icli liabe meine Versuche in letzter Zeit wieder aufgenommen und glaube eine liinllnglich grosse Anzahl von Belegen zu liefern, aus welclien man erselien kann, wann man sich mit Siclierheit auf das Resultat der elekBrolytisclien Bleibestimmung verlassen kann. Ich scliicke zunaclist eine Zusammenstellung meiner ana- lytischen Resultate voraus uud werde an der Hand derselben die Bleibestiminung besprechen. Die Flllungen geschahen entweder in der mattirten Platin- schale von Classen oder auf der mattirten uhrglasfdrmigen Scheibe (Durchmesser = 7 cm)’); in den Tabellen bedeutet S die Schale, U die Scheibe, w die Flllung in der Wlrme (60°), k die FBllung in der Kllte; das Fliissigkeitsvolumen betrug durchwegs 150 ccm. Beim Arbeiten mit der uhrglasfdrmigen Elektrode wnrde die Analyse stets unter Auswechselung der Elektrode fortgefiihrt, bis sich kein Superoxyd mehr abschied ; bei Anwendung der Platinschale wurde nach Verlauf ent- sprechender Zeit ein Tlieil der Flussigkeit auf Blei gepruft; schliesslicli wurde die ganze Fliissigkeit mit Ammoniak und Scliwefelammonium auf etwaigen Rleigehalt gepriift. Vortmnn 11, Zur elektrolytisdien Bestimmung des Bleis. Zur elektrolytischen Bestimmung des Bleis; von (2. Voytmann. 285 I I 1 I0,8473) 2 11 1,07391 3 'I 0,8166 5 1.0321 6 1 1,22721 7 1 1,0019 8 I ' 1,1751 !I 1 0,9537 I 4 11,0920i I 1 __ - -_ ._ __--- _-_______ I I I 0,6107 ' 0,6116 - 0,0009 I62,42 1 0,l ' 0,7747 0,7751 I - 0,0004 ,62,47 I 0,l 10,7866 0,7882 1 - 0,0016 I 62,38 I0,Of ' 0,7376 0,7377 I - 0,0001 162,49 1 0,2 0,8851 10,8858 1 - 0,0007 1 62,46 I 0,l 0,7232 0,72321 - I62,51~ 0,1 10,8482 0,84821 - 62,51 I 0,1 0,6885 0,6884 1 + 0,0001 1 62,52 i 0,2 0,7876 0,7884 I - 0,0006 16245 ~ 0,l j 0,8429,0,8426: + O,OOO.? 62,53 I 0,l 10,7583'0,7593' - 0,0010 162.43, 0,l 10,54191 - , - I62,41 j 0,s 0,D4P3( 0,9412 j + 0,0072 I62,98 0,l I j 0,5889 I 0,5894 - 0,0005 62,46 1 0,l I , I + 0,0084 ! 63,08 0,l j w 1 S i l l + 0,0038 ' 62,86 1 0,5 / ( I , \v U - - % g. a s 10 10 10 20 20 5 7,5 7,s 10 7,5 795 10 10 . - ._ LO LO .o 15 15 15 286 lio r t ma n n, Zur elektrolytischen Bestimmung des Bleis. 286 , c) a U Nr. & & ~- li 2311 0,688( 2411 0,795: 26 , 0,950: 25iI 0,545( 30 1,351~ 31 1 0,807: 321 0,765( I - 33 ' 0,806L I - - 35 0,856: - Ange w PbN,O, 36 1,0136 37 0,9424 38 0,7485 39 0,9305 40 1,0321 41 0,8282 42 0,5969 43, 0,8386 46 I 1,0308 d ! PbO, C fund. Zur elektrolytischen Bestimmung des Bleis; von (2. Voytmann. 0,l g Se 0,104 Se ,5g Cr907(KH4& 0,14 g As,O, 0,28g As,O, 0,28 g As,O, 031 g As,O, 10 ccm I/, n-SO,H, ),4010 g Sb,O, 0,303 g Sb,O, - 0,6898 0 6878 + 0,0020 186.83 0,8126 0,7953 + 0,0173 188,4 0,5494 0,5448, + 0,0046 87,3 0.9578 I 0.9503 + 0,0075 ' 87,27 0,9508,0.9399 + 0,0109 187.58 0,8416 0,8411 - 0 0023 I 86,32 0,9539 I 0,9473 + 0,0066 87,18 1,3564 11.3511 + 0,0053 ' 86,92 0,8133 10.8077 1 + 0.0056 187,l8 I ' - +0,0327 19O,2 0,7981 I1 I 0,7656 0,7654 ~ - 0,0002 8fi,61 - '+0,00751 - 0,8139 i I 'I 0,80641 - 0,0003 I86,55 0,8061 I 1,2819 I I - i+0,0128/ - + 0,0036 - 'I 1,2691 - 0.0001 86.56 1,2690 I I 'I 0,8563 -0,0021 1 1 1 - ),8598 1,6945 0,6802 1,6463 0,5403 1,0729 0,6716 1,7582 0,7594 1,5976 0,5978 1,4303 0,4308 1,6072 0,6053 1,7094 0,7110 1,4444 0,4453 1,7539 0,7440 1,7732 ~ 0,7533! + 0,0199 I64,16 ~ + 0,0143 ,63,82 -0,5987 ~ - - 0,0012,62,41' 1 - 0,0002 : 62,49 1 - 0,0005 62,431 0:4 $0,0020 62,711 0,4 - 0,0016 62,351 0,4 1 - 0,0009 /62,34 0 3 + 0,0009 63,34 1 013 1 W W W W W W W k W W W W W W 1 W Vortninnn, Zur elektrolytischeia Bestiwmung des Bleis. 287 I 47 I0,5681 48 , 0,699 I 49 ' 0,am I I - 50 j 0,7621 52 /0,819! 51 I 0,899: I ! ' '1 - 53 j 0,874; ! l - 54 ~ 0,8945 65 0,8942 56 ' 0,6469 57 0,7406 I' 1 - 58 0,8107 59 0,7266 60 0,8876 - 61 0,8739 62 0,3787 63 0,9144 64 1,0264 65 0,7987 66 0,7903 67 0,8429 68 0,9043 11 415 g Fe20, ; 0,5978 1 I1 : - 10,6313 I 0,137 g AlzO, 10,6467 0,645: 0,137 g AJO, 10,6482; 0,6454 0,43 g CUO 10,4656 0,466: 0t40gZnO 10,5357. - 1 ; j I1 1 I I1 I - I 0.6397 j 0,6407 0,91 HgO 10,'8487 10,6308 0,32 AgNO, 0,2804 ~ 0,2734 iN,O, kryst. 1,0 0,7391 '0,7408 g NiN,O, kryst./O,6622 i 0,6600 - ;62,5 + 0,0008 i62,51 + 0,0028 /62,71 - 0,0013 ~ 62,3: + 0,0010 I ,62,6: + 0,0103 ,63,5 I - 0,0003 ' 62,4! Zur elektrolytischen Bestimmung des Bleis; von (2. Voytmann. I - 0,0014 62,3( 0,0031 I 62,8t I - 0,0010 162,4: -f- 0,0179 164,2E + 0,0070 j 64,2 f 0,0022 I 62,7E - 0,0017 IG2,36 1,0 g CoCO, /0,59O8'0,5761 I + 0,0147 64;06 1,0 g CaCO, 0,5761 0,5704 + 0,0047 63,02 1,0 g CaCO, '0,6110 0,6084 + 0,0026 i62,77 3,0 g KNO, - + 0,0013 162,63 1 1 I - 45 - 41 15 10 - 12 - 14 20 20 12 20 20 20 20 15 15 15 5 20 !O !O !O !O 5 Vortmaiin, Zur elektrolytiscken Bestimmztng des Bleis. 288 70 71 72 73 74 75 0,7346 2,O g PTaNO, 0,5384 '0,5302 0,9617 3,Og Nah'O, 0,6951 10,6942 0,8517 3,O g NH,NO, 0,6181 0,fi147 0,7929 3,0 g NH,NO, 0,3737,0,3723 10 ccm 10 ccm I/, n - ~ ~ , ~ , 0j8255 1 I,/. n-SO,H, 0SJ7* 0,7287 0,7199 I a, D, I +0,0082 +0,ooO9 + 0,0034 $0,0014 + 0,0066 63,48 62,59 62,85 62,66 63,20 0,5 0,4 w s k 1 s - - 3 g R - - ._ 15 15 16 24 20 20 20 20 20 Die Bestimmung des Bleis durcli Ftillung als Superoxyd bietet im Falle nur Blei in salpetersaurer Losung vorhanden ist keine Schwierigkeiten, wenn man die von den verschie- denen Autoren angegebenen Vorschriften genau befolgt. Haupt- bedingung ist, dass nicht zu wenig freie SalpetersLure zugegen ist, da sich sonst metallisches Blei an der Kathode abscheidet. Als Grenze kann eiu Gehalt von 7 Volumprocenten Salpeter- slure (D = 1,4) gelten. Im allgemeinen muss bei Flllung au8 kalter Losung mehr Slure vorhanden sein, a19 bei FlIlung aus warmer Losung; die Stromsttirke bezw. Stromdichte kann inner- halb weiter Grenzen schwanken. Ganz anders verhtilt es sicli aber, sowie nocli andere Korper in der Fliissigkeit zugegen sind ; diese beeinflussen fast stets die Bleisuperoxydabscheidung, indem sie dieselbe ent- weder beeintrtichtigen oder sicli mit dem Superoxyd abscheiden, wodurch zu hohe Resultate erzielt werden. Von besonderem Einfluss ist die Anwesenheit von SchwefelsLure, da die elektro- lytische Bleibestimmung von Classen zur Bestimmung des 289 Vor t m (in n , Zur eleh-trolytischen Bestimmung des Bleis. Bleis im Bleiglanz vorgeschlagen wurde; auch Nissenson empfiehlt dieselbe fur kupfer- und antimonhaltigen Bleiglane, wlhrend er sonst fur letzteren die Trockenprobe vorziebt. Es ist merkwurdig, dass bis jetzt auf den schsdlichen Einflnss der Schwefels%ure noch nicht anfmerksam gemacht wurde. 9, Nur in Lunge's ,,Untersuchungsmethoden" 11. Bd. Seite 256 Annden der Chemie 351. Ri1. fiodet sich eine solche Angabe. 19 9, Nur in Lunge's ,,Untersuchungsmethoden" 11. Bd. Seite 256 fiodet sich eine solche Angabe. Zur elektrolytischen Bestimmung des Bleis; von (2. Voytmann. Ihr Einfluss macht sich dadnrch bemerkbar, dass zu hohe Resul- tate erzielt werden und der Niederschlag schn efelshrebaltig wirde). Ich habe eine grosse Anzahl von Versuclien gemacht und stets zu hohe Zablen erhalten (Versuche 14-35, 74, 75). Uebrigens beweisen zwei Beleganalysen Classen's bei der Ana- lyse einer Mischung von Bleinitrat und Kupfersulfat, dass auch er ein nm 0,0006 bezw. 0,0007 g zu hohes Resultat erhielt (,,Quantitative Analyse durch Elektrolyse', 4. Aufl., Seite 227). In neuerer Zeit scheint George A. Guess (Cbemiker-Zeitung Rep. 1906, 67) zu holie Resultate erhalten zu haben, denn er empfiehlt als Umrechnungsfactor statt der theoretischen Zahl 0,866 die praktische Zalil 0,855. Die elektrolytische Abscbeidung des Bleisuperoxyds mochte ich mir so vorstellen, dass durch den elektrisclien Strom das Bleisalz an der Anode in ein Salz des vierwerthigen Bleis (Plumbisalz) ubergefiihrt wird, w elches durch hydrolytische Dissociation in Bleisuperoxyd bezw. dessen Hydrat und freie Slure zerfallt, wie dies auch Lob in seineln ,,Leitfaden der praktischen ElektrochemieU Seite 74 angenommen hat. Bei -4nwesenheit von Schwefelshre entsteht das Plunibisulfat, dessen Dissociation nicbt so vollstgndig ist wie die des Nitrates. Die Dissociation wird durcli Erwlrmen befdrdert, d'ther fallt die Bleibestimmung uberhaiipt in der W b m e besser aus als in der Kalte. Will man bei Anwesenbeit von Schwefelslure gute Resultate erzielen, so verhhrt man am besten so, dass man das gewogene Bleisuperoxyd in Salpeterstiure unter Zusatz von 19 V ortmann, Zur elektrolylischen Bestimtnung des Bleis. 290 wenig OxalsBure lost und die Flllung wiederholt (Versuche 20, 21, 22, 32, 33, 34, 35). Eine zweite weniger gute Methode ist die, dass man das Blei zunachst aua einer mit Seignettesalz nnd Kalilauge her- gestellten alkalischen Losung als Metallschwamm hllt, diesen nach dem Waschen in Salpeterslure lost und nun als Super- oxyd hut (Versueh 44). Die Methode von X e d i c u s (Versuche 28, 29) ist zu uin- stindlieh und giebt leicht auch ein zu liohes Resultat, wahr- scheinlich durCli Spuren von Chlor. Ebeiieo wie Sulfate bewirkt aucli Chromsaure eine Er- hohnng des Resultates (Versuch 38); hier ist das Bleichromat schon qnalitativ leicht erkeonbar, da in Oxalssure und Sal- peterslue das Superoxyd sicli zuerst lost und das gelbe Chro- mat hinterbleibt. Von Sanren wirken schadlich : die Selenslure, die Arsen- und die Pliosphorslnre. Neumann hat den Einflnss der erst,eren beiden beobachtet und gefunden, dass beide auf die Ansscheidusg des Superoxyds verzogernd wirken. Zur elektrolytischen Bestimmung des Bleis; von (2. Voytmann. Nach meinen Vereuchen wirkt die Selenslure wie die Schwefelsiiiure, also erhohend auf das Resultat; zu dieseii Versuchen (Nr. 36, 37) loste ich das Selen erst in Salpeterslure und gab diese Losung zur Losung des Bleisalzes. Bei Arsens&ure dagegen fand ich ebenfalls eine Beein- trlchtigung der Ftillung (Versuch 39). Um bei Anwesenheit von Arsen das Blei elektrolytisch zu bestimmen, fallt man es erst als Metal1 aus einer mit Seignettesalz versetzten alkalischen Losung, lost den Ychwamm nach dem Waschen in Salpeterslure und b l l t nnii als Superoxyd (Versuche 40, 42, 43). Man b l l t am besten in einer Glasschale auf die untere Elektrode mit einem Strom von 0,1--0,2 Ampere und weniger als 2 Volt Spannnng (am besten 1 3 Volt) iiber Nacht, wlscht ohne Unter- brechung des Stromes sorgdltig aus, lost den Schwamm in 20 ccm Salpeterslure (D = 1,4) und h l l t wie sonst. 1st der .Vortmann, Zur elektrolytischen Bestimmung des Bleis. 291 Bleischwamm nicht gut ausgewaschen, so kann durch Zuriick- halten von Alkali die Bestimmung als Superoxyd zu hoch aus- fallen und miisste letztere wiederholt werden. Bleischwamm nicht gut ausgewaschen, so kann durch Zuriick- halten von Alkali die Bestimmung als Superoxyd zu hoch aus- fallen und miisste letztere wiederholt werden. In derselben Weise wie von Arsen muss Rlei auch von Antirnon getrennt werden; sowohl Arsen, wie Antimon miissen als Pentoxyde zugegen sein. Die Trioxyde fuhrt man zu- nBchst in saurer Losung durch Bromwasser in die Pent- oxyde iiber und macht dann erst alkalisch (mit Kalilauge oder Ammoniak). Schwieriger gestaltet sich die Bestimmung des Bleis neben Pliosphorslure. Dieselbe beeintrlchtigt die Filllung desselben als Superoxyd. Bei der Elektrolyse in der WLrme und Zusatz von 2 0 ccm SalpetersBure auf 150 ccm Gesammtlosung haftet der Niederschlag auch auf der mattirten Elektrode schlecht, lost sich bald theilwpise ab und bleibt in der Fliissigkeit sus- pendirt. Bei der Elektrolyse in der Kalte nnter Zusatz von 2 0 ccm Salpetersaure ist die Fallung unvollstLndig und trotz des hohen SIuregehaltes sclieidet sich an der Kathode metalli- sches BIei ab; bei Zusatz von 40-45 ccrn Salpetersbre scheidet sich nur Superoxyd ab, jpdoch ist die Fgllung unvoll- stllndig. Zur Bestimmung des Bleis neben Phosphorslure kann man daber wie bei Anwesenheit von Arsen verfahren, d. h. das Blei zuerst ah Metal1 aus alkalischer, dann als Superoxyd aus salpetersaurer Losung fLllen und eventuell die FBllung als Superoxyd wiederholen (Versuche 49, 50). Zur elektrolytischen Bestimmung des Bleis; von (2. Voytmann. 130, 1032) sol1 man sogar auf 0,3 g Bleisnlfat circa 5 g Ammonnitrat znsetzen. von C. M a r i e (Compt. rend. 130, 1032) sol1 man sogar auf 0,3 g Bleisnlfat circa 5 g Ammonnitrat znsetzen. 0,3 g Bleisnlfat circa 5 g Ammonnitrat znsetzen. Zur elektrolytischen Bestimmung des Bleis; von (2. Voytmann. Bei Anwesenheit von Chlorid oder Jodid erhBlt man eben- falls zu holie Resultate, was bereits bekannt ist (Versuche 51, 32 I). Im Versucli 32 wurde Bleiglanz durch Jodwasserstoff- saure, das Bleijodid mit Salpetersaure zersetzt und diese Losung der Elektrolyse unterworfen. Aber nicht blos die Anfonen, sondern auch die Kationen beeinflussen die Flllung des Bleisnperoxyds fast alle in nn- giinstiger Weise, so dasb man zu hohe Resultate erhklt. Nur 19* 19* V o r t m a n n , Zur eleh-trolytischen Bestimmung des Bleis. 292 das Kupfer macht eine Ausnahme, indem aus salpetersanrer Lbsung von Blei und Kupfer das Bleisuperoxyd rein heraus- fidllt, wie dies bisher auch von anderen Autoren gefunden wurde. Dagegen scheinen alle anderen Elemente eine Erhiihung des Resnltates zu verursachen. Ich habe die FLllung vorgenommen in Gegenwart von Zink, Nickel, Kobalt, Quecksilber, Silber, Eisen, Aluminium, Calcium, Kalium, Natrium, Ammonium und stets zn hohe Zahlen erhalten; die zugesetzten Metalle liessen sich im Superoxyd nachweisen. Die Trennung ist nur dann verl&sslich, wenn man das zuerst gefallte Superoxyd in Sal- petersanre und Oxalsaure lost und die FMlung wiederholt, so dass man aus der Uebereinatimmung des Gewichtes auf die Bichtigkeit der Bestimmung schliessen kann. Die Trennung des Bleis von Kobalt ist in der Kalte schlecht vorzunehmen, da der Niederschlag sich theilweise in Form eines feinen Pulvers beim Waschen ablost. Das Verhalten des Silbers, Wismutlis und Mangans bei der Bleibestimmung ist geniigend bekannt, so dass ich diese Metalle nicht weiter beriicksichtigt habe. Im Versuch 62 wnrde versucht, die Bildung des Silbersuperoxyds durch geringen Alkoholzusatz zu verhindern. hlerkwiirdig ist es, dass die Bleibestimmung auch bei An- wesenheit von Calcium, Kalium, Natrium und Ammonium zu hoch aus8llt; das Superoxyd ist in solchen Fallen salpeter- saurehaltig, denn nacli dem Erwarmen rnit Natriumcarbonat- losung war in letzterer Salpeterszure nachweisbar. Diese Er- scheinung wiirde die oben ausgesprochene Ansicht von der Bildung eines Plnmbinitrats und dessen Dissociation besttitigen; iudem die Neutralsalze die vollstandige Dissociation verhindern, erhalt man zu hohe Resultate. Die Bleibestimmung im Blei- snlfat, bezw. im Bleiglanz wird also ausser in Folge der An- wesenlieit von Schwefrls&urc, auch durcli Ammoniumnitrat un- richtig, da Classen das Bleisulfat erst mit Ammoniak bebandelt snd dann in Salpetershre lost. Nach einer neneren Vorschrift Vortmann , ZUT elektrolytischeti Bestimmung des Bleis. 293 von C. M a r i e (Compt. rend. 130, 1032) sol1 man sogar auf von C. M a r i e (Compt. rend. Zusammenfassung der Resultate. 1) Die elektrolytische Bestimmnng des Bleis als Snper- oxyd ist nur dann zuverUssig, wenn ausser Blei kein anderes Element in der salpetersanren L b n n g ent- halten ist; nnr das Kupfer bildet hier eine Ansnahme. 2) Bei Anwesenheit von Schwefelstinre, Selensgnre, Chrom- sBure erhLlt man zu holie Resultate; bei zweimaliger FBllung des Snperoxyds ist die Bestimmnng richtig. 3) Bei Anwesenheit von Arsen- nnd Phosphorsliure ist die FLllung unvollstgndig; um eine Trennung zu er- zielen muss inan das Blei zuerst als Yetall, sodann als Superoxyd fillen, aber diese Trennnng ist umstgud- lich und daher nicht empfehlenswerth. 4) Bei Anwesenheit aller iibrigen Metalle erhBlt man un- sichere, znmeist zu holie Zahlen. Man kann sich auf die Bestimmung nnr dann verlassen, wenn bei zwei- nialiger FBllung das Gewicht des Superoxyds keine wesentliclie Aendernng erleidet.
https://openalex.org/W2144431773
https://europepmc.org/articles/pmc1501059?pdf=render
English
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Protease nexin-1 expression is altered in human breast cancer
Cancer cell international
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cc-by
5,736
Published: 31 May 2006 Published: 31 May 2006 Cancer Cell International 2006, 6:16 doi:10.1186/1475-2867-6-16 This article is available from: http://www.cancerci.com/content/6/1/16 © 2006 Candia et al; licensee BioMed Central Ltd. ; This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Urokinase-type Plasminogen Activator (uPA), a serine protease, plays a pivotal role in human breast cancer metastasis by mediating the degradation of extracellular matrix proteins and promoting cell motility. In more advanced breast cancers, uPA activity is significantly up regulated and serves as a prognostic indicator of poor patient outcome. Classically, regulation of uPA activity, especially in breast cancers, is thought to be mediated by Type 1 Plasminogen Activator Inhibitor (PAI-1). However, we have recently found that a lesser known natural inhibitor of uPA, Protease Nexin 1 (PN-1), is expressed in normal human mammary tissue. Based on this observation, we investigated if PN-1 is also expressed in human breast cancers where it may contribute to the regulation of uPA and participate in the development of a metastatic phenotype. Results: Using quantitative real-time PCR analysis, we measured PN-1 mRNA expression in tissues obtained from 26 human breast tumor biopsies and compared these values with those obtained from 10 normal breast tissue samples. Since both PAI-1 and uPA expression levels are known to be elevated in metastatic breast cancer, we also measured their levels in our 26 tumor samples for direct comparison with PN-1 expression. We found that PN-1 expression was elevated over that found in normal mammary tissue; an increase of 1.5- to 3.5-fold in 21 of 26 human breast tumors examined. As anticipated, both PAI-1 and uPA mRNA levels were significantly higher in the majority of breast tumors; 19 of 26 tumors for PAI-1 and 22 of 26 tumors for uPA. A quantile box plot of these data demonstrates that the elevated PN-1 expression in breast tumor tissues directly correlates with the increased expression levels found for PAI-1 and uPA. Conclusion: The fact that PN-1 expression is elevated in human breast cancer, and that its increased expression is directly correlated with increases measured for PAI-1 and uPA, suggests that PN-1 may contribute to the regulation of uPA-mediate tumor cell motility and metastatic spread. cellular matrix (ECM). To achieve this elevated degrada- tive capacity, tumor cells express a variety of proteases to digest ECM proteins that typically encapsulate growing, Received: 13 February 2006 Accepted: 31 May 2006 Received: 13 February 2006 Accepted: 31 May 2006 Received: 13 February 2006 Accepted: 31 May 2006 Primary research Open Access Protease nexin-1 expression is altered in human breast cancer Britny J Candia, William C Hines, Christopher M Heaphy, Jeffrey K Griffith and Robert A Orlando* Address: Department of Biochemistry and Molecular Biology, University of NewMexico, School of Medicine, MSC08 4670, 1 University of New Mexico, Albuquerque, New Mexico, 87131, USA ddress: Department of Biochemistry and Molecular Biology, University of NewMexico, School of Medicine, MSC08 exico, Albuquerque, New Mexico, 87131, USA Email: Britny J Candia - bcandia@unm.edu; William C Hines - Curthines@aol.com; Christopher M Heaphy - cheaphy@salud.unm.edu; Jeffrey K Griffith - jkgriffith@salud.unm.edu; Robert A Orlando* - rorlando@salud.unm.edu * Corresponding author Background i g An important characteristic of highly invasive tumor cells is an elevated capacity to degrade the surrounding extra- Page 1 of 7 (page number not for citation purposes) Page 1 of 7 (page number not for citation purposes) http://www.cancerci.com/content/6/1/16 Cancer Cell International 2006, 6:16 http://www.cancerci.com/content/6/1/16 Preparation of tissue sections and RNA isolation p Serial frozen sections of breast samples, 10 µm in width, were mounted on Colorfrost slides (VWR, West Chester, PA) and stored at -70°C. Specimens were stained with hematoxylin/eosin and examined by a board-certified sur- gical pathologist, who assigned a histopathologic grade to the tumor and analyzed the normal tissue. Total RNA from cultured cells and frozen tumor tissue was isolated using silica-based spin-column extraction kits (RNeasy/ DNeasy mini kits, Qiagen, Valencia, CA) according to the manufacturer's protocol. Total RNA was treated with RNase-free DNase I (Ambion, Austin, TX) to eliminate contaminating DNA. RNA integrity was evaluated by aga- rose gel electrophoresis. Materials and methods Breast tissue samples benign tumors [1,2]. It is now well established that pro- teins of the plasminogen activation (PA) system are ele- vated in breast cancer and serve as the primary functional players in ECM degradation [3,4]. Expression of one member of the PA system, the serine protease urokinase (uPA), is significantly upregulated in tumor cells and cat- alyzes the conversion of extracellular plasminogen to plasmin [5]. Plasmin is a broad-spectrum protease that cleaves many ECM proteins, as well as activates certain matrix metalloproteinases [6]. This proteolytic cascade enables highly migratory tumor cells to efficiently degrade their surrounding matrices, exit the primary site of tumor growth and colonize distant secondary sites [7]. In addi- tion to its protease activity which augments breast tumor cell motility, high expression levels of uPA is also a well- established prognostic indicator of poor patient outcome during the course of breast cancer [8,9]. benign tumors [1,2]. It is now well established that pro- teins of the plasminogen activation (PA) system are ele- vated in breast cancer and serve as the primary functional players in ECM degradation [3,4]. Expression of one member of the PA system, the serine protease urokinase (uPA), is significantly upregulated in tumor cells and cat- alyzes the conversion of extracellular plasminogen to plasmin [5]. Plasmin is a broad-spectrum protease that cleaves many ECM proteins, as well as activates certain matrix metalloproteinases [6]. This proteolytic cascade enables highly migratory tumor cells to efficiently degrade their surrounding matrices, exit the primary site of tumor growth and colonize distant secondary sites [7]. In addi- tion to its protease activity which augments breast tumor cell motility, high expression levels of uPA is also a well- established prognostic indicator of poor patient outcome during the course of breast cancer [8,9]. Frozen breast tumor specimens from anonymous patients (n = 26) were obtained from the University of New Mex- ico Cancer Research and Treatment Center Solid Tumor Facility, Albuquerque, New Mexico. In 25 out of 26 cases, tumor grade, tumor size, lymph node status, and the frac- tion of cells in S phase (based on flow cytometry cell cycle analysis) were included within the clinical history pro- vided with each specimen. Anonymous normal breast mRNA (n = 10) originating from female patients where cause of death was unrelated to cancer, were purchased from Ambion (Austin, TX). The normal, control samples were supplied as two equal pools by the company. Cell culture MCF-7 human mammary epithelial cells, were provided by Dr. Steven Abcouwer, Hershey Medical Center, Her- shey, Pennsylvania. MDA-MB-231 metastatic human mammary epithelial cells were obtained from American Type Culture Collection (Rockland, MD). Both cell lines were propagated in Dulbecco modified Eagle's medium (DMEM, Life Technologies/Invitrogen, Carlsbad, CA) supplemented with 10% fetal calf serum (Irvine Scientific, Santa Ana, CA), 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 0.01 mg/ml bovine insulin, and 100 U/ ml penicillin G. Cells were cultured at 37°C with 5% CO2 and passaged once a week. Regulation of extracellular uPA activity is known to occur through the inhibitory properties of type I plasminogen activator inhibitor (PAI-1), a serine protease inhibitor (SERPIN) that is synthesized and secreted often by the same cells that secrete uPA [10]. Because of the close func- tional relationship between uPA proteolytic activity and PAI-1 inhibitory function, it is thought that a well-con- trolled balance of uPA and PAI-1 dictates the extent of cell motility. Protease Nexin-1 (PN-1), another member of the SERPIN family [11], is highly expressed by stromal cells [12] and a potent inhibitor of uPA [10,13]. Interestingly, although PN-1 activity has been extensively studied within the context of neural development, few studies have been reported examining its expression in cancerous tissues and its potential role in cancer progression. PN-1 is expressed by astrocytes and glial cells [14], as well as neu- roblastoma cells [15] where it is thought to promote neu- ronal cell survival [16] and modulate neurite outgrowth [17]. In addition, PN-1 inhibits thrombin-stimulated cell division [18], migration of cerebrellar granular cells [19], and uPA-dependent ECM degradation [20]. Thus, based on findings in other cell types, we hypothesize that PN-1 may contribute to tumor cell motility in advanced stage breast cancer by playing a role in the regulation of uPA activity. To address this hypothesis, we examined the expression of PN-1 in advanced stage human breast can- cer tissues to determine if its expression is altered when compared to normal mammary tissue and to directly compare its expression level to those of PAI-1 and uPA. To accomplish this goal, we used quantitative real-time reverse transcription-PCR (QRT-PCR) to measure PN-1, PAI-1 and uPA expression levels within a set of breast tumor and normal breast tissue samples. Quantitative real-time RT-PCR Q cDNA was synthesized by random decamer-primed reverse transcription of RNA (1 µg) using a TaqMan® Reverse Transcription kit (Applied Biosystems, Foster City, CA) according to the manufacturer's standard proto- col. Negative controls contained RNase-free water substi- tuted for reverse transcriptase. The mRNA levels of PN-1, PAI-1, uPA and TATA-binding protein (TBP) were meas- ured in breast specimens, the MCF-7 mammary epithelial cell line, and the MDA-MB-231 metastatic mammary epi- thelial cell line using the ABgene Absolute SYBR Green Page 2 of 7 (page number not for citation purposes) Cancer Cell International 2006, 6:16 http://www.cancerci.com/content/6/1/16 QRT-PCR assay (Fisher Scientific, Hampton, NH). PN-1 primers were selected to amplify an 81 bp sequence span- ning the intron located between exons 2 and 3. Primer sequences used for PN-1 were 5'-GAAGCAGCTCGCCAT- GGT-3' (forward), 5'-AGACGATGGCCTTGTTGATC-3' (reverse). TBP primer sequences used were 5'-CACGAAC- CACGGCACTGATT-3' (forward), 5'-TTTTCTTGCT- GCCAGTCTGGAC-3' (reverse). Primer sequences used for PAI-1 were 5'-TGCTGGTGAATGCCCTCTACT-3' (for- ward), 5'-CGG TCA TTC CCA GGT TCT CTA-3' (reverse). uPA primer sequences used were 5'-CAC GCA AGG GGA GAT GAA-3' (forward), 5'-CA GCA TTT TGG TGG TGA CTT-3' (reverse) [21]. Final concentration of PN-1, PAI-1 and uPA primers used for amplification was 600 nmol/L forward, 600 nmol/L reverse; 600 nmol/L forward, 900 nmol/L reverse was used for TBP primers. Amplification of PN-1, PAI-1, uPA and TBP cDNA was performed using the MiniOpticon Real-Time PCR Detection System (Bio- rad, Hercules, CA). The cycling parameters used were as follows: 1 cycle, 95°C for 10 min; 50 cycles, 95°C for 15 sec and 60°C for 1 min; 1 cycle, 40°C for 3 min. The PN- 1, PAI-1 and uPA mRNA levels were normalized to TBP mRNA levels using the Comparative CT method and are reported in the figures as fold difference compared to lev- els found in normal mammary tissue. Melting curve anal- yses were performed for all amplifications to verify that only single products were generated from the reactions. Amplicons were sequenced to verify authentic PN-1. The cDNA for human PN-1 was obtained from the I.M.A.G.E. Consortium (ID: 4824856; Genbank: BC042628; Gen- bank: BC042628). compared directly to quantitative PCR values obtained using cDNA generated from normal human mammary tis- sue. We found that PN-1 expression was elevated over that found in normal mammary tissue; an increase of 1.5- to 3.5-fold in 21 of 26 human breast tumors examined (Fig. 1A). Quantitative real-time RT-PCR Since both PAI-1 [24-26] and uPA [24,26] expression levels are known to be elevated in metastatic breast cancer, we measured their levels in our 26 tumor samples for direct comparison with PN-1 expression. As anticipated, both PAI-1 (Fig. 1B) and uPA (Fig. 1C) mRNA levels were significantly higher in the majority of breast tumors; 19 of 26 tumors for PAI-1 and 22 of 26 tumors for uPA. A quan- tile box plot of the data shown in Figure 1 permits a direct comparison of expression levels for PN-1, PAI-1 and uPA (Fig. 2). These data clearly show that PN-1 expression is elevated in the majority of human breast cancers exam- ined and that this elevated expression directly correlates with the expected higher expression levels found for PAI- 1 and uPA. Since the majority of our tumor samples rep- resent advanced stage, grade 2 and 3 breast cancers, we are unable to determine at this time if PN-1 expression levels correlate with tumor grade, lymph node status or patient reoccurrence. PN-1 expression in MCF-7 and MDA-MB-231 breast cancer cells We plan to characterize the mechanism responsible for increased expression of PN-1 in breast cancer and deter- mine its functional role in breast cancer metastasis. To accomplish this goal, we will require a cultured model sys- tem for accurate, controlled assessment of PN-1 promoter status, transcription factor requirements, and tumor cell invasive capacity. MCF-7 and MDA-MB-231 cells are well established cultured lines used extensively to study molec- ular details of breast cancer progression [27]. Hormone- responsive MCF-7 cells have a low invasive capacity and represent earlier stages of breast cancer, while hormone- independent MDA-MB-231 cells are highly invasive and represent more advanced stage breast cancer. To deter- mine if these cell models will be useful for examining PN- 1 function in breast cancer, we performed QRT-PCR anal- ysis to identify if PN-1 expression is disregulated in a com- parable manner to that seen in human breast cancer tissues. We found that MDA-MB-231 cells express 3.5-fold greater levels of PN-1 than MCF-7 cells (Fig. 3). Moreover, increased expression of PAI-1 and uPA were also found in MDA-MB-231 cells as compared to MCF-7. Results Q i Quantitation of PN-1 expression in human breast tumors For QRT-PCR analysis, we designed primers to amplify an 81 bp sequence of PN-1 spanning the splice junction between exons 2 and 3. Spanning a splice junction ensures that amplified products are derived solely from mRNA and not from genomic DNA that might remain in our preparation. In order to test the specificity of these novel primers, we amplified the 81 bp PN-I sequence by straight RT-PCR using RNA purified from a normal human fibroblast cell line (HuFb) and compared the product to that obtained from amplification using the human PN-1 cDNA. We chose to use human fibroblasts since they synthesize and secrete active PN-1 at levels cor- responding to ~1% of all secreted proteins [22,23]. As anticipated, we found that our newly designed primers amplified only the expected 81 bp sequence (data not shown). Discussion Advanced stage breast cancer is accompanied by a dra- matic increase in metastatic potential of epithelial-derived tumor cells. The observed increase in tumor cell motility is aided by increased expression and activity of uPA [4]. For effective tumor cell migration, the proteolytic activity of uPA is thought to be balanced by the inhibitory activity To quantify PN-1 expression in human breast cancers, we obtained 26 samples of breast tumor tissue, purified RNA and generated cDNA from this material. The cDNA were then analyzed by quantitative PCR and the results were Page 3 of 7 (page number not for citation purposes) Page 3 of 7 (page number not for citation purposes) Cancer Cell International 2006, 6:16 http://www.cancerci.com/content/6/1/16 xpression in human breast tumor tissues and normal human m NA expression in human breast tumor tissues and norm ast tumors (T1–T26) and 10 normal breast samples. Normal sa RNA levels for each gene were evaluated by QRT-PCR. Relative ATA binding protein mRNA levels. Comparative CT method was A (C) expression in breast tumor tissue as compared to levels m oled normal samples was calculated and assigned a value of one in the tumor samples. The standard deviation of the normal sam f the mean values obtained from normal mammary tissues. PN-1, PAI-1 and uPA mRNA expression in human breast tumor tissues and normal human mammary tissue Figure 1 PN-1, PAI-1 and uPA mRNA expression in human breast tumor tissues and normal human mammary tissue. RNA was isolated from 26 breast tumors (T1–T26) and 10 normal breast samples. Normal samples were pooled into two equal groups (N1 and N2). mRNA levels for each gene were evaluated by QRT-PCR. Relative levels of PN-1, PAI-1 and uPA mRNA were normalized to TATA binding protein mRNA levels. Comparative CT method was used to calculate fold difference of PN-1 (A), PAI-1 (B) and uPA (C) expression in breast tumor tissue as compared to levels measured in normal breast tissue. The mean value of the two pooled normal samples was calculated and assigned a value of one in order to determine relative fold change of expression within the tumor samples. The standard deviation of the normal samples was 0.263. The box repre- sents one standard deviation of the mean values obtained from normal mammary tissues. Compariso els in 26 br Figure 2 Comparison of PN-1, PAI-1 and uPA mRNA expres- sion levels in 26 breast tumor samples. The box for each gene represents the interquartile range (25–75th per- centile) and the line within this box is the median value. Bot- tom and top bars of the whisker indicate the 10th and 90th percentiles, respectively. Outlier values are indicated (closed squares). QRT-PCR analysis of PN-1, PAI-1 and uPA mRNA expres- sion in MCF-7 and MDA-MB-231 breast cancer cell lines Figure 3 QRT-PCR analysis of PN-1, PAI-1 and uPA mRNA expression in MCF-7 and MDA-MB-231 breast cancer cell lines. PN-1, PAI-1 and uPA message levels were quanti- tated in MCF-7 and MDA-MB-231 cells by QRT-PCR. Expression levels for PN-1, PAI-1 and uPA were normalized to values obtained for TATA binding protein. CT values for each gene obtained from MCF-7 cells were averaged and assigned a value of one to assess relative fold increase in expression in MDA-MB-231 cells. Although studies in the literature investigating a role for PN-1 in cancer progression are limited, our results com- plement and extend data presented in a recent report by Buchholz and colleagues [31]. Their study demonstrated that a highly metastatic pancreatic cancer line overex- pressed PN-1, while a less metastatic subclone showed lit- tle PN-1 expression. The authors also noted that stable PN-1 overexpression in the less metastatic subclone greatly enhanced its local invasiveness in in vivo studies. Our studies expand on these observations by demonstrat- ing an increase in PN-1 expression in human breast cancer tissues. Q y , p g QRT-PCR analysis of PN-1, PAI-1 and uPA mRNA expression in MCF-7 and MDA-MB-231 breast cancer cell lines. PN-1, PAI-1 and uPA message levels were quanti- tated in MCF-7 and MDA-MB-231 cells by QRT-PCR. Expression levels for PN-1, PAI-1 and uPA were normalized to values obtained for TATA binding protein. CT values for each gene obtained from MCF-7 cells were averaged and assigned a value of one to assess relative fold increase in expression in MDA-MB-231 cells. Q y , p g QRT-PCR analysis of PN-1, PAI-1 and uPA mRNA expression in MCF-7 and MDA-MB-231 breast cancer cell lines. PN-1, PAI-1 and uPA message levels were quanti- tated in MCF-7 and MDA-MB-231 cells by QRT-PCR. Expression levels for PN-1, PAI-1 and uPA were normalized to values obtained for TATA binding protein. Discussion , a u e p ess o u a b east tu o t ssues a o a u a a a y t ssue gu e PN-1, PAI-1 and uPA mRNA expression in human breast tumor tissues and normal human mammary tissue. RNA was isolated from 26 breast tumors (T1–T26) and 10 normal breast samples. Normal samples were pooled into two equal groups (N1 and N2). mRNA levels for each gene were evaluated by QRT-PCR. Relative levels of PN-1, PAI-1 and uPA mRNA were normalized to TATA binding protein mRNA levels. Comparative CT method was used to calculate fold difference of PN-1 (A), PAI-1 (B) and uPA (C) expression in breast tumor tissue as compared to levels measured in normal breast tissue. The mean value of the two pooled normal samples was calculated and assigned a value of one in order to determine relative fold change of expression within the tumor samples. The standard deviation of the normal samples was 0.263. The box repre- sents one standard deviation of the mean values obtained from normal mammary tissues. Page 4 of 7 (page number not for citation purposes) Page 4 of 7 (page number not for citation purposes) Page 5 of 7 (page number not for citation purposes) http://www.cancerci.com/content/6/1/16 Cancer Cell International 2006, 6:16 http://www.cancerci.com/content/6/1/16 Comparison of PN-1, PAI-1 and uPA mRNA expression lev- els in 26 breast tumor samples Figure 2 Comparison of PN-1, PAI-1 and uPA mRNA expres- sion levels in 26 breast tumor samples. The box for each gene represents the interquartile range (25–75th per- centile) and the line within this box is the median value. Bot- tom and top bars of the whisker indicate the 10th and 90th percentiles, respectively. Outlier values are indicated (closed squares). of PAI-1 [28,29]. The cycling activities of proteolysis and protease inhibition lead to sequential rounds of cell detachment-reattachment, which in turn leads to an increase in cell motility. Indeed, elevated expression levels of both uPA and PAI-1 are characteristic of advanced stage breast cancers [30]. Interestingly, although PN-1 is struc- turally and functionally related to PAI-1, there have been no studies to date investigating if PN-1 contributes to breast cancer progression in a manner similar to that of PAI-1. To address this gap in knowledge, we examined if PN-1 expression is altered in human breast cancer by quantitating levels of PN-1 expression in human tissue samples obtained from tumor biopsies. In these same samples, we also quantitated PAI-1 and uPA expression levels for direct comparison to PN-1. Our findings indi- cate that PN-1 expression is elevated in the majority of human breast tumor tissues examined and that its expres- sion levels are directly correlated with increases measured for PAI-1 and uPA. We also found that the highly meta- static, MDA-MB-231 breast cancer line expresses 3.5-fold greater levels of PN-1 compared to the non-tumorgenic, MCF-7 breast cancer cell line. This increase in PN-1 is also correlated to increases seen for PAI-1 and uPA in MDA- MB-231 cells. The elevated expression of all three genes is consistent with our measurements in human breast tumor samples. The significant differences in PN-1 expression between non-tumorigenic MCF-7 cells and highly inva- sive MDA-MB-231 cells should provide us with a good basis for identifying the mechanism responsible for altered PN-1 expression seen in breast tissues and allow us to examine PN-1 function in the context of elevated PAI-1 and uPA levels. Taken together, these data indicate that PN-1 expression is increased during breast cancer tumori- genesis and may contribute, along with PAI-1, to uPA- mediated tumor cell motility and a more advanced meta- static phenotype. Authors' contributions BJC carried out the majority of studies and drafted the manuscript. WCH and CMH provided confirmed breast tumor and normal mammary samples. JKG assisted with data interpretation. RAO provided the original conceptual framework for the study, participated in the experimental design and finalized the manuscript for submission. Authors read and approved the final version. Compariso els in 26 br Figure 2 CT values for each gene obtained from MCF-7 cells were averaged and assigned a value of one to assess relative fold increase in expression in MDA-MB-231 cells. Quantitating expression of PAI-1 and uPA is of high prog- nostic value for assessing breast cancer survival outcome [24,25]. Numerous independent studies have shown that patients with low levels of PAI-1 and uPA in their primary tumor tissue have a significantly better survival rate than Page 5 of 7 (page number not for citation purposes) Page 5 of 7 (page number not for citation purposes) Cancer Cell International 2006, 6:16 http://www.cancerci.com/content/6/1/16 http://www.cancerci.com/content/6/1/16 patients with high levels of either factor alone. Recently, the prognostic value of PAI-1 and uPA has been verified by a pooled analysis consisting of >8,000 breast cancer patients [26]. In light of the overlapping protease specifi- cities of PAI-1 and PN-1 [32], together with the estab- lished role of PN-1 in neuronal cell regulation and motility [33,34], we believe it is likely that PN-1 also plays a role in breast cancer progression by contributing to events necessary for increased tumor cell motility. Increased expression of PN-1 by tumor cells may serve to modulate their adhesiveness or motility [35]. Alterna- tively, tumor cell activity may be influenced by tumor- stromal tissue crosstalk [36]. The breast neoplastic stroma contains a heterogeneous cell population composed of fibroblasts, myofibroblasts, and endothelial cells, which are all known to synthesize and secrete significant amounts of PN-1 [37]. Although it remains to be deter- mined the precise mechanism by which PN-1 contributes to breast cancer tumor progression, the results of the present study establish a rationale for further investigation of PN-1 as a modulator of uPA activity in breast tumor cell motility. Future studies will be focused on identifying transcriptional and/or translational mechanisms control- ling PN-1 expression by cancer cells and determining if PN-1 serves as an independent prognostic indicator of breast cancer staging by using a more widely defined sam- ple of tumor tissues, including earlier stage cancers as well as late-stage carcinomas. In addition, the use of laser cap- ture dissection technology will confine our QRT-PCR measurements to tumor tissue and eliminate contribu- tions from surrounding normal mammary tissue that are likely to occur when using surgical specimens. Competing interests The author(s) declare that they have no competing inter- ests. References 1. Price JT, Bonovich MT, Kohn EC: The biochemistry of cancer dis- semination. Critical Reviews in Biochemistry & Molecular Biology 1997, 32(3):175-253. ( ) 2. Dano K, Romer J, Nielsen BS, Bjorn S, Pyke C, Rygaard J, Lund LR: Cancer invasion and tissue remodeling--cooperation of pro- tease systems and cell types. APMIS 1999, 107(1):120-127. y yp , ( ) 3. Carroll VA, Binder BR: The role of the plasminogen activation system in cancer. Seminars in Thrombosis & Hemostasis 1999, 25(2):183-197. Abbreviations uPA, urokinase-type plasminogen activator; PAI-1, plas- minogen activator inhibitor; ECM, extracellular matrix; PA, plasminogen activation; SERPIN, serine protease inhibitor; PN-1, protease nexin-1. Acknowledgements We thank Drs. Dorothy J. VanderJagt and Robert H. Glew (Department of Biochemistry and Molecular Biology, University of New Mexico, School of Medicine) for there valuable input and critical evaluation of this work. This work was supported by the National Institutes of Health Grant #HL63291 (to R.A.O.), National Institutes of Health Initiative to Maximize Student Diversity (IMSD) fellowship (to B.J.C.) and National Institutes of Health Minority Access to Research Careers (MARC) fellowship (to B.J.C.). Conclusion We quantitated PN-1 expression in samples obtained from biopsies of human breast tumors and from normal mammary tissues by QRT-PCR analysis and compared these results to those obtained for PAI-1 and uPA. 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Chorostowska-Wynimko J, Skrzypczak-Jankun E, Jankun J: Plas- minogen activator inhibitor type-1: its structure, biological activity and role in tumorigenesis (Review). International journal of molecular medicine 2004, 13(6):759-766.
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Cryptosporidium spp. and Enterocytozoon bieneusi in introduced raccoons (Procyon lotor)—first evidence from Poland and Germany
Parasitology research
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Parasitol Res (2016) 115:4535–4541 DOI 10.1007/s00436-016-5245-5 Parasitol Res (2016) 115:4535–4541 DOI 10.1007/s00436-016-5245-5 ORIGINAL PAPER ORIGINAL PAPER Cryptosporidium spp. and Enterocytozoon bieneusi in introduced raccoons (Procyon lotor)—first evidence from Poland and Germany Kinga Leśniańska1 & Agnieszka Perec-Matysiak1 & Joanna Hildebrand1 & Katarzyna Buńkowska-Gawlik1 & Agnieszka Piróg2 & Marcin Popiołek1 Received: 3 August 2016 /Accepted: 2 September 2016 /Published online: 14 September 2016 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract The raccoon (Procyon lotor) carnivore native to North America is a fast spreading, invasive species in the Europe now. At the moment, the highest population occupies areas near the German-Polish border. The data on the occur- rence of Cryptosporidium spp. and microsporidia in raccoons is limited to North America’s territory and is totally lacking in the case of their introduction to Europe. Therefore, the objec- tive of this study was to investigate the occurrence of microparasites, i.e., Cryptosporidium spp. and microsporidia in the introduced raccoons obtained from localities in Poland and Germany. A PCR-based approach that permitted genetic characterization via sequence analysis was applied to raccoon fecal samples (n = 49), collected during 2012–2014. All fecal samples were simultaneously tested with the use of genetic markers, and DNA of microsporidia and Cryptosporidium spp. was detected among the examined raccoons. The results of our research confirmed the presence of Cryptosporidium skunk genotype and Enterocytozoon bieneusi NCF2 genotype. The results suggest a possible role of raccoons in the contam- ination of the environment, including urban areas, with pathogens of zoonotic significance as well as their role in the transmission and introduction of new genotypes of microparasites in the areas where P. lotor has not been ob- served yet. To our knowledge, there has been no literature data on the above genotypes detected previously in humans or an- imals from the examined study sites so far. Keywords Raccoon .Cryptosporidiumspp. .Enterocytozoon bieneusi . Genotyping Keywords Raccoon .Cryptosporidiumspp. .Enterocytozoon bieneusi . Genotyping * Agnieszka Perec-Matysiak agnieszka.perec-matysiak@uwr.edu.pl 2 Department of Invertebrates Systematic and Ecology, Institute of Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631 Wrocław, Poland 1 Department of Parasitology, Institute of Genetics and Microbiology, Wrocław University, Przybyszewskiego 63, 51-148 Wrocław, Poland 1 Department of Parasitology, Institute of Genetics and Microbiology, Wrocław University, Przybyszewskiego 63, 51-148 Wrocław, Poland 2 Department of Invertebrates Systematic and Ecology, Institute of Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631 Wrocław, Poland Study areas and collection of material This study was carried out on 49 raccoons, comprising 31 males and 18 females, collected from hunters and road-kills from the area of Kostrzyn on the Oder and Warta Mouth National Park, Poland (n = 32), and from localities near the Müritz National Park, Mecklemburg-Vorpommern, Germany (n = 17) (Fig. 1). A suburban environment of the city of Kostrzyn is located in the surroundings of Warta Mouth National Park (WMNP) (52 °34′ N, 14° 43′ E) which covers about 80 km2 of the Warta River. Here, raccoons occupy relatively small territories and live in high density (0.7–2.5 individuals per 1 km2)—their home ranges overlap with an average of 80 %. This German-Polish border area is a zone of high human activity associated with traffic at petrol stations, restaurants, and hotels. WMNP is a part of Natura 2000 project, which makes it also attractive for tourists. Müritz National Park (MNP) (53° 27′ N, 12° 49′ E) located in Mecklenburg-Vorpommern contains a large amount of p p Enterocytozoon bieneusi and Encephalitozoon spp. are the major microsporidians infecting humans and animals world- wide (Santin and Fayer 2011). At present, over 240 E. bieneusi genotypes have been identified (Matos et al. 2012; Zhao et al. 2015). By internal transcribed spacer (ITS) sequence analysis of E. bieneusi genotypes, eight different groups of all genotypes were established (Karim et al. 2014). A large cluster named as group 1 contains more than 94 % published genotypes of E. bieneusi (Henriques-Gil et al. 2010). The genotypes within this group are found both in humans and animals. Even though some genotypes are genet- ically similar to human pathogenic ones, they have been found only in animals so far, suggesting their zoonotic potential (Henriques-Gil et al. 2010). The remaining genogroups (2–8) are found mostly in specific hosts and wastewater (Guo et al. 2014). Encephalitozoon spp., another microsporidia group, has been generally studied among humans and domestic animals; there is still insufficient information on the role of wild living animals, including raccoons, which may be a potential source of zoonotic contamination with this microsporidia species. Fig. 1 The map of Poland and Germany showing geographical origin (black dots) of wild raccoons obtained for this study Sofar,30speciesandover100genotypesofCryptosporidium have been described in various vertebrate hosts and environmen- tal sources (Kváč et al. 2014). Introduction The knowledge on rac- coon as reservoir hosts of the abovementioned group of para- sites is rather limited and concerns Central and North Americas’ territories (Feng et al. 2007; Guo et al. 2014; Perz and Le Blancq 2001; Snyder 1988; Sulaiman et al. 2003; Zhou et al. 2004). On the other hand, there is no data on these microparasites in the case of invasive European raccoons. Therefore, the aim of this preliminary study was to investi- gate the presence of intestinal microparasites occurring in the raccoon population in newly colonized areas of Western Poland and Germany. Molecular analyses were conducted to identify and genotype Cryptosporidium spp. and microsporidia species emphasizing their zoonotic potential in European raccoons. Introduction The raccoon is a North American carnivore which was intro- duced to Japan and Europe in the 20th century. In Europe, as a result of escaped pets, releases, and escapes from fur farms, raccoons are distributed almost across the whole mainland (Beltrán-Beck et al. 2012). A rapid expansion of this species has been observed in wild environment since the 1980s main- ly on the German territory (Hohmann et al. 2001; Stubbe 1999). At present, the largest European stable population oc- curs in Germany (over one million individuals) (Hohmann et al. 2000; Michler and Michler 2012), but smaller popula- tions inhabit also other European countries (Beltrán-Beck et al. 2012; Schley et al. 2001; Stubbe 1999). In Poland, the first individuals in wildlife were observed in the 1940s (Bogdanowicz and Ruprecht 1987). In the 1980s and the 1990s, a wild population was reported in Western Poland, and since that time, the abundance of the raccoons on the Polish territory has grown rapidly (Bartoszewicz et al. 2008; Bartoszewicz and Okarma 2007; Biedrzycka et al. 2014; Popiołek et al. 2011). Raccoons, which become one of the fastest spreading wild living population, are often found in forested areas as well in urban space near human settlements, where they can find alternative sources of food but also contribute to the transmis- sion of many zoonotic groups of parasites to other wildlife and humans (Kresta et al. 2009). Some studies have shown that species introduced into a novel environment often lose their 2 Department of Invertebrates Systematic and Ecology, Institute of Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631 Wrocław, Poland 4536 Parasitol Res (2016) 115:4535–4541 own parasites during the course of a new population establish- ment (Torchin et al. 2003; Torchin and Mitchell 2004) but also encounter and accumulate parasites that occur in newly colo- nized areas. In addition, there may be a significant probability of raccoons introducing some new parasite species, recorded previously in individuals from North America, into European ones. The raccoon as an alien and invasive species, both wild living and potentially synanthropic, may serve as a susceptible host for opportunistic intestinal parasites. The current epide- miological data on Cryptosporidium spp. and microsporidia has raised public health concerns about the zoonotic nature of transmission of these microparasites. DNA extraction and PCR amplification NestedPCRdetectedE.bieneusiin2of49(4.1%)examinedfecal samples of raccoons. Both positive samples, one obtained for a female and the other one for a male raccoon, were recorded from the area of Poland. The overall prevalence of Cryptosporidium spp. was estimated in 34.7 % (17/49) with infection rates of 38.9 % (7/18) and 32.3 % (10/31) observed in female and male raccoons, respectively. The prevalence of parasites according to the study sites was determined in 43.8 % (14/32) and 17.6 % (3/17) for Poland and Germany, respectively. No statistically sig- nificant differences were found in the occurrence of Cryptosporidiumspp.andE.bieneusibetweenthesamplingareas and the sex of the examined raccoons. In our survey, we did not detect any DNA of Encephalitozoon spp. in raccoons. DNA was isolated from all 49 fecal samples using GeneMATRIX Stool DNA Purification Kit (EURx, Gdańsk, Poland) according to the manufacturer’s instructions. Obtained DNA was stored at −20 °C until further use. PCR amplification was performed on a sets of nested primers amplifying the ITS region of the ribosomal ribonucle- ic acid (rRNA) gene, i.e., EBITS3, EBITS4 and EBITS1, EBITS2.4 for E. bieneusi (Buckholt et al. 2002) and INT580F, INT580R and Msp3, Msp4a for Encephalitozoon spp. (Katzwinkel-Wladarsch et al. 1996). A fragment of Cryptosporidium 18S rRNA and Cryptosporidium oocyst wall protein (COWP) genes were amplified (Pedraza-Diaz et al. 2001; Spano et al. 1997; Xiao et al. 1999). For the amplification of actin genes, we used cycling parameters elab- orated by Sulaiman et al. (2002). For all PCR reactions, negative and positive controls were performed with sterile water and reference DNA, respectively. Secondary PCR prod- ucts were subjected to electrophoresis on a 1.0 % agarose gel and stained with Midori Green (Nippon Genetics Europe GmbH). Products of expected size were purified using QIAquick PCR Purification Kit (Qiagen, Hilden, Germany) and stored at 4 °C until sequencing. The analysis of the ITS region of E. bieneusi revealed the existence of one known genotype in both positive samples, namely NCF2. The phylogenetic analysis showed that the genotype was identical to the ones previously reported in fox (KT750163) and raccoon dog (KU847358) in China and clustered into group 1 (Fig. 2). The isolates from Cryptosporidium positive samples ob- tained from the amplification of 18S rRNA and/or COWP genes were genotyped by the sequence analysis of the actin gene. DNA extraction and PCR amplification The only Cryptosporidium genotype, namely skunk genotype (identified from sequences of the actin gene), was detected in 9 out of 14 actin positive raccoons. Although the obtained sequences were not of the same length, they were identical to the isolate obtained from Eastern fox squirrel (KT027546) (Fig. 3). Isolates from the remaining actin posi- tive raccoons yielded sequences of insufficient quality to include in the analyses. Statistical analysis wetland habitats, especially bog and swamp districts. This area demonstrates a very opportune habitat for raccoon—its population density in the area is twice as much as that in the middle part of Germany (6–8 individuals per 1 km2) (Fischer et al. 2016; Hohmann 1998; Köhnemann and Michler 2008; Muschik et al. 2011). Prevalence was expressed as a ratio of a number of PCR positive samples for Cryptosporidium spp. 18S rRNA or/and COWP genes and the total number of examined samples. Contingency tables were used to compare prevalence between the sex of the raccoons and the different sampling areas using the chi-square test; p < 0.05 was considered statistically sig- nificant (STATISTICA®12). Frozen carcasses were delivered to the laboratory of Department of Parasitology UWr and dissected. Collected fecal samples were kept at −20 °C for further analysis. Each animal was used for only one fecal specimen. Nucleotide sequencing Products were sequenced in both directions on Applied Biosystems ABI PRISM 3100-Avant Sequencer (SEQme, the Czech Republic). The nucleotide sequences obtained in this study were edited using DNA Baser Sequence Assembly soft- ware (Heracle BioSoft SRL Romania) then aligned with refer- ence sequences of Cryptosporidium spp. and E. bieneusi avail- able in GenBank. Phylogenetic analyses were performed using MEGA6 software (Tamura et al. 2013). Trees were inferred by neighbor joining (NJ) method based on the Kimura 2- parameter distance model; bootstrapping was performed using 1000 replicates. Sequences from this study have been deposited in GenBank database under the accession numbers KX639723 and KX621279. Study areas and collection of material Among them, Cryptosporidium hominis and Cryptosporidium parvum are responsible for over 90 % of human cryptosporidiosis cases (Rossle and Latif 2013). Wildlivingmammals,includingcarnivores,havebeendescribed as reservoirs of several Cryptosporidium species, especially C. parvum and Cryptosporidium muris (Fayer et al. 2010; Ryan and Hijjawi 2015) but also Cryptosporidium meleagridis, Cryptosporidium ubiquitum, Cryptosporidium felis, Cryptosporidium canis, Cryptosporidium cuniculus, Cryptosporidiumskunkgenotype,chipmunkgenotype,andother novel genotypes (Chalmers et al. 2009, 2011; Elwin et al. 2012; Li et al. 2014; Plutzer and Karanis 2009; Robinson et al. 2008; Xiao 2010; Xiao et al. 1999). Fig. 1 The map of Poland and Germany showing geographical origin (black dots) of wild raccoons obtained for this study Parasitol Res (2016) 115:4535–4541 4537 Discussion In this study, we have molecularly identified the presence of E. bieneusi NCF2 genotype and Cryptosporidium skunk genotype in the Polish-German population of introduced raccoons. To our knowledge, this has been the first report on these groups of parasites in raccoons colonizing Europe. By now, literature data concerning this issue is based on the Parasitol Res (2016) 115:4535–4541 4538 Fig. 2 The phylogenetic relationship of Enterocytozoon bieneusi genotypes identified in the present study (indicated by solid circles) and others as inferred by a neighbor-joining analysis of ITS sequences. Bootstrapping was performed using 1000 replicates, and the values below 50 % are not shown. The E. bieneusi group terminology is based on the works of Guo et al. (2014), Zhao et al. (2015), and Xu et al. (2016) reports from the area of North America, where raccoon repre- sents the native fauna. Also there are no available studies on the parasites in the population of raccoons introduced to Japan, but there are surveys on the raccoons introduced to Europe and Japan that concern some other bacterial and viral pathogens as well as parasites of protozoan and helminth species (Bauer 2013; Beltrán-Beck et al. 2012; Popiołek et al. 2011). molecular studies conducted by Sulaiman et al. (2003) and Guo et al. (2014) revealed the presence of human pathogenic genotypes i.e., Peru 11, EbpC, WL15, and D genotypes. Additionally, the following raccoon-adapted genotypes were identified WL1-3, WL13, WL15-17, WL24, WL26, and WW6 (Guo et al. 2014; Sulaiman et al. 2003). Cryptosporidium infection has been reported in raccoons (Carlson and Nielsen 1982; Snyder 1988; Zhou et al. 2004; Ziegler et al. 2007). Using indirect immunofluorescent assay, Snyder (1988) found that 13 % of wild raccoons were infect- ed. By using molecular tools, C. parvum infection was found in 1 of 5 (20 %) raccoons from wildlife parks in New York State (Perz and Le Blancq 2001), and 2 of 51 (3.9 %) raccoons were Cryptosporidium skunk genotype positive in wetlands adjacent to the Chesapeake Bay (Zhou et al. 2004). Cryptosporidium skunk genotype and C. ubiquitum were identified in the raccoons and storm water from a New York Our survey has shown that 2 out of 49 fecal samples of raccoons were E. bieneusi positive. During the phylogeny analysis, the detected genotype NCF2, clustered with other genotypes of group 1, suggesting its zoonotic potential. This newly identified E. Fig. 2 The phylogenetic relationship of Enterocytozoon bieneusi genotypes identified in the present study (indicated by solid circles) and others as inferred by a neighbor-joining analysis of ITS sequences. Bootstrapping was performed using 1000 replicates, and the values below 50 % are not shown. The E. bieneusi group terminology is based on the works of Guo et al. (2014), Zhao et al. (2015), and Xu et al. (2016) Parasitol Res (2016) 115:4535–4541 Parasitol Res (2016) 115:4535–4541 Fig. 3 The phylogenetic relationship of Cryptosporidium sp. skunk genotype identified in present study (indicated by solid circles) and others as inferred by a neighbor-joining analysis of the actin gene sequences. Bootstrapping was performed using 1000 replicates, and the values below 50 % are not shown Fig. 3 The phylogenetic relationship of Cryptosporidium sp. skunk genotype identified in present study (indicated by solid circles) and others as inferred by a neighbor-joining analysis of the actin gene sequences. Bootstrapping was performed using 1000 replicates, and the values below 50 % are not shown Fig. 3 The phylogenetic relationship of Cryptosporidium sp. skunk genotype identified in present study (indicated by solid circles) and others as inferred by a neighbor-joining analysis of the actin gene sequences. watershed area (Feng et al. 2007). The Cryptosporidium skunk genotype was detected also in Eastern gray, American red and fox squirrels, river otters, and striped skunks from the area of the USA (Feng et al. 2007; Stenger et al. 2015; Ziegler et al. 2007). The phylogenetic analysis showed that the isolates obtained in the present study were organized in skunk genotype clade containing isolates previously identified among squirrels and skunk. Although uncommon, human infections with skunk genotype have also been reported (Davies et al. 2009; Elwin et al. 2012; Robinson et al. 2008). The wildlife origin of genotypes is increasingly recognized as an important environmental source of Cryptosporidium infec- tion in humans, and shifting boundaries between wildlife and humans could result in the emergence of novel pathogens (Stenger et al. 2015). Considering that more than 75 % of human cases of cryptosporidiosis are determined to have the zoonotic origin and are related to wildlife and domestic animals, studies concerning a wide range of wild living hosts seem to be reasonable. watershed area (Feng et al. 2007). The Cryptosporidium skunk genotype was detected also in Eastern gray, American red and fox squirrels, river otters, and striped skunks from the area of the USA (Feng et al. 2007; Stenger et al. 2015; Ziegler et al. 2007). The phylogenetic analysis showed that the isolates obtained in the present study were organized in skunk genotype clade containing isolates previously identified among squirrels and skunk. Although uncommon, human infections with skunk genotype have also been reported (Davies et al. 2009; Elwin et al. 2012; Robinson et al. 2008). Parasitol Res (2016) 115:4535–4541 The wildlife origin of genotypes is increasingly recognized as an important environmental source of Cryptosporidium infec- tion in humans, and shifting boundaries between wildlife and humans could result in the emergence of novel pathogens (Stenger et al. 2015). Considering that more than 75 % of human cases of cryptosporidiosis are determined to have the zoonotic origin and are related to wildlife and domestic animals, studies concerning a wide range of wild living hosts seem to be reasonable. raccoon dog origin which is another species introduced from the area of East Asia. Cryptosporidium skunk genotype has been detected for the first time in the examined areas suggest- ing a North American origin. Thus, our results have shown that introduced raccoons could be considered as a potential source of human pathogenic Cryptosporidium skunk geno- type and potentially pathogenic E. bieneusi NCF2 genotype. Acknowledgments We are grateful to Dr. M. Krappe (Kratzeburg, Germany) and the staff of BWarta Mouth^ National Park for their help in collecting raccoon samples. Fecal samples of raccoons used in the study have been collected within the National Science Centre, Poland, project no. 2014/15/B/NZ8/00261. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appro- priate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Despite the fact that the raccoon as an alien species has been present in Europe for 80 years, the knowledge about its parasitofauna is still insufficient, especially concerning microparasites. As our results have shown, raccoon as an introduced species lost many of its originally detected Cryptosporidium spp. and E. bieneusi genotypes. On the other hand, it encountered the E. bieneusi genotype which has not been identified either in Europe or in the North America. We suppose that E. bieneusi NCF2 genotype might be of the Discussion bieneusi NCF2 genotype in European raccoons has so far been present only in farmed foxes and raccoon dogs from China (Xu et al. 2016; Zhang et al. 2016). The studies undertaken by Guo et al. (2014) showed that the infection rate of E. bieneusi in raccoons from a New York watershed area was as high as 82 % (18/22). The 4539 References Bartoszewicz M, Okarma H (2007) Szopy nad Wartą. 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Dissertation, University of Götingen Snyder DE (1988) Indirect immunofluorescent detection of oocysts of Cryptosporidium parvum in the feces of naturally infected raccoons (Procyon lotor). J Parasitol 74:1050–1052 Hohmann U, Gerhard R, Kasper M (2000) Home range size of adult raccoons (Procyon lotor) in Germany. Z Säugetierkunde 65: 124–127 Spano F, Putignani L, McLauchlin J, Casemore DP, Crisanti A (1997) PCR-RFLP analysis of the Cryptosporidium oocyst wall protein (COWP) gene discriminates between C. wrairi and C. parvum, and between C. parvum isolates of human and animal origin. FEMS Microbiol Lett 150:207–217 Hohmann U, Voigt S, Andreas U (2001) Quo Vadis raccoon? New visi- tors in our backyards—on the urbanization of an allochthone carni- vore in Germany. In: Gottschalk E, Barkow A, Mühlenberg M, Settele J (eds) Naturschutz und Verhalten, vol 2. UFZ-Berichte, Lepzig, pp 143–148 Stenger BL, Clark ME, Kváč M, Khan E, Giddings CW, Prediger J, McEvoy JM (2015) North American tree squirrels with overlapping ranges host different Cryptosporidium species and genotypes. Infect Genet Evol 36:287–293 Karim MR, Wang R, Dong H, Zhang L, Lib J, Zhanga S, Rumec FI, Qia M, Jiana F, Sund M, Yange G, Zouf F, Ninga C, Xiao L (2014) Genetic polymorphism and zoonotic potential of Enterocytozoon bieneusi from nonhuman primates in China. Appl Environ Microbiol 80:1893–1898 Stubbe M (1999) Procyon lotor (Linnaeus, 1758). In: Jones AJ, Amori G, Bogdanowicz W, Krystufek B, Reijnders P, Spitzenberger F, Stubbe M, Thissen JBM, Vohohralik V, Zima J (eds) The atlas of European mammals. Mitchell Academic Press, London, pp 326–327 Parasitol Res (2016) 115:4535–4541 4541 Sulaiman IM, Lal AA, Xiao L (2002) Molecular phylogeny and evolu- tionary relationships of Cryptosporidium parasites at the actin locus. 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Mol Biol Evol 30:2725–2729 Zhao W, Zhang W, Yang F, Zhang L, Wang R, Cao J, Shen J, Liu A (2015) Enterocytozoon bieneusi in dairy cattle in the Northeast of China: genetic diversity of ITS gene and evaluation of zoonotic transmission potential. J Eukaryot Microbiol 62:553–560 Torchin ME, Mitchell CE (2004) Parasites, pathogens and invasions by plants and animals. Front Ecol Environ 2:183–190 Torchin ME, Lafferty KD, Dobson AP, McKenzie VJ, Kuris AM (2003) Introduced species and their missing parasites. Nature 421:628–630 Zhou L, Fayer R, Trout JM, Ryan UM, Schaefer FW, Xiao L (2004) Genotypes of Cryptosporidium species infecting fur-bearing mam- mals differ from those of species infecting humans. Appl Environ Microbiol 70:7574–7577 Torchin ME, Lafferty KD, Dobson AP, McKenzie VJ, Kuris AM (2003) Introduced species and their missing parasites. Nature 421:628–630 Xiao L (2010) Molecular epidemiology of cryptosporidiosis: an update. 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The unexpected importance of the fifth digit during stone tool production
Scientific reports
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OPEN Alastair J. M. Key1*, Christopher J. Dunmore1 & Mary W. Marzke2 Unique anatomical features of the human hand facilitate our ability to proficiently and forcefully perform precision grips and in-hand manipulation of objects. Extensive research has been conducted into the role of digits one to three during these manual behaviours, and the origin of the highly derived first digit anatomy that facilitates these capabilities. Stone tool production has long been thought a key influence in this regard. Despite previous research stressing the unique derived morphology of the human fifth digit little work has investigated why humans alone display these features. Here we examine the recruitment frequency, loading magnitude, and loading distribution of all digits on the non-dominant hand of skilled flintknappers during four technologically distinct types of Lower Palaeolithic stone tool production. Our data reveal the fifth digit to be heavily and frequently recruited during all studied behaviours. It occasionally incurred pressures, and was used in frequencies, greater or equal to those of the thumb, and frequently the same or greater than those of the index finger. The fifth digit therefore appears key to >2 million years of stone tool production activities, a behaviour that likely contributed to the derived anatomy observed in the modern human fifth ray. Forceful precision grips and proficient in-hand manipulation underpin many of the behaviours considered unique to modern humans and our hominin ancestors1–4. While the ability of other primates to manipulate objects with force and/or precision is increasingly being recognised5–9, available evidence still indicates that mod- ern humans more frequently or easily generate greater forces and dexterity during these behaviours10,11. Due to the human thumb’s robust skeletal morphology12,13, unique muscular anatomy14 and representation as a “defin- ing” human feature15, it has been the focus of research into the evolution of hominin manual capabilities16–21. This has often been to the exclusion of the other four digits, in particular the fourth and fifth, whose derived traits are not as well explored and explained. p p Digits two and three have been investigated in multiple important works, partly due to their frequent employ- ment in grips used to wield hammerstones and flaked stone tools2,22,23. www.nature.com/scientificreports www.nature.com/scientificreports Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w 1School of Anthropology and Conservation, University of Kent, Canterbury, Kent, UK. 2School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA. *email: a.j.m.key@kent.ac.uk OPEN Knappers five (A) and four (B) during their LAH reduction sequence. The video stills are taken prior to flakes being removed with hard hammer and soft hammer percussors. Although not visible in the video stills, note the fifth digit’s location beneath the point of impact (indicated with a star) (C) (see also: Supplementary Information Video 1). ulno-palmar aspect of the fifth metacarpal shaft in human hands, suggesting frequent recruitment of this muscle, likely during the opposition of the fifth finger to the thumb34. iti Experimental research during the 1980s and 90s provided insight into the evolution of these uniquely human traits. Marzke and Shackley22 highlighted that the fifth digit was frequently recruited to control stone cores during flake removals and to adjust the flake platform’s angle relative to the hammerstone. Further, the fourth and fifth digits were demonstrated to aid the stabilisation and securing of stone tools and antler billets during their use. More recent studies emphasised the variable, but at times vital, stabilising and manipulative role of the fifth digit during stone tool production and use19,23,32. Other studies of stone tool related activities24 and carrying35 have identified more limited roles for the fourth and fifth digits when compared to the radial digits. However, electro- myographic studies of muscles serving the fifth digit (flexor and abductor digiti minimi muscles) during stone tool production revealed their recruitment during hammerstone strikes32. These muscles were particularly heavily recruited on the non-dominant, core holding hand, where the fifth digit was argued to play a critical role in stabi- lizing the core against hammerstone impact forces32 (Fig. 1). Since the early studies by Marzke and colleagues22,32, there has been little research specifically concerning the evolutionary history of the hominin fifth digit, its unique anatomy36,37, or its role in gripping and in-hand manipulation during stone tool related behaviours38. In turn, our understanding of the evolution of ulnar (digits 4–5) hand morphology in fossil hominins and modern humans is highly limited, particularly when compared to the thumb.it g y p y p Here, we approach the question of why modern humans display derived fifth ray anatomy and increased joint mobility from an experimental perspective. We examine the pressure levels experienced by nine expert knappers across their non-dominant hand during four technologically distinct Lower Palaeolithic stone tool production behaviours (Fig. 1). OPEN To date, analysis of digits four and five is often, but not always24, limited to examining their length relative to the first digit17,25.hitl ti The human fifth digit is relatively independent, unlike the fourth which during flexion and extension can also unintentionally recruit the third and fifth26,27. This independence is in part due to the saddle- shaped articulation for the fifth metacarpal base on the hamate, which allows the fifth metacarpal to flex and rotate at the same time, and better oppose the thumb and the rest of the hand4,28. This morphology also provides for a greater range of movement than in the other non-pollical metacarpals29,30. Movement of the fifth carpometacarpal (CMc) joint in this manner allows for a greater degree of curvature in the transverse metacarpal arch of the human palm relative to other apes29,31. In other great apes the fifth CMc joint is not sellar, and the hook of the hamate buttresses the metacarpal, limiting abduction from the midline of the hand as well as axial rotation, movements that permit opposition of the fifth digit with the first28. Combined with ulnar expansion of the palmar aspect of the fifth metacarpal head the unique morphology of humans at this joint, allows for effective opposition of the fifth digit to the thumb28.iti Opposition of the fifth finger to the rest of the hand, or a grasped object, is crucial to in-hand manipula- tion, the forceful cradle precision grip required to produce and use flaked stone tools2,32, and to manipulating cylindrical objects in a power grip33. The human fifth metacarpal is also unique in being second only to the first metacarpal in robusticity33, reflecting its ability to sustain large loads. In addition, a site-specific concentration of trabecular bone volume has been found beneath the opponens digiti minimi muscle insertion site, along the School of Anthropology and Conservation, University of Kent, Canterbury, Kent, UK. 2School of Human Evolution nd Social Change, Arizona State University, Tempe, AZ, USA. *email: a.j.m.key@kent.ac.uk Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w www.nature.com/scientificreports/ www.nature.com/scientificreports/ www.nature.com/scientificreports ificreports/ Figure 1. Knappers five (A) and four (B) during their LAH reduction sequence. The video stills are taken prior to flakes being removed with hard hammer and soft hammer percussors. Although not visible in the video stills, note the fifth digit’s location beneath the point of impact (indicated with a star) (C) (see also: Supplementary Information Video 1). Figure 1. Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w OPEN Through analyses of pressure distribution, magnitude, and loading frequencies, we investigate the role of the fifth digit during stone tool production, the biomechanical stress it experiences, and how this relates to the type of stone tool being produced. Further, we compare these data directly with the other non-pollical digits to explore the comparative evolutionary history of the radial and ulnar sides of the hominin hand within a Lower Palaeolithic behavioural context. Results P In comparison, the distal phalanx of digits three and four were not heavily loaded during the reduction behaviours. Nor were the proximal phalanges of digits one, three, four or five. Pressure magnitude. Maximum recorded pressures are considerable, frequently ranging between 150– 250 kPa (Supplementary Information Table 1). Across all extracted peak values, however, pressures exceed- ing 100 kPa were relatively rare (Supplementary Information Fig. 1; Supplementary Information Tables 6–9). Typically, 30–50% of pressure values for all sensors in all reductions ranged between 20–40 kPa (Supplementary Tables 12–15.f Beyond these values there are differences between sensors and reduction types. Consistent with the pressure distribution results, DP1, DP2, DP5, IP3, PP2, and PP3 returned pressure values of 40–60 kPa 20–30% of the time, while DP3, DP4, IP2, PP1, PP4, and PP5 displayed these values < 20% of the time (often <10%). The sen- sors that frequently (30–50%) returned values < 20 kPa were most often proximally located (PP1, PP3, PP4 and PP5), but also include IP2 and DP3. Only DP1, DP2, and DP5 repeatedly returned >20% of their values as being 60 kPa or greater across all four reductions. g Pressures above 100 kPa were rare. In total, there were 89, 112, 255 and 90 values > 100 kPa during the OF, EAH, LAH and PP behaviours, respectively. Differences between reduction types were not, however, propor- tionate to the number of mass removal events in each. Indeed, proportionately, PP behaviours more frequently recorded values >100 kPa. Of these, the majority of values were recorded on DP1 during the OF, EAH and PP behaviours, while DP1, DP2 and DP5 all displayed ~50 of these values during the LAH reduction. Mean peak pressure values accord with the range data already described, with all sensors ranging between 25–65 kPa, dependent on the type of reduction undertaken and the position of the sensor on the hand (Fig. 3). Recruitment frequency. Recruitment frequency data identify DP1, DP2, PP2, IP3, and DP5 as the five most recurrently loaded sensors (Table 1). They experience loading during 60–90% of all analysed manual behaviours in all tool production types. The remaining sensors display recruitment frequencies ranging between 13–63%, with the proximal phalanges of digits one, three, four and five typically being the lowest. In three out of four behaviours, DP5 is the most frequently loaded sensor. The only exception is the Oldowan reduction, where the thumb is recruited most often. Results P Pressure distribution. Post-hoc Dunn’s tests between the twelve sensors during the four reduction types are presented in the accompanying Supplementary Information Tables 2–5. These statistical comparisons highlighted significant differences in pressure between sensors distributed across the hand during all reduction behaviours (Figs 1 and 2). On almost all occasions, the sensor on the distal phalanx of the thumb (DP1) experienced signif- icantly greater relative pressure than all other sensors during the four tool production strategies (p = <0.0001). The only two exceptions were during the late Acheulean handaxe (LAH) sequence, where the sensors on the distal phalanx of the second (DP2) and fifth (DP5) digit, recorded no significant pressure differences relative to DP1 (Supplementary Information Table 4). pp y DP2 and DP5 sensors are the next most heavily recruited across all four behaviours (Supplementary Information Tables 2–5). For both sensors the LAH and platform preparation (PP) data returned the greatest number of significant differences, each displaying substantially greater pressure than nine and seven other sen- sors, respectively. The other two reductions (Oldowan flake [OF] and early Acheulean handaxe [EAH]) returned six significant differences for these two sensors, thus still indicating their heavy recruitment. No significant differ- ences were observed between DP2 and DP5 across all four comparisons, indicating their similar pressure levels. Results are less consistent across the four behaviours for the remaining sensors (Supplementary Information Tables 2–5). Interestingly, sensors on the intermediate phalanges of digits two and three (IP2, IP3) and the prox- imal phalanx of digit two (PP2) also experienced heavy loading, returning between three and six significantly www.nature.com/scientificreports/ Figure 2. Colour maps detailing the distribution of mean pressure data (top row) and frequency of recruitment data (bottom row) during the four stone tool production behaviours. Figure 2. Colour maps detailing the distribution of mean pressure data (top row) and frequency of recruitment data (bottom row) during the four stone tool production behaviours. greater results relative to the other sensors, in each of the four reduction types. Although relative to DP1, DP2 and DP5 these values were usually reduced. In comparison, the distal phalanx of digits three and four were not heavily loaded during the reduction behaviours. Nor were the proximal phalanges of digits one, three, four or five. greater results relative to the other sensors, in each of the four reduction types. Although relative to DP1, DP2 and DP5 these values were usually reduced. Results P It is notable that all sensors, bar DP1 and IP3, display increased recruitment fre- quencies during the LAH and PP behaviours, relative to the Oldowan and EAH sequences. This is particularly clear for DP2 and DP5, where recruitment frequencies are as high as 90% and 88% during the PP behaviours, respectively (Table 1). Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w Discussion h d We have recorded the distribution, magnitude, and frequency of pressures acting on the non-dominant hand of skilled flintknappers during multiple stone tool production procedures. Our results reveal a unique radio-ulnar loading pattern observed in no other Plio-Pleistocene manual behaviours analysed to date. The uniqueness of this pattern lies in the heavy recruitment of the fifth finger, alongside that of the thumb and index finger. These data help explain derived manual anatomy in fossil hominins and modern humans.it Our data indicate substantial loading on distal aspects of the thumb, second and fifth digits, and although more limited, also proximally on the second and third digits. Other phalanges returned lower loading levels. This distribution is consistent across records of mean and maximum pressure magnitude and loading frequency (Fig. 2). Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w www.nature.com/scientificreports/ Figure 3. Boxplots displaying pressures experienced across the twelve sensors examined here. Data from the Oldowan (A), Early Acheulean Handaxe (B), Late Acheulean Handaxe (C) and Platform Preparation (D) reduction behaviours are depicted. Blue plots correspond to sensors on distal phalanges, while pink and red are sensors on intermediate and proximal phalanges, respectively. ‘D’, ‘I’ and ‘P’ correspond to the distal phalanx, intermediate phalanx and proximal phalanx sensors, respectively. Sensors numbers correspond to the respective digit. Figure 3. Boxplots displaying pressures experienced across the twelve sensors examined here. Data from the Oldowan (A), Early Acheulean Handaxe (B), Late Acheulean Handaxe (C) and Platform Preparation (D) reduction behaviours are depicted. Blue plots correspond to sensors on distal phalanges, while pink and red are sensors on intermediate and proximal phalanges, respectively. ‘D’, ‘I’ and ‘P’ correspond to the distal phalanx, intermediate phalanx and proximal phalanx sensors, respectively. Sensors numbers correspond to the respective digit. Discussion h d Sensor PD1 PP1 PD2 IP2 PP2 PD3 IP3 PP3 PD4 PP4 PD5 PP5 OF (n = 523) Instances 377 160 334 169 340 102 335 131 115 70 331 145 Frequency (%) 78 31 64 32 65 20 64 25 22 13 63 28 EAH (n = 789) Instances 499 214 524 263 532 168 496 219 154 151 555 242 Frequency (%) 69 27 66 33 67 21 63 28 20 19 70 31 LAH (n = 1251) Instances 761 432 909 666 920 438 669 582 413 481 962 644 Frequency (%) 63 35 73 53 74 35 53 47 33 38 77 51 PP (n = 271) Instances 194 155 242 171 229 137 162 130 104 121 238 140 Frequency (%) 75 57 90 63 85 51 60 48 39 45 88 52 Table 1. Digit recruitment frequencies expressed as a percentage relative to the total number of manual behaviours recorded. Table 1. Digit recruitment frequencies expressed as a percentage relative to the total number of manual behaviours recorded. Previous studies of manual loading during Plio-Pleistocene activities have either not investigated the fifth digit18,19,39,40, or identified reduced loading relative to digits one-to-three24,35. Our results uniquely demonstrate the fifth digit to be heavily and frequently loaded during stone tool production; being equal second in terms of loading magnitude, and in three out of four reduction types, the most frequently recruited. It therefore appears that the fifth digit could have experienced selective pressure in response to these high demands, subsequent to the onset of habitual freehand stone tool production after ~2.6 Mya.hii t The significantly greater pressures experienced by the thumb, relative to digits two-to-five, during the OF, EAH and PP behavioural sequences is consistent with previous experimental research examining loading during stone tool production in both the non-dominant and dominant hand19,24. Combined, these three studies support the hypothesis that the production of flaked stone tools likely contributed to the robust first digit skeletal and musculature anatomy observed in the hominin lineage3,4.it High loading on the fifth digit is not necessarily surprising given previous grip analyses and electromyo- graphic studies of stone tool production19,22,32. Nevertheless, it is surprising that the magnitude and frequency of this loading is greater or equal to that of the thumb in some instances and similar to that of the second digit. Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w www.nature.com/scientificreports/ www.nature.com/scientificreports/ the dominant arm41. As percussors strike a core supported in this way a proportion of the impact force propagates through the stone and removes the flake. This force will disperse through all manual elements in contact with the core proportionate to hammerstone strike direction, core morphology and manual element distribution across the core’s surface. Understandably, the fifth digit experiences a high proportion of this force due to its positioning in line with the point of impact (Fig. 1). High-speed videos (800 f/s) in Supplementary Information Video 1 high- light the dispersion of force through the fifth digit. It is evident that during both hard hammer and soft hammer flake detachments the fifth digit is directly beneath the point of impact, with reaction forces extending the digit dorsally. To prevent hyperextension and the loss of the flake by not being supported, it is essential for the fifth digit to resist these forces, in turn resulting in the high pressures recorded here. Additionally, the essential role of the thumb in securing the core into to the hand can also be observed.it g High loading on the distal fifth digit, particularly during platform preparation events and when securing the core against the leg, may also result from its ability to oppose the thumb when creating a secure inclusive grip around a core3. Certainly, as the most ulnarly located digit, when abducted it extends the reach of the hand and can directly oppose the thumb across the midpoint of the palm. Increased pressure values on the fifth digit dur- ing the production of late Acheulean handaxes (LAH, PP), in particular, can be attributed to their low thickness to width ratios, smaller size, increased shaping, and greater requirement to remove long, elongated ‘thinning’ flakes38,42,43.h l The magnitude of loads experienced by digits on the non-dominant hand have been demonstrated to be considerable. Indeed, the pressure ranges recorded here are broadly equal to those observed on the dominant hand of knappers18,24,39, a note of importance given recent statements to the contrary. The upper limits of 150–250 kPa detailed here are consistent with pressures recorded from the dominant hand of the same individuals39 and non-skilled individuals24 during flake tool production.hf gl p There do, however, appear to be differences in the frequency with which high loads are experienced on indi- vidual phalanges (sensors) between the non-dominant and dominant hand. www.nature.com/scientificreports/ Certainly, here pressures above ~100 kPa are infrequent and account for a low proportion of data values (Supplementary Information Tables 6–9). In part, this may reflect differences in experimental design as all mass removal events, no matter how small, were recorded in the present study. Additionally, previous dominant hand research has typically utilized stop-and-start knapping sequences that are less typical of natural knapping behaviours18,24,39. We do, however, also consider this to reflect important recruitment pattern differences between the dominant and non-dominant hand during stone tool production. Certainly, in addition to their non-dominant hand knappers frequently support cores using their leg and palm, consequently providing an additional surface to distribute forces. Moreover, cores typically have larger surface areas that, as identified here, more frequently recruit ulnarly located digits and proximally located phalanges during their manipulation. Dominant hand pressure distribution appears to focus solely on digits one-to-three24. When compared at a whole hand level (i.e. cumulative peak pressures from 12 identically located sensors), however, the non-dominant hand experiences cumulative loading magnitudes roughly four times as large as the dominant hand24,38. g Loading frequencies on the non-dominant hand broadly mirror the distribution of variation in pressure mag- nitude, including the heavy recruitment of the fifth distal phalanx. It is, perhaps, not surprising that these metrics of manual recruitment are related, however these metrics provide details essential for understanding the derived traits observed in the human hand24. Our frequency data broadly corroborates previous findings that the first digit on the non-dominant hand is recruited more often than the second or third during stone tool production19.hit gt g p The data presented here underlines the important role played by the fifth digit during stone tool production and helps explain the derived anatomy observed in the modern human fifth digit. It is interesting that many of distinctively human features of the fifth ray are first seen among current hominin fossils in Homo naledi44, dated to 236–325 ka45, and in Neandertals36. Its heavy and frequent recruitment, which is occasionally greater or equal to the thumb, and the same or greater than the index finger, hints at the complex array of recruitment patterns likely experienced by the hominin hand during the Plio-Pleistocene. To date, investigations into the derived anat- omy of the modern human hand have, understandably, focused on lithic-related behaviours. www.nature.com/scientificreports/ However, numerous manual activities likely undertaken by early hominins, and perhaps essential to their survival and reproductive success, have not yet been examined (e.g. digging stick and spear use, manipulating food, grooming). While work has started to address this deficit7,24,35,46, further studies investigating such behaviours are necessary if we are to fully understand the evolutionary history of the hominin hand. Certainly, as highlighted here, the demands placed on early hominin hands were likely far more diverse than current evidence indicates. Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w Discussion h d As previously detailed19,22,32, the fifth digit is often located directly beneath or very close to the point of impact when flakes are removed via freehand percussion (Fig. 1). This allows flakes to be supported during removals and their platforms to be directed towards the knapper’s body and, importantly, their dominant hand; in turn, allowing per- cussors to accurately and repeatedly strike flake platforms using free-flowing and comfortable arching motions by Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w Material and Methods Stone tool production procedures. Pressure values were recorded from the non-dominant hand of participants using a wireless Novel Pliance® pressure system comprising of ten 17 × 17 mm sensors and two 10 × 10 mm sensors (Figs 1 and 3). Sensors were attached to the palmar side of the distal phalanges of digits one- five, the intermediate phalanges of digits two and three, and the proximal phalanges of digits one-five. The two 10 × 10 mm sensors were secured to the distal and proximal phalanges of the fifth digit. Double-sided tape, Velcro straps and finger cots secured each sensor. Sensors were ‘zeroed out’ prior to data collection and all pressure data were recorded at a rate of 50 Hz.l Nine experienced flintknappers took part in the study (all were capable of consistently producing late Lower Palaeolithic handaxes when required). Each was asked to undertake three stone tool production sequences; Oldowan flake and core production, early Acheulean handaxe, and late Acheulean handaxe production. Hard hammer percussion was used in all three sequences. Soft hammer percussion and platform preparation events were only used during the LAH reduction. All tool production events were recorded using a HD video camera. Knappers were allowed to produce tools at their own pace and using their own hammerstones and billets. Ethical approval was granted by the School of Anthropology and Conservation Ethics Committee (University of Kent; www.nature.com/scientificreports/ Ref. Ares 19065). All individuals gave informed consent and experiments were conducted in accordance with industry (AAPA) guidelines. Ref. Ares 19065). All individuals gave informed consent and experiments were conducted in accordance with industry (AAPA) guidelines. Pressure data. Sensors collected data throughout each reduction sequence, however, pressure data extracted for analysis only refers to manual behaviours that removed mass from the core. Within Oldowan flake and EAH reductions this only referred to attempted flake detachments, while the LAH sequence also included PP events (see also38). Prior to starting a reduction knappers forcefully pinched between the thumb and index finger. This created a point of known manual pressure that was easily identifiable in both the pressure data and the video recording. Subsequently, behaviours observed in the video could be matched with their accompanying pressure output and it was possible to identify individual mass removal events within the pressure data stream. y Each sensor’s peak pressure during each mass removal event was extracted for analysis. Material and Methods During attempted flake detachments, peak pressures were extracted from two second intervals (one second prior to and after the point of impact). Platform preparation events were variable in duration and peak pressures were identified as the highest values recorded from the start to end of these behaviours. Digits are intermittently recruited when secur- ing stone cores19, and in turn, pressure values of 0 kPa were at times recorded by sensors during mass removal events. To avoid examining loading as a combined function of peak pressures and the frequency of digit recruit- ment, pressure records of zero were excluded from analyses (other than those examining loading frequency). In turn, statistical comparisons of distribution and magnitude focus solely on peak pressure differences between digits when they are actively recruited to manipulate a core. g y y p Data from all participants were combined for each of the statistical analyses performed. Participant seven’s distal sensor on the first digit broke during data collection. All analyses for this sensor are, therefore, derived from the remaining eight knappers and are adjusted accordingly. Supplementary Tables 1–15 reveal that mean, stand- ard deviation, and range pressure values remain stable across the other 11 sensors with and without participant seven; hence the continued inclusion of their data in the other sensors. Statistical analysis. Previous investigations of manual loading during stone tool related behaviours have focused on pressure distribution18, magnitude38,39, magnitude and distribution28, force magnitude40 or force dis- tribution and digit recruitment frequency19. Here, we conduct analyses of pressure distribution, magnitude and frequency. Each is analysed independently for the Oldowan flake, EAH and LAH reduction sequences. The LAH sequence was separated further into flake removals (LAH) and platform preparation events (PP), in turn creating four stone tool behaviours. Pressure distribution. To examine how loading varies across the non-dominant hand peak pressure records were compared between sensors. Shapiro-Wilk tests confirmed that all 48 sets of peak pressure data sets (twelve sensors across four reduction types) were not normally distributed (p = < 0.05). In turn, Kruskal-Wallis and post-hoc Dunn’s tests were used for these comparisons. Relative pressure measures were used to investigate load- ing distribution throughout the hand; absolute pressures could have led to erroneous results if knappers with particularly high or low values had individually favoured a particular finger. Relative data were calculated by dividing each knapper’s pressures by their average per knapping behaviour. Material and Methods Participant seven was not included in this analysis as the loss of one sensor would create non-comparable averages for the other sensors on this hand. Significance was assumed at p < 0.05 subsequent to a Bonferroni correction. Pressure magnitude. Beyond basic descriptive data for each sensor during each reduction type (Supplementary Information Table 1), magnitude of peak pressure was examined between sensors relative to the frequency that specific loading values were recruited. Specifically, the pressure range recorded during this exper- iment (0–252.5 kPa) were divided into thirteen 20 kPa segments (e.g. 0–20, 20.1–40, 40.1–60) and the percentage of peak pressure records for each sensor falling into these values were recorded. Recruitment frequency. Recruitment frequency was recorded as the percentage of times that a sensor experienced a load during mass removal events relative to the total number of flake detachments and platform preparation events that were undertaken during that reduction. For example, the total number of flake removals attempted across the nine participant’s Oldowan core reductions was 523. Of these flake removal events, the distal sensor on the thumb registered a load >0 kPa 377 times. In turn, this sensor had a recruitment frequency of 72%. This calculation was repeated for all twelve sensors in each of the four reduction behaviours. Data availabilityh y The data supporting this article have been uploaded as electronic supplementary material. Received: 27 June 2019; Accepted: 31 October 2019; Published: xx xx xxxx Received: 27 June 2019; Accepted: 31 October 2019; Published: xx xx xxxx Received: 27 June 2019; Accepted: 31 October 2019; Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w 5. Pouydebat, E., Gorce, P., Coppens, Y. & Bels, V. Biomechanical study of grasping according to the volume of the object: human versus non-human primates. J. of Biomech. 42(3), 266–272 (2009). g p gy 4. Kivell, T. L. Evidence in hand: recent discoveries and the early evolution of human manual manipulation. Phil. Trans. R. Soc. B. 370, 20140346 (2015). p J ( y ) 2. Marzke, M. W. Precision grips, hand morphology, and tools. Am. J. Phys. Anth. 102, 91–110 (1997). 3. Marzke, M. W. Tool making, hand morphology and fossil hominins. Phil. Trans. R. Soc. B. 368, 20120422 (2013). p J f ( ), ( ) 6. Pouydebat, E., Reghem, E., Borel, A. & Gorce, P. Diversity of grip in adults and young humans and chimpanzees (Pantroglodytes) Behav. Brain. Res 218(1), 21–28 (2011). References Faisal, A., Stout, D., Apel, J. & Bradley, B. The manipulative complexity of Lower Palaeolithic stone toolmaking. PloS One 5, e13718 (2010).h 44. Kivell, T. L. et al. The hand of Homonaledi. NatComm. 6, 8431 (2015). h 45. Hawkes, J. et al. New fossil remains of Homonaledi from the Lasedi Chamber, South Africa. E-Life e24232 (2017). h 45. Hawkes, J. et al. New fossil remains of Homonaledi from the Lasedi Chamber, South Africa. E-Life e242 46. Marzke, M. W. & Marzke, R. F. Evolution of the human hand: approaches to acquiring, analysing and interpreting the anatomical evidence. J. Anatomy. 197, 121–140 (2000). 46. Marzke, M. W. & Marzke, R. F. Evolution of the human hand: approaches to acquiring, analysing and interpreting the anatomical evidence. J. Anatomy. 197, 121–140 (2000). 46. Marzke, M. W. & Marzke, R. F. Evolution of the human hand: approaches to acquiring, analysing and interpreting the anatomical evidence. J. Anatomy. 197, 121–140 (2000). References Shrewsbury, M. M., Marzke, M. W., Linscheid, R. L. & Reece, S. P. Comparative morphology of the pollical distal phalanx. Am Phys. Anth. 121(1), 30–47 (2003).h y 17. Almécija, S., Smaers, J. B. & Jungers, W. L. The evolution of human and ape hand proportions. Nat. Comms. 6, 7717 (2015). 18. Williams, E. M., Gordon, A. D. & Richmond, B. G. Hand pressure distribution during Oldowan stone tool production. J. Human. Evo. 62, 520–532 (2012).hl 19. Key, A. & Dunmore, C. J. The evolution of the hominin thumb and the influence exerted by the non-dominant hand during stone tool production. J. Human. Evo. 78, 60–69 (2015).i p 20. Feix, T., Kivell, T. L., Pouydebat, E. & Dollar, A. M. Estimating thumb-index finger precision grip and manipulatio extant and fossil primates Interface 12(106) 20150176 (2015) 0. Feix, T., Kivell, T. L., Pouydebat, E. & Dollar, A. M. Estimating thumb-index finger precision grip and manipulation potential in extant and fossil primates. Interface 12(106), 20150176 (2015). 0. Feix, T., Kivell, T. L., Pouydebat, E. & Dollar, A. M. Estimating thumb-index finger precision grip and manipulation potential in extant and fossil primates. Interface 12(106), 20150176 (2015). y gi g p g p p p extant and fossil primates. Interface 12(106), 20150176 (2015). p f 21. Skinner, M. M. et al. Human-like hand use in Australopithecus africanus. Science 347(6220), 395–399 (2015). M. et al. Human-like hand use in Australopithecus africanus. Scien 21. Skinner, M. M. et al. Human-like hand use in Australopithecus 2. Marzke, M. W. & Shackley, M. S. Hominid hand use in the Pliocene and Pleistocene: evidence from experimental archaeology and comparative morphology. J. Human. Evo. 15, 439–460 (1986). p p gy 3. Key, A., Merritt, S. R. & Kivell, T. L. 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EMG study of hand muscle recruitment during hard hammer percussion manufacture of Oldowan tools. Am. J. Phys. Anth. 105, 315–332 (1998). 31. Reece, S. Getting a grip: functional morphology of the fifth ray in eight catarrhine species. (PhD thesis: Arizona State University, 2005). 32. Marzke, M. W. et al. EMG study of hand muscle recruitment during hard hammer percussion manufacture of Oldowan tools. Am. 2. Marzke, M. W. et al. EMG study of hand muscle recruitment during hard hammer percussion manufacture of Oldowan tools. Am J. Phys. Anth. 105, 315–332 (1998). y 3. Marzke, M. W., Wullstein, K. L. & Viegas, S. F. Evolution of the power (“squeeze”) grip and its morphological correlates in hominids Am. J. Phys. Anth. 89(3), 283–298 (1992). y 4. Stephens, N., Kivell, T., Pahr, D., Hublin, J. & Skinner, M. Trabecular bone patterning across the human hand. J. Human. Evo 123 1–23 (2018). 35. Key, A. Manual loading distribution during carrying behaviors: implications for the evolution of the hominin hand. References 1. Napier, J. Hands. (Princeton University Press, 1993). p y 2. Marzke, M. W. Precision grips, hand morphology, and tools. Am. J. Phys. Anth. 102, 91–110 (1997) 2. Marzke, M. W. Precision grips, hand morphology, and g p gy 4. Kivell, T. L. Evidence in hand: recent discoveries and the early evolution of human manual manipulation. Phil. Trans. R. Soc. B. 370, 20140346 (2015). Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w www.nature.com/scientificreports/ 7. Marzke, M. W., Marchant, L. F., McGrew, W. C. & Reece, S. P. Grips and hand movements of chimpanzees during feeding in Mahale Mountains National Park, Tanzania. Am. J. Phys. Anth. 156, 317–126 (2015). y 8. Bardo, A., Borel, A., Meunier, H., Guery, J.-P. & Pouydebat, E. Behavioural and functional strategies during tool use tasks in bonobos. Am. J. Phys. Anth 161(1), 125–140 (2016). y 9. Neufuss, J., Robbins, M.M., Baeumer, J., Humle, T. & Kivell, T.L. Manual skills for food processing by maountain gorillas (Gorilla beringei beringei) in Bwindi Impenetrable National Park, Uganda. Bio. J. Linnaean. Soc. bly071 (2018)t g g g 0. Christel, M. Grasping techniques and hand preferences in Hominoidea in Hand of Primates. (eds Preuschoft, H. & Chivers, D. J. 91–108 (Springer, 1993). p g 11. Bardo, A., Cornette, R., Borel, A. & Pouydebat, E. Manual function and performance in humans, gorillas and orangutans during the same tool use task. Am. J. Phys. Anth. 16(4), 21–836 (2017). y 2. Wong, A. L., Meals, C. G. & Ruff, C. B. Computed tomographic analysis of the internal structure of the metacarpals and its implications for hand use. pathology, and surgical intervention. Anatom. Sci. Int 93(2), 231–237 (2018).hi p gy g alletta, L., Stephens, N. B., Bardo, A., Kivell, T. L. & Marchi, D. Three-dimensional geometric morphometric analysis of the first etacarpal distal articular surface in humans, great apes and fossil hominins. J. Human. Evo. 132, 119–136 (2019). 13. Galletta, L., Stephens, N. B., Bardo, A., Kivell, T. L. & Marchi, D. Three-dimensional geometric morphometric analysis of th metacarpal distal articular surface in humans, great apes and fossil hominins. J. Human. Evo. 132, 119–136 (2019). 14. Diogo, R., Richmond, B. G. & Wood, B. Evolution and homologies of primate and modern human hand and forearm muscles, with notes on thumb movements and tool use. J. Human. Evo. 63(1), 64–78 (2012). 15. Susman, R. L. Fossil evidence for early hominid tool use. Science 265(5178), 1570–1573 (1994). 16. References PloS One 11, e0163801 (2016). ( ) 36. Niewoehner, W. A. Neanderthal hands in their proper perspective in Neanderthals revisited: New Approaches and Perspectives (eds Harvati, K. & Harrison, T.) 157–190 (Springer, 2006). g 37. Domalain, M., Bertin, A. & Daver, G. Was Australopithecus afarensis able to make the Lomekwian stone tools? Towards a realistic biomechanical simulation of hand force capability in fossil hominins and new insights on the role of the fifth digit. Comptes. Rendus. Palevol 16(5–6), 572–584 (2017). ( ) ( ) 38. Key, A. & Dunmore, C. J. Manual restrictions on Palaeolithic technological behaviours. Peer J. 6, e5399 (2018). y g 39. Key, A., Dunmore, C. J., Hatala, K. G. & Williams-Hatala, E. M. Flake morphology as a record of manual pressure during stone tool production. J. Arch. Sci. Rep. 12, 43–53 (2017). p p 0. Rolian, C., Lieberman, D. E. & Zermeno, J. P. Hand biomechanics during simulated stone tool use. J. Human. Evo. 61, 26–41 (2011) 40. Rolian, C., Lieberman, D. E. & Zermeno, J. P. Hand biomechanics during simulated stone tool use. J. Human. Evo. 61, 26–41 (2011). 41. Williams, E. M., Gordon, A. D. & Richmond, B. G. Upper limb kinematics and the role of the wrist during stone tool production. Am. J. Phys. Anth. 143(1), 134–145 (2010). 40. Rolian, C., Lieberman, D. E. & Zermeno, J. P. Hand biomechanics during simulated stone tool use. J. Human. Evo. 61, 26–41 (2011). 41. Williams, E. M., Gordon, A. D. & Richmond, B. G. Upper limb kinematics and the role of the wrist during stone tool production. Am. J. Phys. Anth. 143(1), 134–145 (2010). g ( ) 41. Williams, E. M., Gordon, A. D. & Richmond, B. G. Upper limb kinematics and the role of the wrist during stone tool production. Am. J. Phys. Anth. 143(1), 134–145 (2010). y 42. Whittaker, J. C. Flinknapping: Making and Understanding Stone Tools. (University of Texas Press, 1994) 42. Whittaker, J. C. Flinknapping: Making and Un J pp g g g ( y ) 43. Faisal, A., Stout, D., Apel, J. & Bradley, B. The manipulative complexity of Lower Palaeolithic stone toolmaking. PloS One 5, e13718 (2010).h J pp g g g ( y ) 43. Faisal, A., Stout, D., Apel, J. & Bradley, B. The manipulative complexity of Lower Palaeolithic stone toolmaking. PloS One 5, e13718 (2010).h pp g g g y 43. Author contributions A.K. and C.D. conceived the study following earlier work by M.M.; A.K. designed and organised data collection; A.K. and C.D. collected the data; A.K. and C.D. analysed the data; all authors wrote the manuscript. Acknowledgements The authors would like to thank Tracy Kivell for loan of the Novel pressure sensor system and Erin Marie Williams-Hatala for advice on its use. We are grateful to all knappers for their participation in the study. The Supplementary Information videos were recorded with the kind assistance of Jesse Young and Metin Eren at Kent State University using equipment from Northeast Ohio Medical University. We are grateful to three anonymous reviewers who provided helpful suggestions to improve this article. A.K. was supported by a British Academy Postdoctoral Fellowship (pf160022) during this research. C.D. is funded by E.R.C. Starting Grant #336301. Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w www.nature.com/scientificreports/ Author contributions A.K. and C.D. conceived the study following earlier work by M.M.; A.K. designed and organised data collection; A.K. and C.D. collected the data; A.K. and C.D. analysed the data; all authors wrote the manuscript. Competing interests The authors declare no competing interests. Additional information Supplementary information is available for this paper at https://doi.org/10.1038/s41598-019-53332-w. Correspondence and requests for materials should be addressed to A.J.M.K. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Cre- ative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not per- mitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2019 Additional information Supplementary information is available for this paper at https://doi.org/10.1038/s41598-019-53332-w. Correspondence and requests for materials should be addressed to A.J.M.K. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Cre- ative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not per- mitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2019 Scientific Reports | (2019) 9:16724 | https://doi.org/10.1038/s41598-019-53332-w
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Effect of immunonutrition on colorectal cancer patients undergoing surgery: a meta-analysis
International journal of colorectal disease
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cc-by
6,547
Abstract Abstract Purpose Immunonutrition has been used to prevent the complications after colorectal elective surgery. This systematic review aimed to analyze and assess the effect of immunonutrition on colorectal cancer patients who received elective surgery. Purpose Immunonutrition has been used to prevent the complications after colorectal elective surgery. This systematic review aimed to analyze and assess the effect of immunonutrition on colorectal cancer patients who received elective surgery. Methods Three electronic databases (Medline, Embase, Cochrane) were used to search the latent studies which investigated the effects of enteral immunonutrition (EIN) compared with standard enteral nutrition (EN) or parenteral immunonutrition (PIN) compared with standard parenteral nutrition (PN) on colorectal cancer patients who are undergoing surgery until 21st of April, 2017. Meta-analysis was conducted to calculate odd risk (OR), mean difference (MD), or standard mean difference (SMD) with 95% confidence interval (CI), and heterogeneity was tested by Q test. ( ) g y y Q Results Nine publications were included. The meta-analysis results presented that EIN improved the length of hospital stay (pooled MD, 2.53; 95% CI, 1.29–3.41), infectious complications (pooled OR, 0.33; 95% CI, 0.21–0.53) which contains the Surgical Site Infections (pooled OR, 0.25; 95% CI, 0.22–0.58) and Superficial/Deep incisional infections (pooled OR, 0.27; 95% CI, 0.12–0.64); meanwhile, PIN improved the length of hospital stay (pooled MD, 2.66; 95% CI, 0.62–4.76), IL-6 (pooled MD, −6.09; 95% CI, −10.11 to −2.07), CD3 (pooled MD, 7.50; 95% CI, 3.57–11.43), CD4 (pooled MD, 5.47; 95% CI, 2.54–8.40), and CD4/CD8 (pooled MD, 0.50; 95% CI, 0.22–0.78); the level of CD8 was lower (pooled MD, −4.32; 95% CI, −7.09 to − 1.55) in PIN. Conclusion Immunonutrition could be an effective approach to enhance the immune function of colorectal cancer patients undergoing elective surgery and to improve the clinical and laboratory outcomes. Keywords Immunonutrition . Colorectal cancer . Meta-analysis . Surgery 1 School of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Box 21, 138 Xianlin Road, Nanjing 210023, China Effect of immunonutrition on colorectal cancer patients undergoing surgery: a meta-analysis ing Xu1 & Xian Sun1 & Qianqian Xin1 & Ying Cheng1 & Zhen Zhan1 & Junfeng Zhang1 & Juan Wu1 Accepted: 31 December 2017 /Published online: 15 January 2018 # The Author(s) 2018. This article is an open access publication International Journal of Colorectal Disease (2018) 33:273–283 https://doi.org/10.1007/s00384-017-2958-6 International Journal of Colorectal Disease (2018) 33:273–283 https://doi.org/10.1007/s00384-017-2958-6 ORIGINAL ARTICLE * Juan Wu wujuan1213@hotmail.com * Junfeng Zhang zhangjunfeng5_5@163.com Introduction homeostasis, defense mechanisms and inflammatory re- sponse, which would increase the rate of postoperative com- plications and prolong hospital stay [2, 3]. As nutritional sta- tus being a key factor to influence the clinical outcomes, nu- trition support has been widely used for elective colorectal surgery patients. Recently, many researchers argued that immunonutritional formulas supplemented with biologically active nutrients were more effective than standard nutrition intervention in improving inflammation, promoting the wound healing and shortening the length of hospital stay (LOS) after operation. Colorectal cancer is one of the most commonly diagnosed cancers in the world [1]. Although early colorectal cancer patients could be treated successfully by surgery, major oper- ation itself possibly cause the dysfunction of the host Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00384-017-2958-6) contains supplementary material, which is available to authorized users. The nutrients of immunonutrition formula usually include arginine, omega-3 fatty acid, glutamine and RNA, etc. Omega-3 fatty acid could reduce the platelet-adhesive endo- thelial interactions and the synthesis of proinflammatory ei- cosanoids, while it could stimulate the produce of glutathione which can decrease oxidative injury [4–6]. Arginine is the sole substrate for nitric oxide (NO) synthesis, which is a crucial Int J Colorectal Dis (2018) 33:273–283 274 (Bglutamine^) OR (Bomega-3 fatty acid^) OR (BRNA^) AND (Bparenteral nutrition^) OR (Benteral nutrition^) OR (Bimmunonutrition^). Appropriate Medical Subject Heading (MeSH) terms were combined in the search builder. The re- sults were imported into the management software Endnote X7 to extract data and delete duplicate references. element of innate antimicrobial immunity in the host’s first line of defense [7]. It also plays an important role in maintain- ing the physiological balance of gastrointestinal tract [8] and regulating the metabolism of many kinds of lymphocyte [9]. Glutamine, as the major fuel source for macrophages, lym- phocytes, and enterocytes, could increase the level of gut mu- cosal glutathione, thereby reduce free radical availability, and decrease inflammation [10, 11]. The protective effect of glu- tamine on intestinal mucosa might be attributed to the induc- tion of heat shock protein (HSP) synthesis. Enhanced expres- sion of HSPs (in particular HSP70) has been shown to be responsible for glutamine-mediated cellular protection after inflammatory cytokine-induced cellular injury [12–14]. Deficiency of glutamine may lead to impaired immune func- tion and dysfunction of intestinal epithelium [15]. Data extraction and quality assessment The information and data in all eligible studies were extracted: basic characteristics of each study (first author, publication year, country, sample size, age of the participants), study de- sign (elements in immunonutrition formula, nutritional sup- port duration, approach of the nutritional support), and out- comes of interest (clinical outcomes, immune and biochemical indices). To date, meta-analysis has focused on immunonutrition with digestive system cancer and upper gastrointestinal surgery pa- tients [21, 22], but pooled results about immunonutrition on colorectal cancer patients are still lacking. This systematic re- view and meta-analysis were done to evaluate whether immunonutrition could be beneficial to colorectal cancer pa- tients, and the conclusion will provide a higher level evidence regarding usage of immunonutrition on colorectal cancer pa- tients undergoing surgery. The quality of included investigations was assessed accord- ing to the Cochrane Collaboration tool published in the Cochrane Handbook for Systematic Reviews of Interventions (Version 5.1.0). BRisk of bias^ consisting chiefly of six do- mains: random sequence generation, allocation concealment, blinding of participants and personnel, blinding of outcome assessment, incomplete outcome data, selective reporting, and other bias. Each domain was graded as Blow risk of bias,^ Bhigh risk of bias,^ or Brisk of bias unclear.^ Study selection The inclusion criteria for this study were as follows: (i) studies designed as randomized controlled trials (RCTs), (ii) patients with colorectal neoplasms who received surgery, (iii) interven- tion of trials was EN vs EIN; PN vs PIN, (iv) both EIN and PIN included at least one of the following nutrients: Arginine, Glutamine, Omega-3 fatty acid. Although immunonutrition has been used in clinics for more than 20 years, the findings have not been uniform in all reports nor conclusive. For example, one literature ap- proved to use immunonutrition to patients undergoing major surgery regardless of their baseline nutritional status [16], while two literatures suggested that immunomodulating diets have no quantifiable efficacy in well-nourished patients [17, 18]. Senkal et al. [19] revealed a significant reduction of com- plications receiving immunonutrition on day 3, while Lobo et al. [20] revealed that enteral immunonutrition formula had no advantage over traditional EN formula. Studies beyond the inclusion criteria or originally pub- lished in language other than English or Chinese were excluded. Study characteristics rate was used, we transferred it into events number by sample size. If multiple intervention patterns were imple- mented in one study, we took them as multiple indepen- dent studies. Outcomes of continuous and dichotomous data were measured using fixed-effect model or random- effect model. The heterogeneity among eligible studies was tested by Q test based on chi-square distribution and I2 value. Fixed-effect model was used if no signifi- cant heterogeneity (I2 < 50%) existed among studies; oth- erwise, random-effect model was applied. We removed one or two studies to explore the heterogeneity source and recombined the remaining data to assess the sensitiv- ity of the results. P value < 0.05 was considered statisti- cally significant. rate was used, we transferred it into events number by sample size. If multiple intervention patterns were imple- mented in one study, we took them as multiple indepen- dent studies. Outcomes of continuous and dichotomous data were measured using fixed-effect model or random- effect model. The heterogeneity among eligible studies was tested by Q test based on chi-square distribution and I2 value. Fixed-effect model was used if no signifi- cant heterogeneity (I2 < 50%) existed among studies; oth- erwise, random-effect model was applied. We removed one or two studies to explore the heterogeneity source and recombined the remaining data to assess the sensitiv- ity of the results. P value < 0.05 was considered statisti- cally significant. Characteristics of nine studies were outlined in Table 1. In summary, perioperative (n = 4) [23–25, 28], preoperative (n = 1) [26], and postoperative (n = 4) [27, 29–31] interven- tions were included in this meta-analysis. Six studies taken EN vs EIN [23–28] and three taken PN vs PIN [29–31]. Laboratory indicators including biochemical indices and im- mune indices (e.g., T cell subsets, cytokines, and immuno- globulin) were measured both before and after the surgery in EN/EIN; in PN/PIN, they were measured 1 day and 1 week after the surgery, respectively; the clinical outcomes including LOS, readmission, and complications were measured within 30 days after surgery. Nine studies provided a total of 1004 participants diagnosed with colorectal cancer, including 866 participants received the EN/EIN nutrition support and 138 received the PN/PIN nutri- tion support. In the EN/EIN group, the ratio of control group and intervention group is 433:433; the ratio of control group and intervention group in PN/PIN group is 69:69. Study characteristics More char- acteristics of participants such as age, gender, weight, BMI, and the situation of metastasis were listed in Table 2. Results Two thousand eight hundred seventy-four studies were screened out through the initial search: 1531 from Medline database, 1068 from Embase database, and 275 from CENTRAL. After removal of duplicates and irrelevant arti- cles, 38 full-text articles remained of which 26 studies were excluded for not meeting the inclusion criteria. Three of the remaining 12 studies were excluded with data unable to syn- thesize. Eventually, nine studies [23–31] (six of the EN vs EIN and three of the PN vs PIN) were included for this meta- analysis (Fig. 1). Search strategy Statistical analysis was performed by Revman 5.3. For continuous outcome, mean and standard deviation (SD) of each study was extracted for calculating pool effect. One study conducted by Moya [23] described continuous data by mean and standard error (SE); we transferred it into SD through formula: SD = SE × √N (N = sample size). Mean difference (MD) was used as effect size when the unit and order of magnitude adopted in all studies were consistent; otherwise, standardized mean difference (SMD) was used. Odds ratio (OR) and 95% confidence interval (CI) were adopted as effect size for dichotomous outcome; events number in intervention and control group was extracted for calculating pooled effect. If effective The meta-analysis was performed in accordance with the PRISMA guidelines. This systematic review was registered with the International Prospective Register of Systematic Review (PROSPERO), and the registration number is CRD42016049748. Potential studies were searched on Medline (via PubMed), Embase (via OVID), and Cochrane Central Register of Controlled Trials (CENTRAL) from in- ception to April 2017. The terms and keywords were as fol- lows: (Bcolon/rectal/colorectal neoplasms^) OR (Bcolon/rec- tal/colorectal cancer^) OR (Bcolon/rectal/colorectal adenomas^) AND (Bnutritional support^) OR (Bnutrition^) OR (Bnutritional sciences^) OR (Barginine^) OR Int J Colorectal Dis (2018) 33:273–283 275 Quality assessment Most studies had a clear description of their random sequence generation. Three studies used a computer random number generator [28–30], one used an envelope [25], two used the Full-text artical analysis n=38 Duplicates,irrelevant records screened: n=2836 Records identified through Pubmed searching n=1531 Records identified through Embase searching n=1068 Records identified through Cochrane searching n=275 Included studies n=9 Full-text articals excluded n=29 Cannot find full text n=11 Included patients with other tumors n=4 Outcomes not matching inclusion criteria n=7 Systematic reviews n=2 Languages not in english or chinese n=2 Data can not be merged n=3 Fig. 1 Flow diagram of the literature search and studies selection process Fig. 1 Flow diagram of the literature search and studies selection process Fig. Quality assessment 1 Flow diagram of the literature search and studies selection process Records identified through Pubmed searching n=1531 276 Int J Colorectal Dis (2018) 33:273–283 Table 1 Characteristics of the included studies Author [Ref] Year Country Duration of supplementa- tion Lost to follow up (Con / IN) Nutrients Approaches Outcomes before sugery 1 day after surgery 1 week after surgery 0~30 days after surgery Pedro Moya [24] 2016 Spain 7 days prior to surgery and 5 days after surgery 6/7 Arginine,RNA,n3FA EN Oral Albumin,prealbumin, transferrin Albumin,prealbumin, transferrin Readmission,anastomotic leak,ileus,Infectious complications,Urinary tract infections,Superficial/Deep incisional infetious,Organ/Space infectious,SSI,Respiratory infections Pedro Moya [23] 2016 Spain 7 days prior to surgery and 5 days after surgery 0/0 Arginine,RNA,n3FA EN Oral Readmission,wound infection,Anastomotic leak,ileus,Infectious complications,Respiratory infections L.S.Sorensen [25] 2013 Denmark 2 days prior to surgery and 7 days after surgery 0/0 n3FA EN Oral Readmission,wound infection,Anastomotic leak,ileus,Urinary tract infections,Respiratory infections Hisanaga Horie [26] 2006 Japan From 6 to 2 days before surgery NG Arginine,RNA,n3FA EN Oral albumin Anastomotic leak,ileus,Urinary tract infections,Superficial/Deep incisional,Organ/Space,SSI,Respiratory infections Rong Chen [27] 2005 China From 1 to 7 days after surgery NG Glutamine,Arginine,n3FA EN Nasointestinal tube albumin,prealbumin, Transferrin,CD4,CD8 albumin,prealbumin, Transferrin Marco Braga1 [28] 2002 Italy 5 days prior to surgery 0/0 EN Oral LOS,Anastomotic leak,Infectious complications Marco Braga2 [28] 2002 Italy 5 days prior to surgery and 4 days after surgery 0/0 EN Oral,jejunal infusion LOS,Anastomotic leak,Infectious complications Mingwei Zhu [29] 2012 China From 1 to 8 days after surgery 0/0 n3FA PN/peripherally-inserted central catheter CD4,CD8,CD4/CD8, IL-6,TNFα CD4,CD8,CD4/CD8, IL-6,TNFα Bin Liang [30] 2008 China From 1 to 7 days after surgery 0/1 n3FA PN/central venous catheter/Peripheral catheter CD4,CD8,CD3, CD4/CD8,IL-6, TNFα CD4,CD8,CD3, CD4/CD8,IL-6, TNFα Jingxiang Song [31] 2004 China From 2 to 7 days after surgery NG Glutmine PN/Peripheral venous catheter CD4,CD8,CD3, CD4/CD8 CD4,CD8,CD3, CD4/CD8 Ref reference, Con control, IN immunonutrition, Marco Braga1 preoperative, Marco Braga2 peri-operative, NG not given, n3FA omega-3 fatty acids Int J Colorectal Dis (2018) 33:273–283 277 web-based randomization [23, 24], and three studies did not give the sufficient information [26, 27, 31]. Among them, three studies appropriately performed the allocation conceal- ment [23–25]. Blinding of participants and personnel was conducted in four studies [25, 28–30]. Blinding of participants and personnel was conducted in five studies [25–28, 30, 31]. The remaining studies had no sufficient information about blinding. Effect of enteral immunonutrition on laboratory index No pooled results of laboratory index were found significantly different between EN and EIN in this meta-analysis (Supplementary Table 2). Effect of enteral immunonutrition on clinical outcome indicators after surgery The meta-analysis showed that EIN group had a shorter LOS than EN group. Fixed-effect pooled MD was 2.35 (95% CI, 1.29–3.41) with null heterogeneity (I2 = 0%) (Fig. 2a). Infectious complications were reduced in EIN group for the fixed-effect pooled OR 0.33(95% CI, 0.21–0.53); no hetero- geneity was detected (I2 = 0%) (Fig. 2b). Surgical Site Infections (SSI) and Superficial/Deep incisional infections were reduced in EIN group; the fixed-effect pooled OR was 0.25 (95% CI, 0.11–0.58) in SSI and 0.27(95% CI, 0.12–0.64) in Superficial/Deep incisional infections; no heterogeneity was detected (I2 = 0%) (Fig. 2c, d). Other outcomes, such as anastomotic leak, ileus, organ/space infections, urinary tract infections, respiratory infections, and readmission, were not significantly different between two groups (Supplementary Table 1). Quality assessment Two studies reported the drop-out before conducting the immunonutrition [24, 30]; therefore, corresponding do- main was graded as Blow risk.^ All nine included studies showed the pre-specified outcomes in the pre-specified way. The assessment of risk of bias outcome of each study is sum- marized in Tables 3 and 4. Table 2 Patients characteristics of the included studies Moya 2016 [24] Moya 2016 [23] Sorensen 2013 [25] Horie 2006 [26] Chen 2005 [27] Braga 20021 [28] Braga 20022 [28] Zhu 2012 [29] Liang 2008 [30] Song 2004 [31 Variables (control/intervention) Sample size 128/129 61/61 74/74 34/33 36/36 50/50 50/50 28/29 21/21 20/20 Age* 68/70 68/69 71/69 63/69 58.1/57.9 61.8/63.0 61.8/60.5 70.8/69.8 59.19/55.80 56 Sex (male/female) Control 69/53 27/34 36/38 18/16 18/18 31/19 31/19 11/17 15/6 26/14 Intervention 62/60 30/31 44/30 25/8 20/16 30/20 8/22 16/13 10/10 BMI 26.64/27.05 NG 26/26 22.8/22.8 NG NG NG 23.2/22.9 23.92/23.38 NG Metastasis 13/15 NG 5/5 NG NG NG NG 0/0 0/0 NG Weight NG NG 76/77 58/59 59/62 NG NG NG 65.4/63.50 NG Effect of parenteral immunonutrition on clinical outcome indicators after surgery PIN intervention could shorten the LOS compared to PN. Pooled MD was 2.66 (95% CI, 0.62–4.76), and the homoge- neity was well (I2 = 0%) (Fig. 3). Effect of parenteral immunonutrition on laboratory index CD8 and IL-6 were decreased in the PIN group than those in PN group 1 week after the surgery. Effect of parenteral immunonutrition on laboratory index Braga 2002 Chen 2005 Horie 2006 Liang 2008 Moya 2016 Moya 2016 Song 2004 Sorensen 2013 Zhu 2012 Random sequence generation (selection bias) low risk unknown risk unknown risk low risk low risk low risk unknown risk low risk low risk Allocation concealment (selection bias) unknown risk unknown risk unknown risk high risk low risk low risk unknown risk low risk unknown risk Blinding of participants and personnel (performance bias) low risk unknown risk unknown risk low risk high risk high risk unknown risk low risk low risk Blinding of outcome assessment (detection bias) low risk low risk unknown risk low risk high risk high risk low risk low risk unknown risk Incomplete outcome data (attrition bias) low risk low risk low risk low risk low risk low risk low risk low risk low risk Selective reporting (reporting bias) low risk low risk low risk low risk low risk low risk low risk low risk unknown risk Other bias low risk high risk low risk low risk low risk low risk low risk low risk low risk Effect of parenteral immunonutrition on laboratory index CD8 and IL-6 were decreased in the PIN group than those in PN group 1 week after the surgery. CD8 and IL-6 were decreased in the PIN group than those in PN group 1 week after the surgery. 278 Int J Colorectal Dis (2018) 33:273–283 Braga 2002 Chen 2005 Horie 2006 Liang 2008 Moya 2016 Moya 2016 Song 2004 Sorensen 2013 Zhu 2012 Random sequence generation (selection bias) low risk unknown risk unknown risk low risk low risk low risk unknown risk low risk low risk Allocation concealment (selection bias) unknown risk unknown risk unknown risk high risk low risk low risk unknown risk low risk unknown risk Blinding of participants and personnel (performance bias) low risk unknown risk unknown risk low risk high risk high risk unknown risk low risk low risk Blinding of outcome assessment (detection bias) low risk low risk unknown risk low risk high risk high risk low risk low risk unknown risk Incomplete outcome data (attrition bias) low risk low risk low risk low risk low risk low risk low risk low risk low risk Selective reporting (reporting bias) low risk low risk low risk low risk low risk low risk low risk low risk unknown risk Other bias low risk high risk low risk low risk low risk low risk low risk low risk low risk Pooled MD for CD8 was −4.32 (95% CI, −7.09 to −1.55) and −6.09 (95% CI, −10.11 to −2.07) for IL-6 (Fig. 4a, b). CD3, CD4/CD8, and CD4 increased in PIN group 1 week after the surgery. Combined MD for CD3 was 7.50 (95% CI, 3.57–11.43), CD4/CD8 was 0.50 (95% CI, 0.22–0.78), and CD4 was 5.47 (95% CI, 2.54–8.40) (Fig. 4c–e). In order to find the source of relative high heterogeneity of CD4, a study conducted by Zhu et al. [29] was removed and I2 reduced to zero; meanwhile, pooled MD of CD4 level reached 7.59 (95% CI, 3.97–11.22) (Fig. 4f). Discussion In the present meta-analysis, we evaluated the benefits of immunonutrition in patients with colorectal cancer after sur- gery. Overall, the pooled results supported the usage of EIN in colorectal cancer patients, for the improvement of postopera- tive complications and reduction of LOS, compared with EN. Meanwhile, PIN strategy also showed to be beneficial for patients’ LOS and cellular immune function parameters. Regarding the proinflammatory factors, the PIN group had a lower serum IL-6 level than that in the PN group, and the increased CD4, CD4/CD8, and CD3 T lymphocytes in the PIN group were reasonably observed, which reflect the en- hancing immune function. Colorectal cancer is the third most commonly diagnosed cancer in males and the second in females, and the mortality rate ranked fourth in males and third in females. Statistics data from IARC showed that the number of new cases of colorectal cancer was 1.4 million and 693,900 cases died in 2012 in the world [1]. Patients of colorectal cancer often suffer from mal- nutrition, especially those undergoing tumorectomy, and the worsening of nutritional status consequently deteriorated the surgical outcomes. Thus, nutrition intervention has been the focal point of postoperative recovery [32]. Despite the standard nutrition support could reverse nitrogen imbalance and promote patients’ nutritional status, it did little contribution in improving the immune function. Thus, many researchers advocated the usage of immunonutrition in colorectal cancer patients. A growing body of studies suggests that the immunonutrition could reduce the postoperative complications and shorten the LOS in surgical patients, and it also lower toxic effect after the chemoradiotherapy, such as nausea, vomiting, bloating, abdom- inal pain, diarrhea, or constipation [33]. Immunonutrition for- mula usually includes arginine, omega-3 fatty acid, glutamine and RNA, etc. Andrade et al. [34] found dietary arginine could preserve the intestinal mucosa and tend to decreased inflamma- tion by histologic analysis. Glutamine supplementation in enteral/parenteral nutrition was able to reduce septic complica- tions, accelerate wound healing, and shorten LOS [35]. However, not all the studies showed the beneficial effects of immunonutrition. For example, Giger-Pabst et al. Discussion [36] found Int J Colorectal Dis (2018) 33:273–283 279 Table 4 The percentage of each bias for all the included studies Low risk (%) High risk (%) Unknown risk (%) Random sequence generation (selection bias) 66.67 0 33.33 Allocation concealment (selection bias) 33.33 11.11 55.56 Blinding of participants and personnel (performance bias) 44.44 22.22 22.22 Blinding of outcome assessment (detection bias) 55.55 22.22 22.22 Incomplete outcome data (attrition bias) 100 0 0 Selective reporting (reporting bias) 88.89 0 11.11 Other bias 88.89 11.11 0 immunonutrition [39]. The above results indicated that the ef- fects of immunonutrition would be different when the condi- tions are different. Patient characteristics of demographic, sam- ple size, control group selection, different administration dose, and duration may be the sources of heterogeneity [40]. In this meta-analysis, the present results confirmed that the that preoperative oral supplementation with an immune- enriched diet for 3 days did not improve postoperative outcome in patients with gastrointestinal cancer, and meanwhile, no pos- itive effects of immunonutrition support were found in ICU patients [37, 38]; furthermore, a study including 1223 critically ill adults showed harmful effects of early administration of a b c d Fig. 2 Forest plot comparison between EN and EIN for clinical index. a LOS. b Infectious complications. c SSI. d Superficial/deep incisional infection Braga 20021 preoperative group, Braga 20022 perioperative group b Fig. 2 Forest plot comparison between EN and EIN for clinical index. a LOS. b Infectious complications. c SSI. d Superficial/deep incisional infections, Braga 20021 preoperative group, Braga 20022 perioperative group Fig. 2 Forest plot comparison between EN and EIN for clinical index. a LOS. b Infectious complications. c SSI. d Superficial/deep incisional infections, Braga 20021 preoperative group, Braga 20022 perioperative group Int J Colorectal Dis (2018) 33:273–283 280 Fig. 3 Forest plot comparison between PN and PIN for LOS Fig. 3 Forest plot comparison between PN and PIN for LOS EN and PN were two different drug delivery routes. In general, EN is prior to PN in clinical practice. PN is used immunonutrition support did work for the patients with colo- rectal cancer. immunonutrition support did work for the patients with colo- rectal cancer. a b c d e f ig. 4 Forest plot comparison between PN and PIN for laboratory index. a CD8. b IL-6. c CD3. d CD4/CD8. Conclusion only in patients with the following conditions: not feasible or tolerated for EN, unable to receive and absorb adequate amounts of oral/enteral feeding for at least 7 days due to postoperative complications impairing gastrointestinal function [41]. In this meta-analysis, we also found a dif- ferent effect between EIN and PIN. EIN mainly improved the clinical outcomes such as SSI and Superficial/Deep incisional infection. However, PIN mainly increase the immune function and reduce inflammation through sever- al laboratory indices, such as raised level of CD4, CD4/ CD8, and CD3 T lymphocytes and decreased serum level of IL-6. only in patients with the following conditions: not feasible or tolerated for EN, unable to receive and absorb adequate amounts of oral/enteral feeding for at least 7 days due to postoperative complications impairing gastrointestinal function [41]. In this meta-analysis, we also found a dif- ferent effect between EIN and PIN. EIN mainly improved the clinical outcomes such as SSI and Superficial/Deep incisional infection. However, PIN mainly increase the immune function and reduce inflammation through sever- al laboratory indices, such as raised level of CD4, CD4/ CD8, and CD3 T lymphocytes and decreased serum level of IL-6. Immunonutrition is beneficial for colorectal cancer pa- tients undergoing surgery. It may decrease the rate of postoperative complications, shorten LOS, and enhance immune function. Immunonutrition could be encouraged in the clinical treatment. More studies with specific tim- ings (preoperative, perioperative, and postperative) are needed for better understanding of immunonutrition in clinical practice. Use of immunonutrition within an ERAS may be more effective. Whether immunonutrition has a long-time effect of patients also needs to be clarified in future. Enhanced recovery after surgery (ERAS) protocols are de- signed to accelerate recovery after surgery [42]. Several stud- ies have demonstrated that ERAS protocols can reduce mor- bidity and shorten the LOS following colorectal surgery [43–48]. Two of the included studies evaluated benefits of immunonutrition on colorectal cancer patients within an ERAS [23, 24]. The wound infection decreased in both of the two studies. However, reduction of infectious complica- tions occurred only in patients undergoing laparoscopic sur- gery. Those results indicated the potential effect difference of immunonutrition in patients undergoing laparoscopic and open surgery. Acknowledgements This work was supported by the National Natural Science Foundation (81473458, 81473593) and the Jiangsu Qing Lan Project (JSQL-2014). Conclusion This work was also supported partly by the Priority Academic Program Development of Jiangsu Higher Education Institutions (Integration of Chinese and Western Medicine) and the Project of Clinical Scientific Research of Medicine State Administration of TCM (JDZX2015089). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. There are different opinions regarding the mechanisms of immunonutrition on immune function and inflamma- tion. Two reports found glutamine could raise secretion of sIgA in the intestine and prevent the translocation of intestinal microbiota [49, 50]. Costa et al. [51] found that supplementation with arginine prevented the increases in intestinal permeability and bacterial transfer caused by exertional hyperthermia and indicated that dietary L- arginine supplementation preserves the integrity of the intestinal epithelium. Those may be the possible explana- tion of the positive effect of immunonutrition in patients with colorectal cancer in this meta-analysis. Discussion e CD4 a b c d e f 4 Forest plot comparison between PN and PIN for laboratory index. a CD8. b IL-6. c CD3. d CD4/CD8. e CD4 Int J Colorectal Dis (2018) 33:273–283 281 References J Pharm Pract 24(1):70–77. https://doi.org/10.1177/ 0897190010388142 28. Braga M, Gianotti L, Vignali A, Carlo VD (2002) Preoperative oral arginine and n-3 fatty acid supplementation improves the immunometabolic host response and outcome after colorectal re- section for cancer. Surgery 132(5):805–814. https://doi.org/10. 1067/msy.2002.128350 16. Braga M (2012) Perioperative immunonutrition and gut function. Curr Opin Clin Nutr Metab Care 15(5):485–488. https://doi.org/10. 1097/MCO.0b013e3283567d8f 29. 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Andrade ME, Santos RD, Soares AD, Costa KA, Fernandes SO, de Souza CM, Cassali GD, de Souza AL, Faria AM, Cardoso VN (2016) Pretreatment and treatment with L-arginine attenuate weight loss and bacterial translocation in dextran sulfate sodium colitis. JPEN J Parenter Enteral Nutr 40(8):1131–1139. https://doi.org/10. 1177/0148607115581374 21. Wong CS, Aly EH (2016) The effects of enteral immunonutrition in upper gastrointestinal surgery: a systematic review and meta-anal- ysis. Int J Surg 29:137–150. https://doi.org/10.1016/j.ijsu.2016.03. 043 35. Lorenz KJ, Schallert R, Daniel V (2015) Immunonutrition—the influence of early postoperative glutamine supplementation in enteral/parenteral nutrition on immune response, wound healing and length of hospital stay in multiple trauma patients and patients 22. Zhang Y, Gu Y, Guo T, Li Y, Cai H (2012) Perioperative immunonutrition for gastrointestinal cancer: a systematic review Int J Colorectal Dis (2018) 33:273–283 283 after extensive surgery. 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Heyland D, Muscedere J, Wischmeyer PE, Cook D, Jones G, Albert M, Elke G, Berger MM, Day AG, Canadian Critical Care Trials G (2013) A randomized trial of glutamine and antioxidants in critical- ly ill patients. N Engl J Med 368(16):1489–1497. https://doi.org/10. 1056/NEJMoa1212722 49. Ren W, Wang K, Yin J, Chen S, Liu G, Tan B, Wu G, Bazer FW, Peng Y, Yin Y (2016) Glutamine-induced secretion of intestinal secretory immunoglobulin a: a mechanistic perspective. Front Immunol 7:503. https://doi.org/10.3389/fimmu.2016.00503 40. McCowen KC, Bistrian BR (2003) Immunonutrition: problematic or problem solving? Am J Clin Nutr 77(4):764–770 50. Zou XP, Chen M, Wei W, Cao J, Chen L, Tian M (2010) Effects of enteral immunonutrition on the maintenance of gut barrier function and immune function in pigs with severe acute pancreatitis. JPEN J Parenter Enteral Nutr 34(5):554–566. https://doi.org/10.1177/ 0148607110362691 41. Weimann A, Braga M, Carli F, Higashiguchi T, Hübner M, Klek S, Laviano A, Ljungqvist O, Lobo DN, Martindale R, Waitzberg DL, Bischoff SC, Singer P (2017) ESPEN guideline: clinical nutrition in surgery. Clin Nutr 36(3):623–650. https://doi.org/10.1016/j.clnu. 2017.02.013 51. Costa KA, Soares AD, Wanner SP, Santos R, Fernandes SO, Martins Fdos S, Nicoli JR, Coimbra CC, Cardoso VN (2014) L- arginine supplementation prevents increases in intestinal perme- ability and bacterial translocation in male Swiss mice subjected to physical exercise under environmental heat stress. J Nutr 144(2): 218–223. https://doi.org/10.3945/jn.113.183186 42. Wilmore DW, Kehlet H (2001) Management of patients in fast track surgery. BMJ 322(7284):473–476. https://doi.org/10.1136/bmj. 322.7284.473 43. Adamina M, Kehlet H, Tomlinson GA, Senagore AJ, Delaney CP (2011) Enhanced recovery pathways optimize health outcomes and resource utilization: a metaanalysis of randomized controlled trials
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Evaluating outreach activities: overcoming challenges through a realist ‘small steps’ approach
Perspectives
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Abstract: Practitioners are being placed under increasing pressure to evaluate the success of their outreach activities, both by government and by their own universities. Based in a reductionist doctrine of ‘evidence-based practice’, there is a desire to demonstrate the effectiveness and value-for-money across activities that now account for around £175 million per year across England. This article examines some of the difficulties in evaluating the complex social world of outreach and suggests a ‘small steps’ approach to overcome some of these. This uses the idea of a transformative ‘theory of change’ as a framework for understanding the particular contribution made by discrete activities within a wider portfolio, providing a more reliable form of inference than attempts to ‘prove’ impact over longer timeframes. Introduction For some time, there has been concern about the effectiveness of outreach activities (e.g. summer schools, university taster days and mentoring schemes) that are designed to encourage disadvantaged individuals to apply to higher education. This is perhaps inevitable for any high- profile and high-cost social policy, especially during a period of austerity; the latest figures show outreach activities totalling nearly £175 million in England (Office for Fair Access [OFFA], 2016). The recent national strategy document lays out a clear expectation: ‘It is essential to understand which approaches and activities have the greatest impact, and why. An improved evidence base, and a robust approach to evaluation, are critical in helping the sector and partners to understand which of their activities are most effective and have the greatest impact on access, student success and progression, so enabling effort to be focused on these areas’ (Department of Business, Innovation and Skills [BIS], 2014, p.9). With slightly softer rhetoric, the recent OFFA strategic plan makes a similar point, signalling its intent to use ‘…an evidence-based approach to more actively challenge and engage with universities and colleges to make sustained and faster progress towards their targets across the student lifecycle’ (OFFA, 2015, p.12). This fits within a wider doctrine of ‘evidence-based practice’ in education, sometimes colloquially known as ‘what works’. The idea is simple: to focus resources on activities that have strong evidence for effectiveness. The reality is significantly more problematic, as generating unequivocal evidence in complex social fields is notoriously difficult (Donaldson, Christie and Mark, 2009; Pawson, 2013; Lingenfelter, 2016). Outreach is clearly such a field, with its long timescales, diverse settings and myriad influences. This complexity is exacerbated without a clear definition of ‘effectiveness’ in place. Current government policy aims ‘to double the proportion of people from disadvantaged backgrounds entering university in 2020 compared to 2009’ (BIS, 2016, p. 54), additionally focusing on increasing the proportion entering elite universities. Conversely, individual universities are duty bound to direct their outreach activities towards meeting the requirements of the Access Agreements that they negotiate with OFFA. These are generally couched in competitive terms of meeting recruitment targets of disadvantaged students to that specific university (McCaig, 2015; Rainford, in press). Senior university managers are inevitably keen to avoid censure (or worse) from OFFA and ensure that their admissions remain buoyant, alongside wider social justice motivations. Introduction The tension here is obvious: a university can meet its targets (and ostensibly be effective) for recruiting disadvantaged students without impacting at all on the national targets if it is simply capturing a greater share of the existing applicant pool; a ‘zero sum game’ where outreach is conflated with recruitment and universities seek easy wins, leading to few additional students being encouraged into higher education. This ‘confusion of successes’ is an added challenge to practitioners: is it success against institutional or national targets that matters – effectiveness for one university or for society in general? Outreach activities are often focused on changing attitudes to higher education by, for example, making it appear desirable, achievable or ‘normal’. However, other changes may also occur in terms of knowledge, behaviours or social relations. This article therefore focuses on evaluating whether and how activities lead to change. This change could be the explicit intention to enter higher education or, more likely, an intermediate state such as increased motivation at school, having a clear career goal or developing more self-confidence. ‘Effectiveness’ is used hereafter in an informal sense of judging the amount of change which can be ascribed to an activity. In other words, it is an assessment of what did happen with respect to participants relative to what would have happened otherwise – often described as the ‘counterfactual’ situation. Similarly, ‘causality’ is used informally to indicate the certainty that an activity is directly responsible for this change. These complexities underline the need for a considered and critical approach to evaluation that generates credible claims to knowledge. This article is aimed at those expected to generate or assess such claims, including researchers, practitioners, university managers and experienced evaluators applying their expertise to outreach activities. It draws on the findings of the recent Assessing Impact and Measuring Success project led by the authors (removed for review). Inter alia, this study found that 32 percent of university outreach managers had concerns about the quality of evidence available to them, while 91 percent were seeking to improve their evaluation processes. This article is methodologically agnostic, concerning itself instead with broad principles that can usefully underpin all forms of evaluation. It might appropriately be positioned within the ‘realist’ tradition developed and advocated by Pawson (2006, 2013) which engages with the intricate realities of how human choices are made within complex social fields. Introduction In particular, it looks at how we might better understand the impact of outreach in terms of transformational changes that are reflected in the choices made by young people who have been subject to deeply-ingrained educational inequalities. It also obliquely questions whether an evaluative focus on institutionally- driven ideas of success is actually a distraction from the wider issues of social justice that outreach is intended to address. Five challenges for evaluating outreach This section briefly explores five key epistemological challenges that are inherent within evaluations of outreach work and which any successful approach needs to consider, mitigate as far as possible and preferably overcome. They are not intended to be exhaustive, but rather a starting point for critiquing any proposed approach, including the tracking and trials approaches outlined above; indeed, the former are likely to be susceptible to 1 and 3, while the latter are more likely to be challenged by 2, 4 and 5. Dominant approaches to outreach evaluation At the time of writing, two approaches to evaluating outreach work are attaining a form of dominance in the field, yet both have shortcomings:  The ‘tracking’ approach. This has widespread support among current practitioner- managers (removed for review) and is generally based on collecting data on individuals over time with respect to (a) their involvement in activities, (b) their changing attitudes and choices, and (c) school outcomes including qualifications. These data are then used to explore the effectiveness of individual activities or a whole programme by identifying how attitudes and behaviours shift in step with outreach activities.  The ‘trials’ approach. This is emerging as a ‘borrowing’ from medicine and seeks to use techniques like randomised controlled trials to isolate a direct causal effect of activities. This has historically strong support in the US, albeit that there are growing critical voices about its claims (e.g. Bickman and Reich, 2009; Scriven, 2016; Lingenfelter, 2016). It is not currently widely used in the UK, although some practitioners believe it offers something of a ‘gold standard’ (removed for review). 1. Selection and self-selection biases A longstanding tenet of outreach is to target activities at individuals within identified disadvantaged groups who are felt likely to benefit from them (e.g. Department for Education and Employment, 2000; BIS, 2014). This is clearly appropriate in seeking to overcome structural educational inequalities by providing more support to those most in need, but it is heightened further where resources are constrained. From the evaluation perspective, this creates a strong selection bias within any data collected. The participants are not representative of the school or area from which they are drawn, but form a rarefied subgroup that have been selected for a particular purpose – i.e. because they are deemed to be potentially ‘in the market’ for higher education. This is further complicated where targeted young people, their families or their schools are able to absent themselves from the activity, either through a choice to opt-out (e.g. a refusal to participate) or a failure to opt-in – whether active (e.g. not completing a form) or passive (e.g. not being aware of the activity). If an activity requires an opt-in or where there are significant numbers of opt-outs, then self-selection bias is layered on top of the selection bias outlined above. Those families already positively predisposed towards education are likely to disproportionately take up opportunities compared to those ‘hard-to-reach’ families who might benefit more but who may be less likely to participate due to various forms of exclusion (Boag-Munroe and Evangelou, 2012). Evaluations which seek to compare the (self-)selected group with an unselected group as a counterfactual analysis are therefore likely to be fallacious and will usually over-estimate effectiveness as the two groups are likely to have different demographic profiles and pre-activity attitudes towards education. 2. Priming and social desirability effects The challenge with evaluating activities designed to shift attitudes is that young people very quickly become attuned to the idea that there are a ‘correct’ collection of attitudes to express to practitioners, teachers and parents. This is a form of social desirability bias; a well-attested phenomenon in social research whereby the participant will reproduce what they understand to be the required responses in order to please, impress or reassure the researcher. This potentially compromises both the reliability and validity of the evaluation data collected from young people about their educational experiences (Bowman and Seifert, 2011) Similarly, if a young person has been engaged in an activity that is designed to impart certain knowledge about higher education, it is likely that they will reflect this back to evaluators and others in the short term, especially if they are also asked about what they will do in the future. In the context of outreach, a taster day is very likely to generate short-term results that suggest an increased likelihood of attending university as this has been the purpose of the day and the events are fresh in the young person’s mind. Unless it is effectively internalised or regularly reinforced, this priming will fade over time as the information and experiences fall out of memory. As a result, the effectiveness of activities are likely to appear greater the closer in time the data are collected. 3. Deadweight and leakage The linked phenomena of leakage and deadweight are relevant to any social policy which is predicated on targeting certain individuals, including participation in higher education (removed for review). Leakage occurs when the targeting method fails and relatively advantaged individuals are erroneously included within the target group. Aside from the wastage of resources, this is challenge for evaluation as it will tend to cause an over-estimation of an activity’s effectiveness by capturing individuals who were always likely to apply to university. This might occur, for example, where relative advantaged children in a school serving a disadvantaged area are included in general classroom-based activities. Deadweight is a more complex idea. It relates to the targeting of individuals who meet the relevant criteria of disadvantage, but who would have followed the desired path without the activity; in other words, a disadvantaged young person who is already on the pathway to higher education without the need for outreach activities, even if they themselves are not aware of it at the time. Clearly, this is very difficult to assess from the practitioner’s perspective, as it involves engaging with future decisions yet to be made by a young person who cannot know at, say, the age of 13 what their intentions will turn out to be at the age of 17. In this instance, changes in reported intention can be erroneously assigned to activities that happen to coincide, without there being a causal relationship. In particular, this is a risk when evaluating lengthy programmes of activities that occur over several years, which can appear very effective simply by selecting high-achieving, but disadvantaged, young people who would almost certainly have progressed anyway (Croll and Attwood, 2013). The inability to predict future choices makes the construction of a viable comparison group problematic; indeed, improving this prediction would be a useful goal for future research. 4. Complexity and bounded rationality Social fields like participation in higher education are inherently complex. It is, however, easy to slip into a reductionist mindset of viewing outreach activities as quasi-scientific interventions, where a specific stimulus leads inexorably to a measurable result (Doyle and Griffin, 2012; Pawson, 2013). Within this mindset, the objective of the practitioner is to devise the ‘right’ portfolio of activities and the role of the evaluator is to confirm ‘what works’ by demonstrating unequivocal causal changes. The reality is very different. The lives of all young people are ‘messy’ as they are buffeted by myriad experiences and influences – some planned, but many accidental. The beliefs and expectations of their families, schools and communities will shape their own attitudes and ambitions. The intersection of their gender and ethnicity will also play a role, as will other social factors like disability or sexuality. All of these elements are then mediated through the prism of personality – itself mutable in the process of becoming an adult. Furthermore, Simon’s (e.g. 1979, 1997) seminal work on bounded rationality compelling asserts the limits of human decision-making. This is not to say that young people are inherently irrational, but that their decisions about higher education will be dictated by the information available to them, their own subjective priorities, the time available and judgements about likelihoods and risk. Humans also tend to make intuitive decisions that are grounded in emotions and a range of unconscious heuristics (Kahneman, 2003). Given this complexity of environment and decision-making, the idea of an outreach activity having a predictable causal outcome on a young person’s decisions appears thoroughly misguided. Activities will affect certain groups or individuals more than others – indeed, they may be actively negative for some. Similarly, the impact may be positive from the perspective of the practitioner in one element (e.g. raising motivation for schoolwork), but negative in another (e.g. making apprenticeships seem more attractive than university). The same activity run twice with different individuals or in different places may well have markedly different outcomes. This complexity means that effectiveness of activities will never be static or predictable. An activity can only be judged to have been successful at one time and in one context – and probably only with some of the participants (Pawson, 2013). This must limit the inferences that can be drawn about effectiveness and the life expectancy of those inferences. 5. Confounding factors and non-linearity 4. Complexity and bounded rationality It also makes conclusions about certain types of activity in the abstract particularly problematic – e.g. a claim that ‘summer schools are effective’ – especially as every university will provide their own ‘flavour’ of the activity with different staff and resources (Hoare and Mann, 2014). 5. Confounding factors and non-linearity From its inception, outreach has generally been conceived as a process rather than as a single event in time. It is assumed, probably rightly, that shifting the knowledge, beliefs, attitudes and behaviours of young people takes concerted effort over a series of encounters – especially where there are ingrained expectations from their families, their schools or their communities acting to prevent that change (Gorard et al., 2006). In its most extreme incarnations, it is a ten-year process spanning mid primary through to late secondary schooling. In a related point to the previous one, one temptation may be to seek to evaluate changes in young people over this time period as if the efforts of practitioners are the only influence when, in reality, there are many confounding factors at work. In particular, the impact of the school and its teachers, where young people spend far more time than in outreach activities, are very likely to effect changes to knowledge about and attitudes towards higher education (Winterton and Irwin, 2012; Fuller, 2014). Within a long-term, but punctuated, programme of activities, there is a risk of erroneously ascribing changes to those activities rather than what might occur in between: is it the activities offered that are effective or the day-to-day influence of teachers? It may even be the ongoing partnership between a university and a school which impacts on the knowledge, expectations and ethos embodied in the latter, rather than any direct effect of activities. Within a structured and long-term series of activities with a young person, there is also the risk of assuming that there is a linear and positive cumulative effect over time – i.e. that each activity goes a little way further to tipping them towards higher education. This is likely to be fallacious. As noted earlier, some activities may have negative effects from the perspective of higher education (e.g. by suggesting alternative routes) or may only have an effect months later when reflected upon, perhaps in conjunction with other experiences. Alternatively, two activities might only prove effective when offered several months apart, providing mutual reinforcement, with neither being effective in isolation. This non-linearity makes conclusions about causality and effectiveness problematic. Realist evaluation As a springboard, this article uses Pawson’s (2006, 2013) idea of ‘realist’ evaluation. This approach places the individual’s choices at the heart of the evaluation, ‘recognising that the fate of social policy lies in the real choices of choice makers and [evaluation’s] task is to explain the distribution and consequences of those choices’ (Pawson, 2013, p. 71). Human choice is seen as the driving force for changes in behaviour, so the purpose of an activity is to provide circumstances where changes can take place. The idea of direct causality between activity and change is dismissed as simplistic in a complex social field with multiple confounding influences. In particular, it rejects ‘medicalised’ approaches to evaluation that derive from a basic stimulus-effect model of human behaviour. Pawson (2006, p.25) emphasises the ‘messiness’ of social fields and argues that the only appropriate question is ‘What works for whom and in what circumstances?’, rather than seeking authoritative statements about effectiveness that are decontextualized from people, setting or time: ‘the ludicrous idea that evaluators and researchers are able to tell policy-makers and practitioners exactly what works in the world of policy interventions’ (ibid, p.170). A key idea of realist evaluation is that a planned activity within a social field is the embodiment of a ‘theory of change’ – it represents some conception of how an individual might be ‘moved’ from one state to another. This might be a deliberate process, based in the expertise of the practitioner or social theory, or a tacit one based on beliefs, prior experiences or borrowing from elsewhere. Pawson sees this transformational theory of change as being the focus of evaluation rather than the outcomes of the activity, with the purpose of evaluation being to interrogate and hone this theory. This approach embraces the inherent complexity of fields like outreach and the bounds on human rationality, with a desire to understand the complex web of factors as work and how to influence them, rather than seeking to ignore or eliminate them in pursuit of simplistic causal relationships and dubious measures of effectiveness. Realist evaluation Realist evaluation rejects this as likely to create misleading results with over-confident conclusions, while remaining silent on how to improve practice: ‘There is […] no concealing the reality that the same intervention can trigger change in myriad ways, and no way of camouflaging the truth that the different contexts in which programmes are implemented are as wide as society is wide’ (Pawson, 2013, pp. 29-30). A ‘small steps’ approach This section outlines a potential alternative approach, broadly within the realist tradition, to both conceiving and evaluating outreach activity based on ‘small steps’. This is intended to signal a partial rejection both of long-term tracking (although this may have value for understanding key junctures at which change occurs) and of unwieldy and over-engineered trials (although they may have some value in evaluating short-term activities). It also denotes a conceptualisation of participation in higher education as a process with many intermediate steps which young people take and which evaluators must heed. It attempts to provide a means of addressing issues of effectiveness while overcoming some of the challenges outlined above. It is methodologically neutral, in that it is compatible with a range of data collection methods – both quantitative and qualitative – which need to be designed around the intervention, the participant group and the practitioners involved. Rather, we suggest five principles to guide how evaluation is conceived and undertaken, relating to theories of change, measurement, causality, timescales and disadvantage:  Articulation of a clear theory of change. Outreach activities are, at their heart, about causing change within individuals. If practitioners expect to cause change, then they need to have a clear articulation of the mechanisms by which they expect this to occur at the individual level – a theory of change. As well as attending to outcomes, which is an obvious concern of evaluation, the starting point of the individual needs to be recognised alongside a deep engagement with psychological, sociological and psychosocial processes; indeed, the first and last of these have been somewhat neglected within theorisations of participation in general. For example, practitioners wanting to ‘raise aspirations’ need to be clear what an aspiration is, how it is formed and how it is crystallised in reference to others. This clarity then provides a framework for evaluation which focuses on individual and group processes in sequence (i.e. a logic chain). The theory of change can then be evaluated in terms of its effectiveness in describing processes and predicting outcomes, to be further honed through reflective practice and empirical research.  Criticality about causality. The complexity and non-linearity outlined above is problematic for drawing strong conclusions about an activity and its causal effects on individuals. The trial approach attempts to resolve this by focusing on the outcomes of participants relative to a (preferably randomised) group of non-participants. A ‘small steps’ approach If well-executed, this can provide some evidence as to whether an intervention is effective (self-selection, priming and confounding issues notwithstanding), but not the more important question of why it is effective. This sort of evaluation risks reducing activities to a form of ‘magic box’ where nothing is known about the processes within it. Indeed, it may fail to identify if the effective element is incidental to the activity rather than integral to it – e.g. the personal relationships developed alongside the activity. Instead, we advocate evaluating the success of activities in terms of these intermediate processes – i.e. the logic chain within the theory of change. In general, the research community knows surprisingly little about the effects of interventions on educational disadvantage (Gorard and See, 2013). Instead, much is assumed by practitioners and it is in these areas of small change that evaluations focusing on causality might best be used.  Criticality about measurability. While some of the measures used to understand widening participation are broadly reliable and valid (e.g. examination results or the submission of a university application), many are more subjective and readily contestable. In particular, evaluations often rely on easily-collected self-reports of attitudes and future intentions from young people (or teachers and parents) – measuring the measurable. Validity here is very uncertain, especially given priming and social desirability effects. In order to ensure evaluation through measures with strong reliability and internal validity, we suggest eschewing attitudinal measures in favour of those based on knowledge or behaviours – e.g. asking about the number of university websites visited rather than a possible future intention to apply. Future research may be able to reveal which of such measures are strongly correlated with future behaviours and can therefore be used as a proxy. Greater use of pre/post and quasi-experimental designs are also likely to support a more robust approach to the identification of changes.  Using appropriate timescales. There is a tension between evaluating individual activities over a short time period and evaluating whole programmes over very long periods, potentially measured in years. While the desire for the latter is understandable, we suggest that it is probably unattainable due to complexity and the dominance of the confounding factors in young people’s lives, as well as the difficulty in undertaking a counterfactual analysis. A ‘small steps’ approach Where there certainly is value is in tracking young people’s attitudes at regular points in time, with appropriate distance from major activities to mitigate social desirability and priming effects. Instead, we suggest that evaluative efforts are focused on individual activities. If a robust theory of change for each activity is evidenced and there is an overarching theory of change for the integrated programme, then there is unlikely to be a need to evaluate the programme as a whole – and efforts to do so are likely to be vexed for the reasons discussed above. It is more important to have confidence in each intervention in its own terms, relative to its theory of change, especially in universities which employ a ‘pick and mix’ approach where young people receive a varying portfolio of activities built around their unique needs.  A focus on educational disadvantage. Evidence is building that differences in participation rates between socioeconomic groups results from the accumulated educational disadvantages faced by some young people, rather than being an issue around aspirations in the late-teenage years (e.g. Crawford, 2014; Whitty, Hayton and Tang, 2015). As such, it is not only morally important that outreach should address itself more directly to these structural inequalities, but it provides a useful distinction between effectiveness as conceived as challenging disadvantage as opposed to success in recruitment for a specific university; we suggest that evaluation also needs to recognise this distinction. Inequalities in attainment are clearly key, but other areas that have been somewhat neglected include challenging negative expectations from adults surrounding young people, broadening career horizons and providing high-quality advice and guidance (removed for review). Conclusion This article does not seek to provide a toolkit for evaluation, but rather to identify challenges to be mitigated and principles that are likely to underpin effective evaluation practice. We do not claim that the ‘small steps’ approach we advocate provides a full solution to the vexed issues outlined in the first half of the article. However, we do feel that it does provide a sounder basis than the existing and emerging orthodoxies with their focus on excessive timeframes or certifying ‘the best’ interventions. Perhaps the most important element of this is the focus on the social and individual theory of change embodied within an activity. In particular, our approach respects the role of practitioners as reflective professionals who, with help from evaluators, can refine their theories of change and the resulting practices. We have contextualised our small steps approach within a period of policy that is marked by what we have typified as a ‘confusion of successes’. On the one hand, the recent White Paper (BIS, 2016) commits to doubling participation rates for disadvantaged young people, however the main policy levers used on individual universities instils a competitive market where targets can just as easily be met by targeted recruitment activities as those designed to challenge educational inequalities. We believe this risks distorting evaluation activity to focus on attempts to demonstrate value-for-money against simplistic and inward-looking institutional recruitment outcomes (removed for review). Our final point, then, is to encourage practitioners to refocus their evaluative efforts back on effectiveness in addressing structural educational inequalities, in particular through improving young people’s attainment, broadening the educational and occupational opportunities available to them and offering guidance to help them realise their ambitions. References References Bickman, L. and S. Reich. 2009. Randomized controlled trials: a gold standard with feet of clay? In S. Donaldson, C. Christie and M. Mark (eds.) What counts as credible evidence in applied research and evaluation practice? Thousand Oaks: Sage. Boag-Munroe, G. and M. Evangelou. 2012. From hard to reach to how to reach: A systematic review of the literature on hard-to-reach families. Research Papers in Education 27(2): 209- 239. Bowman, N. and T. Seifert. 2011. Can college students accurately assess what affects their learning and development? Journal of College Student Development 52(3): 270-290. 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Donaldson, S., Christie, C. and Mark, M. (eds.) 2009. What counts as credible evidence in applied research and evaluation practice? Thousand Oaks: Sage. Doyle, M. and M. Griffin. 2012. Raised aspirations and attainment? A review of the impact of Aimhigher (2004–2011) on widening participation in higher education in England. London Review of Education 10(1): 75-88. Fuller, C. 2014. Social capital and the role of trust in aspirations for higher education. Educational Review, 66(2): 131-147. Gorard, S., N. Adnett, H. May, K. Slack, E. Smith and L. Thomas. 2006. Overcoming the barriers to higher education. Stoke-on-Trent: Trentham. Gorard, S. and B.H. See. 2013. Overcoming disadvantage in education. Abingdon: Routledge. Gorard, S. and B.H. See. 2013. Overcoming disadvantage in education. Abingdon: Routledge. Hoare, T. and R. Mann. 2012. The impact of the Sutton Trust’s Summer Schools on subsequent higher education participation. London: Sutton Trust. Kahneman, D. 2003. Maps of bounded rationality: psychology of behavioural economics. American Hoare, T. and R. Mann. 2012. The impact of the Sutton Trust’s Summer Schools on subsequent higher education participation. References London: Sutton Trust. Kahneman, D. 2003. Maps of bounded rationality: psychology of behavioural economics. American Economic Review 93(5): 1449-1475. Kahneman, D. 2003. Maps of bounded rationality: psychology of behavioural economics. American Kahneman, D. 2003. Maps of bounded rationality: psychology of behavioural economics. American Economic Review 93(5): 1449-1475. Kahneman, D. 2003. Maps of bounded rationality: psychology of behavioural economics. American Economic Review 93(5): 1449-1475. Lingenfelter, P. 2016. “Proof”, policy and practice: understanding the role of evidence in improving education. Sterling: Stylus Publishing. Lingenfelter, P. 2016. “Proof”, policy and practice: understanding the role of evidence in improving education. Sterling: Stylus Publishing. 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Targeting of widening participation measures by elite institutions: widening access or simply aiding recruitment? Awaiting publication in Perspectives: Policy and Practice in Higher Education. DOI: 10.1080/13603108.2016.1148645 Scriven, M. 2016. Roadblocks to recognition and revelation. American Journal of Evaluation 37(1): 27-44. Simon, H. 1979. Rational decision-making in business organisations. American Economic Review 69(4): 493-513. Simon, H. 1979. Rational decision-making in business organisations. American Economic Review 69(4): 493-513. Simon, H. 1997. An empirically based microeconomics. Cambridge: Cambridge University Press. Simon, H. 1997. An empirically based microeconomics. Cambridge: Cambridge University Press. Winterton, M. and Irwin, S. 2012. Teenage expectations of going to university: the ebb and flow of influences from 14 to 18. Journal of Youth Studies 15(7): 858-874. Winterton, M. and Irwin, S. 2012. Teenage expectations of going to university: the ebb and flow of influences from 14 to 18. Journal of Youth Studies 15(7): 858-874. Whitty, G., A. Hayton and S. Tang. 2015. References Who you know, what you know and knowing the ropes: a review of evidence about access to higher education institutions in England. Review of Education 3 (1): 27-67. Whitty, G., A. Hayton and S. Tang. 2015. Who you know, what you know and knowing the ropes: a review of evidence about access to higher education institutions in England. Review of Education 3 (1): 27-67.
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Modelling infectious diseases with relapse: a case study of HSV-2
Theoretical biology and medical modelling
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*Correspondence: toshikazu.kuniya@gmail.com 3Department of Applied Mathematics, Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, 657-8501 Kobe, Japan Full list of author information is available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 DOI 10.1186/s12976-017-0059-4 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 DOI 10.1186/s12976-017-0059-4 Abstract Background: Herpes Simplex Virus Type 2 (HSV-2) is one of the most common sexually transmitted diseases. Although there is still no licensed vaccine for HSV-2, a theoretical investigation of the potential effects of a vaccine is considered important and has recently been conducted by several researchers. Although compartmental mathematical models were considered for each special case in the previous studies, as yet there are few global stability results. Results: In this paper, we formulate a multi-group SVIRI epidemic model for HSV-2, which enables us to consider the effects of vaccination, of waning vaccine immunity, and of infection relapse. Since the number of groups is arbitrary, our model can be applied to various structures such as risk, sex, and age group structures. For our model, we define the basic reproduction number ℜ0 and prove that if ℜ0 ≤1, then the disease-free equilibrium is globally asymptotically stable, whereas if ℜ0 > 1, then the endemic equilibrium is so. Based on this global stability result, we estimate ℜ0 for HSV-2 by applying our model to the risk group structure and using US data from 2001 to 2014. Through sensitivity analysis, we find that ℜ0 is approximately in the range of 2-3. Moreover, using the estimated parameters, we discuss the optimal vaccination strategy for the eradication of HSV-2. Conclusions: Through discussion of the optimal vaccination strategy, we come to the following conclusions. (1) Improving vaccine efficacy is more effective than increasing the number of vaccines. (2) Although the transmission risk in female individuals is higher than that in male individuals, distributing the available vaccines almost equally between female and male individuals is more effective than concentrating them within the female population. Keywords: Multi-group SVIRI epidemic model, Relapse, Basic reproduction number, Global asymptotic stability, Herpes Simplex Virus Type 2, Vaccination Jinliang Wang1, Xiaoqing Yu1, Heidi L. Tessmer2, Toshikazu Kuniya3* and Ryosuke Omori2,4 Jinliang Wang1, Xiaoqing Yu1, Heidi L. Tessmer2, Toshikazu Kuniya3* and Ryosuke Omori2,4 Background Herpes Simplex Virus Type 2 (HSV-2) is one of the most common sexually trans- mitted diseases, and has infected about 417 million people aged 15-49 worldwide [1]. Although there is still no licensed vaccine for HSV-2, a theoretical investigation of the potential effects of a vaccine is considered important and has recently been con- ducted by several researchers (see [2–4]). In [2, 3], compartmental epidemic models with vaccination for HSV-2 were considered and the effectiveness of the vaccina- tion was discussed in connection with the basic reproduction number ℜ0 (see [5]) Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 2 of 20 through numerical simulations. However, there was little discussion about the stability of each equilibrium. As observed in several papers on epidemic models with vaccina- tion (see, for instance, [6–8]), backward bifurcation can occur at ℜ0 = 1 for some special models and ℜ0 < 1 does not necessarily imply the global asymptotic sta- bility of the disease-free equilibrium, that is, the eradication of the disease. In that case, the vaccination effort solely to make ℜ0 < 1 has less significance. There- fore, a global stability analysis is critical for theoretically justifying the epidemiological discussion. In [4], Lou et al. considered a compartmental epidemic model for HSV-2 with age and risk group structures and discussed the effectiveness of the vaccination together with the global stability analysis of each equilibrium. In their study, the vaccination was limited to female individuals, who are known to be the high-risk group for HSV- 2, and it was concluded that such a vaccination strategy can reduce the total infections in both females and males. However, to support their conclusion, we need to consider a more general model in which male individuals can also benefit from the vaccina- tion and show that the optimal distribution ratio of the vaccines is 1 to 0 for female and male individuals. In this paper, we consider such a general model and investi- gate the optimal distribution ratio of the vaccines. As opposed to their conclusion, our result shows that distributing the vaccines almost equally to females and males is more effective for the eradication of HSV-2 than concentrating them within the female population. Background To consider the effect of vaccination with imperfect immunity, SVIR epidemic models are often formulated, in which the total population is subdivided into the suscepti- ble (S), vaccinated (V), infective (I) and recovered (R) populations (see, for instance, [2, 6–10]). However, to take into account the relapse of HSV-2 (see [2, 11]), it is necessary to also consider a direct transition from R to I. Thus, in this paper, we formulate a multi-group SVIRI epidemic model for HSV-2, which enables us to con- sider the effects of vaccination, of waning vaccine immunity, and of infection relapse. Since the number of groups is arbitrary, our model can be applied to various struc- tures such as risk, sex, and age group structures. In the empirical portion of this paper, we apply our model to the risk group structure and estimate the basic reproduc- tion number ℜ0 for HSV-2 by using data from the US from 2001 to 2014. Since the infective population of HSV-2 seems to be in endemic equilibrium, the estimation of ℜ0 must be carried out under the global asymptotic stability of the endemic equilib- rium. However, in general, the global asymptotic stability of the endemic equilibrium is not trivial. Recently, multi-group epidemic models have been studied by many authors [10, 12–24]. One of the most effective approaches for global stability analysis of multi- group epidemic models is the graph-theoretic approach developed by Guo et al. [14]. Since our model has a quite complex form with the paths from V to S (the wan- ing of vaccine-induced immunity), R to I (relapse) and distributed time delay, the global asymptotic stability analysis is challenging. In this paper, by applying the graph- theoretic approach as in [14] together with an approach of max function as in [10], we prove that if ℜ0 > 1, then the endemic equilibrium is globally asymptotically stable, whereas if ℜ0 ≤1, then the disease-free equilibrium is so. Based on this theoretical result, we estimate ℜ0 for HSV-2 by using US data from 2001 to 2014. By using the Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 3 of 20 estimated parameters, we discuss the optimal vaccination strategy for the eradication of HSV-2. The general multi-group SVIRI epidemic model (A6) The survival probability for recovered individuals in group i ∈N , who spent time t in the recovered class, is Pi(t) := exp(−  t 0 δi(η)dη), where δi(η) denotes the relapse risk for individuals who spent time η in the recovered class in group i. For each i ∈N , δi ∈L1 loc,+(0, +∞) and  +∞ 0 δi(η)dη = +∞. (A6) The survival probability for recovered individuals in group i ∈N , who spent time t in the recovered class, is Pi(t) := exp(−  t 0 δi(η)dη), where δi(η) denotes the relapse risk for individuals who spent time η in the recovered class in group i. For each i ∈N , δi ∈L1 loc,+(0, +∞) and  +∞ 0 δi(η)dη = +∞. (A6) The survival probability for recovered individuals in group i ∈N , who spent time t in the recovered class, is Pi(t) := exp(−  t 0 δi(η)dη), where δi(η) denotes the relapse risk for individuals who spent time η in the recovered class in group i. For each i ∈N , δi ∈L1 loc,+(0, +∞) and  +∞ 0 δi(η)dη = +∞. Under assumptions (A1)-(A2), we see that the time variation of Ni(t), i ∈N is governed by the following differential equation: N′ i(t) = bi −μiNi(t), i ∈N . (1) N′ i(t) = bi −μiNi(t), i ∈N . (1) From the variation of constants formula, we easily see that limt→+∞Ni(t) = bi/μi =: N∗ i , i ∈N . Hence, without loss of generality, we can assume that Ni(t) ≡N∗ i , i ∈N . Then, under assumptions (A1)-(A4), we obtain the differential equations for Si(t) and Vi(t), i ∈N as follows: From the variation of constants formula, we easily see that limt→+∞Ni(t) = bi/μi =: N∗ i , i ∈N . Hence, without loss of generality, we can assume that Ni(t) ≡N∗ i , i ∈N . Then, under assumptions (A1)-(A4), we obtain the differential equations for Si(t) and Vi(t), i ∈N as follows: S′ i(t) =bi −Si(t) n  j=1 βij Ij(t) N∗ j −(μi + vi) Si(t) + ωiVi(t), (2) V ′ i (t) =viSi(t) −σiVi(t) n  j=1 βij Ij(t) N∗ j −(μi + ωi) Vi(t). The general multi-group SVIRI epidemic model The general multi-group SVIRI epidemic model Let n ∈N be the number of groups and let N := {1, 2, · · · , n}. Let Ni(t) be the sexually active population in group i ∈N at time t. Let us divide Ni(t) into four sub- populations: susceptible Si(t), vaccinated Vi(t), infective Ii(t), and recovered Ri(t). Thus, Ni(t) = Si(t) + Vi(t) + Ii(t) + Ri(t) for all i ∈N . We make the following assumptions: (A1) The number of individuals becoming sexually active in group i ∈N per unit time is bi > 0. (A1) The number of individuals becoming sexually active in group i ∈N per unit time is bi > 0. (A2) The per capita rate of removal from the sexual activity in group i ∈N is μi > 0. (A3) The coefficient for disease transmission from infective individuals in group j ∈N to uninfected (susceptible or vaccinated) individuals in group i ∈N is βij ≥0. The matrix (βij)i,j∈N is irreducible. The vaccine efficacy in group i ∈N is σi ∈[0, 1] and the force of infection to vaccinated individuals in group i ∈N is weakened by multiplying σi. That is, (A3) The coefficient for disease transmission from infective individuals in group j ∈N to uninfected (susceptible or vaccinated) individuals in group i ∈N is βij ≥0. The matrix (βij)i,j∈N is irreducible. The vaccine efficacy in group i ∈N is σi ∈[0, 1] and the force of infection to vaccinated individuals in group i ∈N is weakened by multiplying σi. That is, λS i (t) := n  j=1 βij Ij(t) Nj(t) and λV i (t) :=σi n  j=1 βij Ij(t) Nj(t), i ∈N are the forces of infection to susceptible and vaccinated individuals in group i ∈N at time t ≥0, respectively. Here we assume standard incidence. (A4) The per capita vaccination rate for susceptible individuals in group i ∈N is vi > 0. The per capita rate for the waning of vaccine-induced immunity for vaccinated individuals in group i ∈N is ωi ≥0. (A5) The per capita recovery rate of infective individuals in group i ∈N is γi > 0. (A5) The per capita recovery rate of infective individuals in group i ∈N is γi > 0. The general multi-group SVIRI epidemic model (3) S′ i(t) =bi −Si(t) n  j=1 βij Ij(t) N∗ j −(μi + vi) Si(t) + ωiVi(t), (2) (2) V ′ i (t) =viSi(t) −σiVi(t) n  j=1 βij Ij(t) N∗ j −(μi + ωi) Vi(t). (3) (3) Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 4 of 20 Biology and Medical Modelling (2017) 14:13 Page 4 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 4 of 20 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 4 of 20 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 4 of 20 Under assumptions (A5)-(A6), the recovered population in group i ∈N at time t is given by Under assumptions (A5)-(A6), the recovered population in group i ∈N at time t is given by Ri(t) =  +∞ 0 γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ =  t −∞ γiIi(ξ)e−μi(t−ξ)e−  t−ξ 0 δi(η)dηdξ, i ∈N . (4) =  t −∞ γiIi(ξ)e−μi(t−ξ)e−  t−ξ 0 δi(η)dηdξ, i ∈N . (4) (4) By differentiating (4), we obtain the following integro-differential equation for Ri(t), i ∈N . R′ i(t) =γiIi(t) −μiRi(t) −  t −∞ δi(t −ξ)γiIi(ξ)e−μi(t−ξ)e−  t−ξ 0 δi(η)dηdξ =γiIi(t) −μiRi(t) −  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ. (5) (5) From (1)-(5) we obtain the integro-differential equation for Ii(t), i ∈N as follows. I′ i(t) = (Si(t) + σiVi(t)) n  j=1 βij Ij(t) N∗ j −(μi + γi)Ii(t) +  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ. Under this setting, we arrive at the following main model in this paper. ⎧ ⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎨ ⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎩ S′ i(t) = bi −Si(t) n  j=1 βij Ij(t) N∗ j −(μi + vi)Si(t) + ωiVi(t), V ′ i (t) = viSi(t) −σiVi(t) n  j=1 βij Ij(t) N∗ j −(μi + ωi) Vi(t), I′ i(t) = (Si(t) + σiVi(t)) n  j=1 βij Ij(t) N∗ j −(μi + γi)Ii(t) +  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ, i ∈N . (6) (6) +  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ, i ∈N . Note that the differential equation of Ri(t), i ∈N can be omitted since it does not appear in the above three equations. The equilibria of system (6) can be obtained as the solution of the following algebraic equations. The general multi-group SVIRI epidemic model ⎧ ⎪⎪⎪⎪⎪⎪⎪⎨ ⎪⎪⎪⎪⎪⎪⎪⎩ 0 = bi −Si n j=1 βij Ij N∗ j −(μi + vi)Si + ωiVi, 0 = viSi −σiVi n j=1 βij Ij N∗ j −(μi + ωi) Vi, 0 = (Si + σiVi) n j=1 βij Ij N∗ j −(μi + γi −Qi)Ii, i ∈N , (7) (7) where Qi :=  +∞ 0 δi(ξ)γie−μiξe−  ξ 0 δi(η)dηdξ, i ∈N . Note that Note that Qi <γi  +∞ 0 δi(ξ)e−  ξ 0 δi(η)dηdξ = γi −e−  ζ 0 δi(η)dη +∞ 0 = γi, i ∈N . Hence, we have μi + γi −Qi > 0 for all i ∈N . Hence, we have μi + γi −Qi > 0 for all i ∈N . Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 5 of 20 It is easy to see that the trivial solution of (7) such that Ii = 0 for all i ∈N always exists. It is called the disease-free equilibrium of system (6) and we write it as E0 := S0 1, V 0 1 , 0, S0 2, V 0 2 , 0, · · · , S0 n, V 0 n, 0 ∈R3n + , where S0 i := bi μi μi + ωi μi + vi + ωi , V 0 i := vi μi + ωi S0 i = bi μi vi μi + vi + ωi , i ∈N . Existence of the endemic equilibrium E∗:= S∗ 1, V ∗ 1 , I∗ 1, · · · , S∗ n, V ∗ n , I∗ n ∈R3n + such that I∗ i > 0 for all i ∈N will be discussed in connection with the basic reproduction number ℜ0, which is defined as the expected number of secondary cases produced by a typical infected individual during its entire period of infectiousness at the initial invasion phase into a fully susceptible population, and given by the spectral radius of the next generation matrix (see [25]). Let F := ⎛ ⎜⎜⎝ S0 1 + σ1v0 1 β11 N∗ 1 · · · S0 1 + σ1v0 1 β1n N∗n ... ... ... S0 n + σnv0 n βn1 N∗ 1 · · · S0 n + σnv0 n βnn N∗n ⎞ ⎟⎟⎠and V := diag 1≤i≤n (μi + γi −Qi) . The general multi-group SVIRI epidemic model Then, according to [25], the next generation matrix is given by K := FV−1 = ⎛ ⎜⎜⎜⎝ S0 1+σ1V 0 1 β11 (μ1+γ1−Q1)N∗ 1 · · · S0 1+σ1V 0 1 β1n (μn+γn−Qn)N∗n ... ... ... (S0 n+σnV 0 n)βn1 (μ1+γ1−Q1)N∗ 1 · · · (S0 n+σnV 0 n)βnn (μn+γn−Qn)N∗n ⎞ ⎟⎟⎟⎠. K := FV−1 = ⎛ ⎜⎜⎜⎝ S0 1+σ1V 0 1 β11 (μ1+γ1−Q1)N∗ 1 · · · S0 1+σ1V 0 1 β1n (μn+γn−Qn)N∗n ... ... ... (S0 n+σnV 0 n)βn1 (μ1+γ1−Q1)N∗ 1 · · · (S0 n+σnV 0 n)βnn (μn+γn−Qn)N∗n ⎞ ⎟⎟⎟⎠. Hence, the basic reproduction number ℜ0 is defined by Hence, the basic reproduction number ℜ0 is defined by Hence, the basic reproduction number ℜ0 is defined by ℜ0 := ρ(K), (8) (8) ℜ0 := ρ(K), where ρ(·) denotes the spectral radius of a matrix. We will obtain the global stability results for (6) in connection with ℜ0 (see the “Results” section). The special multi-group SVIRI epidemic model for HSV-2 The general model (6) can be applied to analyze the field data of HSV-2 epidemics. Sim- ilar to other sexually transmitted infections, the risk factor for HSV-2 infection is sexual behavior. To describe the heterogeneity of HSV-2 infection risk between host individu- als, we characterize the group as the combination of sex and their sexual behavior. We consider the following levels of sexual activity: x = 0, 1, 2, · · · , 5 meaning the number of sexual partners within the last 12 months, where x = 5 implies the number of sexual part- ners is 5 or more. Let y ∈{1, 2} denote the sex, 1 denotes male and 2 denotes female. Then, the risk group is characterized by i ∈{1, 2, · · · , 12} in the following way: i = 2xi + yi, where (xi, yi) =  (m −1, 1) if i = 2m −1, (m −1, 2) if i = 2m, m = 1, 2, · · · , 6. For example, i = 2 corresponds to (xi, yi) = (0, 2) and implies the group of female indi- viduals with no sexual partners and i = 11 corresponds to (xi, yi) = (5, 1) and implies the group of male individuals with 5 or more sexual partners. Then, (6) can be written as follows: Page 6 of 20 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 ⎧ ⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎨ ⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎩ S′ i(t) = bi −Si(t) 12  j=1 βij Ij(t) N∗ j −(μi + vi)Si(t) + ωiVi(t), V ′ i (t) = viSi(t) −σiVi(t) 12  j=1 βij Ij(t) N∗ j −(μi + ωi) Vi(t), I′ i(t) = (Si(t) + σiVi(t)) 12  j=1 βij Ij(t) N∗ j −(μi + γi)Ii(t) +  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ, i ∈{1, 2, · · · , 12}. (9) (9) ⎪⎪⎪⎩i ∈{1, 2, · · · , 12}. Note that (9) is a special case of (6). In this section, we assume that δi(ξ) ≡δi > 0 for all i ∈{1, 2, · · · , 12}. Note that the assumption (A6) is satisfied. In this case, we have: Note that (9) is a special case of (6). In this section, we assume that δi(ξ) ≡δi > 0 for all i ∈{1, 2, · · · , 12}. Note that the assumption (A6) is satisfied. The special multi-group SVIRI epidemic model for HSV-2 In this case, we have:  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ =δi  +∞ 0 γiIi(t −ξ)e−μiξe−δiξdξ =δiRi(t), i ∈{1, 2, · · · , 12}. Hence, together with the Eq. 5 of Ri(t), (9) can be simplified to the following multi-group SVIRI epidemic model. Hence, together with the Eq. 5 of Ri(t), (9) can be simplified to the following multi-group SVIRI epidemic model. ⎧ ⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎨ ⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎩ S′ i(t) = bi −Si(t) 12  j=1 βij Ij(t) N∗ j −(μi + vi)Si(t) + ωiVi(t), V ′ i (t) = viSi(t) −σiVi(t) 12  j=1 βij Ij(t) N∗ j −(μi + ωi) Vi(t), I′ i(t) = (Si(t) + σiVi(t)) 12  j=1 βij Ij(t) N∗ j −(μi + γi)Ii(t) + δiRi(t), R′ i(t) = γiIi(t) −(μi + δi) Ri(t), i ∈{1, 2, · · · , 12}. (10) (10) Vi(t)) 12  j=1 βij Ij(t) N∗ j −(μi + γi)Ii(t) + δiRi(t), No vaccine against HSV-2 infection is currently available, so we ignore the vaccinated class Vi, i ∈{1, 2, · · · , 12} in the estimation of ℜ0. Then, (10) can be rewritten as follows. ⎧ ⎪⎪⎪⎪⎪⎪⎪⎪⎪⎨ ⎪⎪⎪⎪⎪⎪⎪⎪⎪⎩ S′ i(t) = bi −Si(t) 12  j=1 βij N∗ j Ij(t) −μiSi(t), I′ i(t) = Si(t) 12  j=1 βij N∗ j Ij(t) −(μi + γi)Ii(t) + δiRi(t), R′ i(t) = γiIi(t) −(μi + δi) Ri(t), i ∈{1, 2, · · · , 12}. (11) (11) The basic reproduction number ℜ0 for (11) is obtained as the spectral radius of the following matrix. The basic reproduction number ℜ0 for (11) is obtained as the spectral radius of the following matrix. ⎛ ⎜⎜⎜⎝ S0 1 μ1+γ1−Q1 β1,1 N∗ 1 · · · S0 1 μ12+γ12−Q12 β1,12 N∗ 12 ... ... ... S0 12 μ1+γ1−Q1 β12,1 N∗ 1 · · · S0 12 μ12+γ12−Q12 β12,12 N∗ 12 ⎞ ⎟⎟⎟⎠, Biology and Medical Modelling (2017) 14:13 P Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 7 of 20 where Qi = δiγi/(μi + δi) and we write βij as βi,j for improved readability. where Qi = δiγi/(μi + δi) and we write βij as βi,j for improved readability. where Qi = δiγi/(μi + δi) and we write βij as βi,j for improved readability. Transmission rates between the risk groups i and j, βij, depend on sexual behavior and sex. We modeled βij as follows; βij = ρxiyiρxjyjRxixjSyiyj. The special multi-group SVIRI epidemic model for HSV-2 (12) (12) βij = ρxiyiρxjyjRxixjSyiyj. The meaning of each symbol for βij is as follows. The meaning of each symbol for βij is as follows. The meaning of each symbol for βij is as follows. • ρxiyi denotes the HSV-2 infection risk for the risk group i. The risk group is stratified by sex and the number of partners within the last 12 months, the risk group i denotes the individuals whose number of partners within the last 12 months is xi and sex is yi. ρxiyi is given by; ρxiyi = cyi(xi + 1)φ. ρxiyi = cyi(xi + 1)φ. Here, similar to previous modelling studies of sexually transmitted infections, we modeled the relationship between infection risk and sexual behavior by a power law function [26]. Here, similar to previous modelling studies of sexually transmitted infections, we modeled the relationship between infection risk and sexual behavior by a power law function [26]. • c denotes the sex specific HSV-2 transmission coefficient. • φ denotes the exponent parameter describing the heterogeneity of the infection risk between different sexual behaviors. • R denotes the mixing matrix between the risk groups defined by sexual behavior, x; • R denotes the mixing matrix between the risk groups defined by sexual behavior, x; Rxixj = qδxixj + (1 −q) y ρxyNxy x y ρxyNxy . This is the classical one-parameter ‘preferred mixing’ formulation, proposed by [2 This is the classical one-parameter ‘preferred mixing’ formulation, proposed by [27]. • δ denotes Kronecker’s delta. • δ denotes Kronecker’s delta. • δ denotes Kronecker’s delta. • q denotes assortative coefficient. When q = 0, the mixing between risk groups defined by sexual behavior is ‘proportionately mixing’, and the mixing is ‘fully assortative mixing’ when q = 1. • q denotes assortative coefficient. When q = 0, the mixing between risk groups defined by sexual behavior is ‘proportionately mixing’, and the mixing is ‘fully assortative mixing’ when q = 1. • S denotes the mixing matrix between sexes; • S denotes the mixing matrix between sexes; • S denotes the mixing matrix between sexes; S =  a 1 −a 1 −a a  . • a denotes the proportion of homosexual behavior. • a denotes the proportion of homosexual behavior. The special multi-group SVIRI epidemic model for HSV-2 We will use the special model (11) with transmission rate (12) to estimate the basic reproduction number ℜ0 for HSV-2 (see the “Results” section), and (10) with (12) to discuss the effectiveness of vaccination strategy (see the “Discussion” section). For the proofs of Proposition 1 and Theorem 1, see the Appendix. For the proofs of Proposition 1 and Theorem 1, see the Appendix. Theorem 1 still works for (10) since it is a special case of (6). In particular, although (10) does not include the integrated time delay, to our knowledge, there is no previous study on the global asymptotic stability of the endemic equilibrium of model (10). From this viewpoint, our main theorem can be regarded as valuable for the empirical study in the subsequent sections. The main theorem The main theorem of this paper is obtained for the general multi-group SVIRI epidemic model (6). Since (6) has an infinite time delay, we define the fading memory space (see, for instance, [28, 29]) as follows: C :=  φ ∈C((−∞, 0] ; R+) : φ(s)e s is uniformly continuous on(−∞, 0] , sup s≤0 |φ(s)|e s < +∞  , (13) C :=  φ ∈C((−∞, 0] ; R+) : φ(s)e s is uniformly continuous on(−∞, 0] ,  sup s≤0 |φ(s)|e s < +∞  , (13) (13) Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 8 of 20 Biology and Medical Modelling (2017) 14:13 Page Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 8 of 20 where is a positive constant such that 0 < < mini∈N {μi}. Let us define the following state space for system (6): where is a positive constant such that 0 < < mini∈N {μi}. Let us define the following state space for system (6):  :=  ψ1, ψ2, · · · , ψn, ˜ψ1, ˜ψ2, · · · , ˜ψn, φ1(·), φ2(·), · · · , φn(·)  ∈R2n + × Cn : 0 < ψi < S0 i , 0 < ˜ψi < V 0 i , φi(0) > 0, 0 < ψi + ˜ψi + φi(0) < bi μi , i ∈N  . (14) (14) The following proposition is proved: The following proposition is proved: The following proposition is proved: Proposition 1  is positively invariant for system (6). Proposition 1  is positively invariant for system (6). The main theorem of this paper is as follows. Theorem 1 Let ℜ0 and  be defined by (8) and (14), respectively. Let ¯ denote the closure of . (i) If ℜ0 ≤1, then the disease-free equilibrium E0 ∈ ¯ of system (6) is globally asymptotically stable in  and there exists no endemic equilibrium E∗in ¯. (ii) If ℜ0 > 1, then the system (6) has the unique endemic equilibrium E∗in  and it is globally asymptotically stable in . Estimation of ℜ0 for HSV-2 Based on Theorem 1, we estimate the basic reproduction number ℜ0 for HSV-2 in the US from 2001 to 2014. For the estimation of ℜ0, we use the special model (11) with transmission rate (12). Note that (11) corresponds to the case where vi = σi = ωi = 0 for all i ∈ {1, 2, · · · , 12}. Although the case where vi = 0 for all i ∈ {1, 2, · · · , 12} is excluded under assumption (A4), it is easy to check in a completely similar way as in the Appendix that the global stability result similar to Theorem 1 holds. Previous study derived the value of δi and γi from empirical data, δi and γi are param- eterized based on [30], 1/δi = 78.5 days and 1/γi = 13 days for all i ∈{1, 2, · · · , 12}. Here note that we can regard μi as the removal rate from our system, which is given by the sum of the sexual-inactivation rate and the mortality rate among those who are sexually active. We assume that the sexual life span is 50 years (15-65 years old) and parameterize the mortality rate by the national representative census data in the US [31], μi = 0.0231 per year for all i ∈{1, 2, · · · , 12}. Based on the previous stud- ies [32] and [33], we obtain the estimations q = 0.3 and a = 0.02, respectively (see Table 1). Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 9 of 20 Table 1 The model parameters and related estimates Parameter Meaning Value Reference δi (i = 1, 2, · · · , 12) Relapse risk 1/78.5 [30] γi (i = 1, 2, · · · , 12) Recovery rate 1/13 [30] μi (i = 1, 2, · · · , 12) Rate of removal from sexual activity 0.0231 [31] q Assortative coefficient 0.3 [32] a Proportion of homosexual behavior 0.02 [33] c1 Transmission coefficient for male 0.228 Estimated c2 Transmission coefficient for female 1.78 Estimated φ Exponent parameter 0.700 Estimated ℜ0 Basic reproduction number 2.07 Estimated Using the observed data of sero-prevalence of HSV-2 in the US from 2001 to 2014 reported by [34], sex specific transmission coefficient c and the exponent parameter φ were estimated by maximum likelihood estimation. Estimation of ℜ0 for HSV-2 The estimated c are, transmission coefficient for male, c1 = 0.228 (95% CI 0.225 to 0.231), transmission coefficient for female, c2 = 1.78 (95% CI 1.75 to 1.81), exponent parameter φ = 0.700 (95% CI 0.693 to 0.707) and estimated ℜ0 = 2.07 (95% CI 2.03 to 2.11). Sexual behavior shows wide variation between host individuals. To assess the sensitivity of sexual behavior to ℜ0 of HSV-2, we conducted a sensitivity analysis of the parameters describing sexual behavior, i.e., the proportion of homosexual partnership a and assorta- tivity coefficient for the mixing between risk groups q. Fig. 2 shows the relation of a and q to estimated ℜ0, ℜ0 increase if i) a increases, and ii) q decreases. The realistic variations of a and q [36, 37] can induce the variation of ℜ0, which is approximately demonstrated in the range of 2-3. Sexual behavior shows wide variation between host individuals. To assess the sensitivity of sexual behavior to ℜ0 of HSV-2, we conducted a sensitivity analysis of the parameters describing sexual behavior, i.e., the proportion of homosexual partnership a and assorta- tivity coefficient for the mixing between risk groups q. Fig. 2 shows the relation of a and q to estimated ℜ0, ℜ0 increase if i) a increases, and ii) q decreases. The realistic variations of a and q [36, 37] can induce the variation of ℜ0, which is approximately demonstrated in the range of 2-3. Estimation of ℜ0 for HSV-2 Since the antibody against HSV-2 infection (IgG) provides life-long immunity [35], we fitted I+R to the observed data of the number of sero-positive cases for the estimation of c and φ. To estimate c and φ, endemic equilibria of Ii and Ri were solved numerically with varied c1 and c2 and φ, and the set of c1 and c2 maximizing the likelihood function was explored. The likelihood function for c1 and c2 is given by L(c1, c2, φ) =  T  i pmf  bin  Ndata i,T , I∗ i (ci, c2, φ) + R∗ i (c1, c2, φ) N∗ i  , Pdata i,T  . Here pmf denotes the probability mass function, bin denotes a binomial distribution, Ndata i,T denotes the observed data of the size of the risk group i in sampling year T, and Pdata i,T denotes the observed data of the number of HSV2-seropositive cases in the risk group i in sampling year T, respectively. For the confidence interval (CI) of the estimated parameter, profile likelihood-based confidence intervals were calculated. Using estimated c and φ the basic reproduction number ℜ0 for HSV-2 in the US was calculated. Figure 1 shows the comparison between the observed data of sero-prevalence of HSV-2 and the model esti- mates. The estimated c are, transmission coefficient for male, c1 = 0.228 (95% CI 0.225 to 0.231), transmission coefficient for female, c2 = 1.78 (95% CI 1.75 to 1.81), exponent parameter φ = 0.700 (95% CI 0.693 to 0.707) and estimated ℜ0 = 2.07 (95% CI 2.03 to 2.11). Here pmf denotes the probability mass function, bin denotes a binomial distribution, Ndata i,T denotes the observed data of the size of the risk group i in sampling year T, and Pdata i,T denotes the observed data of the number of HSV2-seropositive cases in the risk group i in sampling year T, respectively. For the confidence interval (CI) of the estimated parameter, profile likelihood-based confidence intervals were calculated. Using estimated c and φ the basic reproduction number ℜ0 for HSV-2 in the US was calculated. Figure 1 shows the comparison between the observed data of sero-prevalence of HSV-2 and the model esti- mates. Discussion Using the demographic and epidemiological parameters obtained above, we discuss the effectiveness of each vaccination strategy. We investigate the sensitivity of the basic repro- duction number ℜ0 to the vaccination parameters, that is, the vaccination rate among Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 10 of 20 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 10 of 20 1.0 0.8 0.4 0.2 0.0 0.6 0 1 2 3 4 5+ The number of partner within 12 months Sero-prevalence of HSV-2 among male 1.0 0.8 0.4 0.2 0.0 0.6 Sero-prevalence of HSV-2 among female The number of partner within 12 months 0 1 2 3 4 5+ a b 2001-2002 2003-2004 2005-2006 2007-2008 2009-2010 2011-2012 2013-2014 2001-2002 2003-2004 2005-2006 2007-2008 2009-2010 2011-2012 2013-2014 Year Year Estimate Estimate Fig. 1 Comparison between the observed data of sero-prevalence of HSV-2 and the model estimates 1.0 0.8 0.4 0.2 0.0 0.6 0 1 2 3 4 5+ Sero-prevalence of HSV-2 among male a 2001-2002 2003-2004 2005-2006 2007-2008 2009-2010 2011-2012 2013-2014 Year Estimate The number of partner within 12 months 1.0 0.8 0.4 0.2 0.0 0.6 Sero-prevalence of HSV-2 among female The number of partner within 12 months 0 1 2 3 4 5+ b 2001-2002 2003-2004 2005-2006 2007-2008 2009-2010 2011-2012 2013-2014 Year Estimate Fig. 1 Comparison between the observed data of sero-prevalence of HSV-2 and the model estimates b The number of partner within 12 months Fig. 1 Comparison between the observed data of sero-prevalence of HSV-2 and the model estimates susceptible population v and the vaccination efficacy σ. Here we have assumed that vac- cination is conducted with the same rate v for the susceptible population over time. For simplicity, we assume that the efficacy of vaccine σ is the same for all risk groups. We first consider the case that vaccination rate v is the same between males and females. In this case, the basic reproduction number ℜ0 with different σ when v varies over (0, 1) is shown in Fig. 3. We see from Fig. 3 that, if σ is 0.3 or smaller, ℜ0 can be less than 1. On the other hand, if σ is 0.4 or larger, ℜ0 cannot be less than 1 for any v ∈(0, 1). Discussion This implies that decreasing σ is more important than increasing 5 4 3 2 1 The basic reproduction number R0 The proportion of homo-sexual partnerships a 0.02 0.04 0.06 0.08 0.0 0.1 0.2 0.3 0.4 0.5 5 4 3 2 1 The basic reproduction number R0 Assortativity coefficient q a b Fig. 2 Sensitivity analysis with respect to the parameters describing sexual behavior a and q 5 4 3 2 1 The basic reproduction number R0 The proportion of homo-sexual partnerships a 0.02 0.04 0.06 0.08 0.0 a 0.1 0.2 0.3 0.4 0.5 5 4 3 2 1 The basic reproduction number R0 Assortativity coefficient q b b Fig. 2 Sensitivity analysis with respect to the parameters describing sexual behavior a and q Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 11 of 20 Fig. 3 The relation of v to estimated ℜ0 with different σ v to reduce the basic reproduction number ℜ0. That is, improving the vaccine effi- cacy is more important for the eradication of HSV-2 than increasing the number of vaccines. We next discuss the optimal sex ratio of the vaccinated population to control HSV-2. HSV-2 infection is observed among females more frequently than males, “opportunistic” vaccination can induce higher vaccination coverage among females than males. To assess the optimal sex ratio of the vaccination rate, we expand the vaccination rate v as follows; v1 = pv, v2 = (1 −p)v, v : total vaccination rate. Conclusion In this paper, we have formulated the multi-group SVIRI epidemic model (6), which enables us to consider the effects of vaccination, the waning of vaccine-induced immunity, and relapse. We have defined the basic reproduction number ℜ0 and proved Theorem 1, which states that if ℜ0 ≤1, then the disease-free equilibrium E0 is globally asymp- totically stable, whereas if ℜ0 > 1, then the endemic equilibrium E∗is so. Based on Theorem 1, we have estimated the basic reproduction number ℜ0 for HSV-2 as 2.07 (95% CI 2.03 to 2.11) by using US HSV-2 data from 2001 to 2014. Through the sen- sitivity analysis for uncertain parameters on sexual behavior, we have found that ℜ0 is approximately in the range of 2-3. Furthermore, using sensitivity analysis for vacci- nation parameters, we have discussed the effectiveness of the vaccination. As a result, we have come to the following conclusions. (1) Improving vaccine efficacy is more effective than increasing the number of vaccines. (2) Although the transmission risk in female individuals is higher than that in male individuals, distributing vaccines almost equally to females and males is more effective than concentrating them within the female population. v1 = pv, v2 = (1 −p)v, v : total vaccination rate. Here p denotes the sex ratio of vaccination. Figure 4 shows the relationship between p, σ and ℜ0, we assumed v = 0.9 as the representative value. Interestingly, small or large p increases ℜ0. This implies that vaccination biased to females (small p) or males (large p) can result in persistence of the disease. In particular, it is noteworthy that the curves in Fig. 4 are almost symmetric with respect to p and the minimum is attained near the center p = 0.5. This implies that vaccination distributed equally to females and males is optimal for the eradication of the disease even though the transmission coefficient for males is lower than that for females. Fig. 4 The relation of p and σ to estimated ℜ0 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 12 of 20 We define the following matrix, which corresponds to the next generation matrix: We define the following matrix, which corresponds to the next generation matrix: M0 := V−1F = ⎛ ⎜⎜⎜⎝ S0 1+σ1V 0 1 β11 (μ1+γ1−Q1)N∗ 1 · · · S0 1+σ1V 0 1 β1n (μ1+γ1−Q1)N∗n ... ... ... (S0 n+σnV 0 n)βn1 (μn+γn−Qn)N∗ 1 · · · (S0 n+σnV 0 n)βnn (μn+γn−Qn)N∗n ⎞ ⎟⎟⎟⎠. (16) (16) In fact, it is easy to see that ρ(M0) = ρ(K) = ℜ0. In fact, it is easy to see that ρ(M0) = ρ(K) = ℜ0. In fact, it is easy to see that ρ(M0) = ρ(K) = ℜ0. First we show that system (6) has no endemic equilibrium E∗∈¯. Let us define the following matrix-valued function on R2n, which is equal to M0 if (S1, V1, · · · , Sn, Vn) = (S0 1, V 0 1 , · · · S0 n, V 0 n): M(S1, V1, · · · , Sn, Vn) := ⎛ ⎜⎜⎝ (S1+σ1V1)β11 (μ1+γ1−Q1)N∗ 1 · · · (S1+σ1V1)β1n (μ1+γ1−Q1)N∗n ... ... ... (Sn+σnVn)βn1 (μn+γn−Qn)N∗ 1 · · · (Sn+σnVn)βnn (μn+γn−Qn)N∗n ⎞ ⎟⎟⎠. Suppose that (S1, · · · , Sn) ̸= (S0 1, · · · , S0 n). Then, from assumptions (A1)-(A6), we see that 0 < M(S1, V1, · · · , Sn, Vn) < M0, where 0 denotes the zero matrix and the inequality implies that it holds for each element and each of the two matrices are not equal. Then, since it follows from assumptions (A1)-(A6) that matrices M0 and M0 + M(S1, V1, · · · , Sn, Vn) are nonnegative and irreducible, we can apply the Perron-Frobenius theorem (see [38, Corollary 2.1.5]) to obtain that ρ (M(S1, V1, · · · , Sn, Vn)) < ρ(M0) ≤1. This implies that the equation M(S1, V1, · · · , Sn, Vn) (I1, · · · In)T = (I1, · · · In)T has only the trivial solution (I1, · · · , In)T = 0, where T denotes the transpose of a vector. This implies that E∗does not exist in ¯. Next we show the global asymptotic stability of E0. It follows from the Perron- Frobenius theorem (see [38, Theorem 2.1.4]) that M0 has a strictly positive left eigenvector (ℓ1, · · · , ℓn), ℓi > 0, i ∈N corresponding to the eigenvalue ρ(M0): (ℓ1, · · · , ℓn) ρ(M0) = (ℓ1, · · · , ℓn) M0. Proof of Proposition 1 Theoretical Biology and Medical Modelling (2017) 14:13 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 13 of 20 The boundedness of the solution of system (6) immediately follows from the fact that N′ i(t) = bi−μiNi(t), S′ i(t) ≤bi−(μi+vi)Si(t)+ωiVi(t) and V ′ i (t) ≤viSi(t)−(μi+ωi)Vi(t) for all t > 0 and i ∈N . This completes the proof. Proof of Proposition 1 We first show the positivity of the solution of system (6). Suppose that there exist t1 > 0 and i∗∈N such that Si(t) > 0 and Vi(t) > 0 for all t ∈[ 0, t1) and i ∈N and min (Si∗(t1), Vi∗(t1)) = 0. By the variation of constants formula, we have from the first equation in the system (6) that Si∗(t1) =Si∗(0)e −  t1 0  n j=1 βi∗jIj(s)/N∗ j +μi∗+vi∗  ds +  t1 0 (bi∗+ ωi∗Vi∗(s)) e −  t1 s  n j=1 βi∗jIj(u)/N∗ j +μi∗+vi∗  duds > 0. Hence, Vi∗(t1) = 0. However, by the variation of constants formula, we have from the second equation in the system (6) that Hence, Vi∗(t1) = 0. However, by the variation of constants formula, we have from the second equation in the system (6) that Vi∗(t) =Vi∗(0)e −  t1 0  σi∗ n j=1 βi∗jIj(s)/N∗ j +μi∗+ωi∗  ds +  t1 0 vi∗Si∗(s)e −  t1 s  σi∗ n j=1 βi∗jIj(u)/N∗ j +μi∗+ωi∗  duds > 0, which is a contradiction. Hence, we see that Si(t) > 0 and Vi(t) > 0 for all t > 0 and ∈N . which is a contradiction. Hence, we see that Si(t) > 0 and Vi(t) > 0 for all t > 0 and i ∈N . Suppose that there exist t2 > 0 and ˜i ∈N such that Ii(t) > 0 for all t ∈[ 0, t2) and i ∈N and I˜i(t2) = 0. By the variation of constants formula, we have from the third equation in the system (6) that Ii(t) =Ii(0)e−(μi+γi)t +  t 0 ⎛ ⎝(Si(s) + σiVi(s)) n  j=1 βij Ij(s) N∗ j + hi(s) ⎞ ⎠e−(μi+γi)(t−s)ds, (15) where hi(t) :=  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ. We see that hi(t) ≥0 for all i ∈N and t ∈[0, t1). Hence, from (15), we have I˜i(t2) > 0, which is a contradiction. Hence, we see that Ii(t) > 0 for all t > 0 and i ∈N . where hi(t) :=  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ. We see that hi(t) ≥0 for all i ∈N and t ∈[0, t1). Hence, from (15), we have I˜i(t2) > 0, which is a contradiction. Hence, we see that Ii(t) > 0 for all t > 0 and i ∈N . Wang et al. We define the following matrix, which corresponds to the next generation matrix: Theoretical Biology and Medical Modelling (2017) 14:13 Hence, the derivative of LDFE gives Hence, the derivative of LDFE gives L′ DFE = n  i=1 ci ⎛ ⎝(Si + σiVi) n  j=1 βij Ij N∗ j −(μi + γi −Qi)Ii ⎞ ⎠ = n  i=1 ℓi ⎛ ⎜⎜⎜⎝ (Si + σiVi) n j=1 βijIj (μi + γi −Qi) N∗ j −Ii ⎞ ⎟⎟⎟⎠ L′ DFE = n  i=1 ci ⎛ ⎝(Si + σiVi) n  j=1 βij Ij N∗ j −(μi + γi −Qi)Ii ⎞ ⎠ = n  i=1 ℓi ⎛ ⎜⎜⎜⎝ (Si + σiVi) n j=1 βijIj (μi + γi −Qi) N∗ j −Ii ⎞ ⎟⎟⎟⎠ = (ℓ1, · · · , ℓn) · (M (S1, V1, · · · , Sn, Vn) −En) · (I1, · · · , In)T ≤(ℓ1, · · · , ℓn) · M S0 1, V 0 1 , · · · , S0 n, V 0 n −En · (I1, · · · , In)T = ρ(M0) −1 (ℓ1, · · · , ℓn) · (I1, · · · , In)T ≤0, (17) = (ℓ1, · · · , ℓn) · (M (S1, V1, · · · , Sn, Vn) −En) · (I1, · · · , In)T ≤(ℓ1, · · · , ℓn) · M S0 1, V 0 1 , · · · , S0 n, V 0 n −En · (I1, · · · , In)T (M0) 1 (ℓ ℓ) (I I )T 0 ≤(ℓ1, , ℓn) M S1, V1 , , Sn, Vn En (I1, , In) = ρ(M0) −1 (ℓ1, · · · , ℓn) · (I1, · · · , In)T ≤0, (17) (17) where En denotes the n-dimensional unit matrix and · denotes the product of vectors. It is easy to see that when ℜ0 < 1, L′ DFE = 0 holds if and only if Ii = 0 for all i ∈N , that is, the solution is in the disease-free equilibrium E0. When ℜ0 = 1, from the third equality in (17), we see that L′ DFE = 0 implies (ℓ1, · · · , ℓn) · M (S1, V1, · · · , Sn, Vn) · (I1, · · · , In)T = (ℓ1, · · · , ℓn) · (I1, · · · , In)T. We define the following matrix, which corresponds to the next generation matrix: (18) (18) Suppose that (S1, V1, · · · , Sn, Vn) ̸= S0 1, V 0 1 , · · · , S0 n, V 0 n . Then (ℓ1, · · · , ℓn) · M (S1, V1, · · · , Sn, Vn) < (ℓ1, · · · , ℓn) · M0 = ρ(M0) (ℓ1, · · · , ℓn) = (ℓ1, · · · , ℓn). Hence, (18) has only the trivial solution such that Ii = 0 for all i ∈N . This implies that L′ DFE = 0 holds only in the disease-free equilibrium E0 ∈ ¯. Consequently, from the LaSalle’s invariance principle (see [39]), we can conclude that the disease-free equilibrium E0 is globally asymptotically stable. We define the following matrix, which corresponds to the next generation matrix: Let ci := ℓi/ (μi + γi −Qi) , i ∈N and Ji(t) :=  +∞ t δi(ξ)γie−μiξe−  ξ 0 δi(η)dηdξ, i ∈N and consider the following Lyapunov function. LDFE (I1, · · · , In) := n  i=1 ci  Ii(t) +  +∞ 0 Ji(ξ)Ii(t −ξ)dξ  . From assumption (A6), Ji(t) ≥0, i ∈N for all t ≥0 and hence, LDFE ≥0 and the equality holds if and only if (I1, · · · , In) ≡0. Note that +∞ Ji(ξ)Ii(t −ξ)dξ ′ =  +∞ 0 Ji(ξ) ∂ ∂t Ii(t −ξ)dξ = −  +∞ 0 Ji(ξ) ∂ ∂ξ Ii(t −ξ)dξ  +∞ 0 Ji(ξ)Ii(t −ξ)dξ ′ =  +∞ 0 Ji(ξ) ∂ ∂t Ii(t −ξ)dξ = −  +∞ 0 Ji(ξ) ∂ ∂ξ Ii(t −ξ)dξ = −[ Ji(ξ)Ii(t −ξ)]+∞ 0 +  +∞ 0 ∂ ∂ξ Ji(ξ)Ii(t −ξ)dξ = QiIi(t) −  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ, i ∈N . = −[ Ji(ξ)Ii(t −ξ)]+∞ 0 +  +∞ 0 ∂ ∂ξ Ji(ξ)Ii(t −ξ)dξ = QiIi(t) −  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ, i ∈N . Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 14 of 20 Wang et al. Proof of (ii) of Theorem 1 components S∗ 1, V ∗ 1 , I∗ 1, · · · , S∗ n, V ∗ n , I∗ n of E∗satisfy the following equations. mponents S∗ 1, V ∗ 1 , I∗ 1, · · · , S∗ n, V ∗ n , I∗ n of E∗satisfy the following equations. bi = S∗ i n  j=1 βij I∗ j N∗ j + (μi + vi)S∗ i −ωiV ∗ i , (19) viS∗ i = σi n  j=1 βij I∗ j N∗ j + (μi + ωi) V ∗ i , (20) (μi + γi −Qi)I∗ i = (S∗ i + σiV ∗ i ) n  j=1 βij I∗ j N∗ j , i ∈N . (21) (19) (20) (21) As in [14], we define θij := S∗ i + σiV ∗ i βijI∗ j /N∗ j , i, j ∈N and As in [14], we define θij := S∗ i + σiV ∗ i βijI∗ j /N∗ j , i, j ∈N and As in [14], we define θij := S∗ i + σiV ∗ i βijI∗ j /N∗ j , i, j ∈N and  := ⎛ ⎜⎜⎜⎜⎜⎜⎜⎜⎝ j̸=1 θ1j −θ21 · · · −θn1 −θ12 j̸=2 θ2j · · · −θn2 ... ... ... ... −θ1n −θ2n · · · j̸=n θnj ⎞ ⎟⎟⎟⎟⎟⎟⎟⎟⎠ . Let ϕ := (ϕ1, · · · , ϕn)T be a basis of the solution space of linear system ϕ = 0. Then, from [14, Lemma 2.1], we see that the dimension of the solution space is 1 and ϕi > 0, i ∈N . In particular, from the form of matrix , the following equality holds. Let ϕ := (ϕ1, · · · , ϕn)T be a basis of the solution space of linear system ϕ = 0. Then, from [14, Lemma 2.1], we see that the dimension of the solution space is 1 and ϕi > 0, i ∈N . In particular, from the form of matrix , the following equality holds. n  j=1 θijϕi = n  j=1 θjiϕj, i ∈N . (22) n  j=1 θijϕi = n  j=1 θjiϕj, i ∈N . (22) Using this ϕ and H(x) := x −1 −ln x ≥H(1) = 0, we consider the following Lyapunov functional to prove the global asymptotic stability of E∗. Proof of (ii) of Theorem 1 If ℜ0 > 1, then (ℓ1, · · · , ℓn) · M S0 1, V 0 1 , · · · , S0 n, V 0 n −En · (I1, · · · , In)T = ρ(M0) −1 (ℓ1, · · · , ℓn) · (I1, · · · , In)T > 0. Hence, we see from the third equality in (17) that in a neighborhood of S0 1, V 0 1 , · · · , S0 n, V 0 n , L′ DFE > 0. This implies the instability of the disease-free equilibrium E0. If ℜ0 > 1, then (ℓ1, · · · , ℓn) · M S0 1, V 0 1 , · · · , S0 n, V 0 n −En · (I1, · · · , In)T = ρ(M0) −1 (ℓ1, · · · , ℓn) · (I1, · · · , In)T > 0. Hence, we see from the third equality in (17) that in a neighborhood of S0 1, V 0 1 , · · · , S0 n, V 0 n , L′ DFE > 0. This implies the instability of the disease-free equilibrium E0. Since the disease-free equilibrium of E0 of system (6) is unstable if ℜ0 > 1, we see from the uniform persistence result of [40] and an argument as in the proof of Proposition 3.3 of [41] that system (6) is uniformly persistent. That is, there exists a positive constant c > 0 such that for any initial value, it holds that lim inft→+∞Si(t) ≥c, lim inft→+∞Vi(t) ≥c and lim inft→+∞Ii(t) ≥c for all i ∈N . Since the uniform persistence together with the uniform boundedness implies the existence of an interior equilibrium (see [42, 43]), we see that system (6) has an endemic equilibrium E∗∈. From (7), we see that the Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 15 of Biology and Medical Modelling (2017) 14:13 Page 15 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 15 of 2 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 15 of 20 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 15 of 20 components S∗ 1, V ∗ 1 , I∗ 1, · · · , S∗ n, V ∗ n , I∗ n of E∗satisfy the following equations. Proof of (ii) of Theorem 1 L′ EE = n  i=1 ϕi   1 −S∗ i Si   bi −Si n  j=1 βij Ij N∗ j −(μi + vi)Si + ωiVi  +  1 −V ∗ i Vi   viSi −σiVi n  j=1 βij Ij N∗ j −(μi + ωi)Vi  +  1 −I∗ i Ii   (Si + σiVi) n  j=1 βij Ij N∗ j −(μi + γi)Ii L′ EE = n  i=1 ϕi   1 −S∗ i Si   bi −Si n  j=1 βij Ij N∗ j −(μi + vi)Si + ωiVi  +  1 −V ∗ i Vi   viSi −σiVi n  j=1 βij Ij N∗ j −(μi + ωi)Vi  +  1 −I∗ i Ii   (Si + σiVi) n  j=1 βij Ij N∗ j −(μi + γi)Ii +  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ  +  +∞ 0 Ji(ξ)I∗ i ∂ ∂t H Ii(t −ξ) I∗ i  dξ  = n  i=1 ϕi   1 −S∗ i Si   S∗ i n  j=1 βij I∗ j N∗ j + (μi + vi)S∗ i −ωiV ∗ i −Si n  j=1 βij Ij N∗ j −(μi + vi)Si + ωiVi  +  1 −V ∗ i Vi   Si S∗ i viS∗ i −σiVi n  j=1 βij Ij N∗ j −(μi + ωi)Vi   I∗ i   n  Ij +  1 −Vi Vi   viSi −σiVi  j=1 βij j N∗ j −(μi + ωi)Vi  +  1 −I∗ i Ii   (Si + σiVi) n  j=1 βij Ij N∗ j −(μi + γi)Ii +  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ  +  +∞ 0 Ji(ξ)I∗ i ∂ ∂t H Ii(t −ξ) I∗ i  dξ  = n  i=1 ϕi   1 −S∗ i Si   S∗ i n  j=1 βij I∗ j N∗ j + (μi + vi)S∗ i −ωiV ∗ i −Si n  j=1 βij Ij N∗ j −(μi + vi)Si + ωiVi  +  1 −V ∗ i Vi   Si S∗ i viS∗ i −σiVi n  j=1 βij Ij N∗ j −(μi + ωi)Vi  +  1 −I∗ i Ii   (Si + σiVi) n  j=1 βij Ij N∗ j −(μi + γi)Ii +  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ  −  +∞ 0 Ji(ξ)I∗ i ∂ ∂ξ H Ii(t −ξ) I∗ i  dξ  = n  i=1 ϕi  μiS∗ i  2 −S∗ i Si −Si S∗ i  + viS∗ i  2 −S∗ i Si −SiV ∗ i S∗ i Vi  + μiV ∗ i  1 −Vi V ∗ i  + ωiV ∗ i  −1 + S∗ i Si + Vi V ∗ i −S∗ i Vi SiV ∗ i + 1 −Vi V ∗ i  + S∗ i n  j=1 βij I∗ j N∗ j  1 −S∗ i Si  + S∗ i + σiV ∗ i n  j=1 βij Ii N∗ j −(Si + σiVi) n  j=1 βij I∗ j N∗ j I∗ i Ij IiI∗ j + (μi + γi)I∗ i  1 −Ii I∗ i  +  1 −Ii I∗ i   +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ  −  +∞ 0 Ji(ξ)I∗ i ∂ ∂ξ H Ii(t −ξ) I∗ i  dξ  . Proof of (ii) of Theorem 1 LEE(S1, V1, I1, · · · , Sn, Vn, In) := n  i=1 ϕi  S∗ i H  Si S∗ i  + V ∗ i H  Vi V ∗ i  + I∗ i H  Ii I∗ i  +  +∞ 0 Ji(ξ)I∗ i H Ii(t −ξ) I∗ i  dξ  . In order to make this function well-defined, without loss of generality, we can restrict our attention to the solution such that Ii(s) = ϕi(s), i ∈N on (−∞, 0], where ϕi(0) = Ii(0) and 0 < mi < ϕi(s) < Mi < +∞, s ∈(−∞, 0] , i ∈N for positive constants mi and Mi, i ∈N . Then, from the positive invariance of set  and the uniform persistence of system (6), we see that the Lyapunov functional LEE is well-defined. Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 16 of 20 Using (19), we can calculate the derivative of LEE as follows. Using (19), we can calculate the derivative of LEE as follows. Proof of (ii) of Theorem 1 j +  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ  +  +∞ 0 Ji(ξ)I∗ i ∂ ∂t H Ii(t −ξ) I∗ i  dξ  = n  i=1 ϕi   1 −S∗ i Si   S∗ i n  j=1 βij I∗ j N∗ j + (μi + vi)S∗ i −ωiV ∗ i −Si n  j=1 βij Ij N∗ j −(μi + vi)Si + ωiVi  +  1 −V ∗ i Vi   Si S∗ i viS∗ i −σiVi n  j=1 βij Ij N∗ j −(μi + ωi)Vi +  Ii   ( i + i i)  j=1 βij N∗ j (μi + γi) i +  +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ  −  +∞ 0 Ji(ξ)I∗ i ∂ ∂ξ H Ii(t −ξ) I∗ i  dξ  = n  i=1 ϕi  μiS∗ i  2 −S∗ i Si −Si S∗ i  + viS∗ i  2 −S∗ i Si −SiV ∗ i S∗ i Vi  + μiV ∗ i  1 −Vi V ∗ i  + ωiV ∗ i  −1 + S∗ i Si + Vi V ∗ i −S∗ i Vi SiV ∗ i + 1 −Vi V ∗ i  + S∗ i n  j=1 βij I∗ j N∗ j  1 −S∗ i Si  + S∗ i + σiV ∗ i n  j=1 βij Ii N∗ j −(Si + σiVi) n  j=1 βij I∗ j N∗ j I∗ i Ij IiI∗ j + (μi + γi)I∗ i  1 −Ii I∗ i  +  1 −Ii I∗ i   +∞ 0 δi(ξ)γiIi(t −ξ)e−μiξe−  ξ 0 δi(η)dηdξ  −  +∞ 0 Ji(ξ)I∗ i ∂ ∂ξ H Ii(t −ξ) I∗ i  dξ  . (23) (23) Now it follows from integration by parts that Now it follows from integration by parts that  +∞ 0 Ji(ξ)I∗ i ∂ ∂ξ H Ii(t −ξ) I∗ i  dξ = −Ji(0)I∗ i H  Ii I∗ i  +  +∞ 0 δi(ξ)γie−μiξe−  ξ 0 δi(η)dηI∗ i H Ii(t −ξ) I∗ i  dξ = −Qi  Ii −I∗ i −I∗ i ln Ii(t) I∗ i  +  +∞ 0 δi(ξ)γie−μiξe−  ξ 0 δi(η)dη  Ii(t −ξ) −I∗ i −I∗ i ln Ii(t −ξ) I∗ i  dξ. Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Wang et al. Proof of (ii) of Theorem 1 Theoretical Biology and Medical Modelling (2017) 14:13 Page 17 of 20 Hence, (23) can be calculated as follows: L′ EE = n  i=1 ϕi  μiS∗ i  2 −S∗ i Si −Si S∗ i  + viS∗ i  2 −S∗ i Si −SiV ∗ i S∗ i Vi  + μiV ∗ i  1 −Vi V ∗ i  + ωiV ∗ i S∗ i Si −S∗ i Vi SiV ∗ i  + S∗ i n  j=1 βij I∗ j N∗ j  1 −S∗ i Si  + S∗ i + σiV ∗ i n  j=1 βij Ii N∗ j −(Si + σiVi) n  j=1 βij I∗ j N∗ j I∗ i Ij IiI∗ j + (μi + γi −Qi)I∗ i  1 −Ii I∗ i  −QiI∗ i ln Ii I∗ i −I∗ i  +∞ 0 δi(ξ)γi Ii(t −ξ) Ii −1 −ln Ii(t −ξ) I∗ i  e−μiξe−  ξ 0 δi(η)dηdξ  . (24) (24) From (21) and (22), we have From (21) and (22), we have From (21) and (22), we have From (21) and (22), we have n  i=1 ϕi (μi + γi −Qi) Ii = n  i=1 ϕi (μi + γi −Qi) I∗ i Ii I∗ i = n  i=1 ϕi S∗ i + σiV ∗ i n  j=1 βij I∗ j N∗ j Ii I∗ i = n  i=1 Ii I∗ i n  j=1 θijϕi = n  i=1 Ii I∗ i n  j=1 θjiϕj = n  i=1 n  j=1 θji Ii I∗ i ϕj = n  i=1 n  j=1 θij Ij I∗ j ϕi = n  i=1 ϕi n  j=1 θij Ij I∗ j = n  i=1 ϕi S∗ i + σiV ∗ i n  j=1 βij Ij N∗ j . Proof of (ii) of Theorem 1 (25) (25) Hence, using (20), (21) and (25), we can calculate (24) as follows: Hence, using (20), (21) and (25), we can calculate (24) as follows: Hence, using (20), (21) and (25), we can calculate (24) as follows: L′ EE = n  i=1 ϕi  μiS∗ i  2 −S∗ i Si −Si S∗ i  + μiV ∗ i  3 −S∗ i Si −SiV ∗ i S∗ i Vi −Vi V ∗ i  + ωiV ∗ i  2 −SiV ∗ i S∗ i Vi −S∗ i Vi SiV ∗ i  + S∗ i n  j=1 βij I∗ j N∗ j  2 −S∗ i Si −SiI∗ i Ij S∗ i IiI∗ j  + σiV ∗ i n  j=1 βij I∗ j N∗ j  3 −S∗ i Si −SiV ∗ i S∗ i Vi −ViI∗ i Ij V ∗ i IiI∗ j  −QiI∗ i ln Ii I∗ i + QiI∗ i ln Ii I∗ i −I∗ i  +∞ 0 δi(ξ)γiH Ii(t −ξ) Ii  e−μiξe−  ξ 0 δi(η)dηdξ  . (26) (26) Using the inequality of arithmetic and geometric means, we see that the first three terms in the right-hand side of (26) are non-positive and equal to zero if and only if (Si, Vi) = S∗ i , V ∗ i , i ∈N . From the positivity of the function H(x), we see that the last term in the Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Page 18 of 20 right-hand side of (26) is non-positive. Proof of (ii) of Theorem 1 Hence, taking the maximum as in [10] and using the graph-theoretic approach as in [14], we can evaluate (26) as follows: L′ EE ≤ n  i=1 ϕi n  j=1 S∗ i + σiV ∗ i βij I∗ j N∗ j × max  2 −S∗ i Si −SiI∗ i Ij S∗ i IiI∗ j , 3 −S∗ i Si −SiV ∗ i S∗ i Vi −ViI∗ i Ij V ∗ i IiI∗ j  = n  i=1 ϕi n  j=1 θij max  2 −S∗ i Si −SiI∗ i Ij S∗ i IiI∗ j , 3 −S∗ i Si −SiV ∗ i S∗ i Vi −ViI∗ i Ij V ∗ i IiI∗ j  =  G∈ w(G)  (i,j)∈A(CG) max  2 −S∗ i Si −SiI∗ i Ij S∗ i IiI∗ j , 3 −S∗ i Si −SiV ∗ i S∗ i Vi −ViI∗ i Ij V ∗ i IiI∗ j  , (27) =  G∈ w(G)  (i,j)∈A(CG) max  2 −S∗ i Si −SiI∗ i Ij S∗ i IiI∗ j , 3 −S∗ i Si −SiV ∗ i S∗ i Vi −ViI∗ i Ij V ∗ i IiI∗ j  , (27) (27) where  denotes the set of all unicyclic graphs included in directed graphs with vertices {1, 2, · · · , n}, G denotes the unicyclic graph included in , w(G) denotes the weight of graph G, CG denotes the unicycle included in G and A(CG) denotes the set of all arcs included in CG. Proof of (ii) of Theorem 1 For instance, for a unicycle CG : 1 →2 →1, we have A(CG) = {(1, 2), (2, 1)} and thus,  (i,j)∈A(CG) max  2 −S∗ i Si −SiI∗ i Ij S∗ i IiI∗ j , 3 −S∗ i Si −SiV ∗ i S∗ i Vi −ViI∗ i Ij V ∗ i IiI∗ j  = max  2 −S∗ 1 S1 −S1I∗ 1I2 S∗ 1I1I∗ 2 , 3 −S∗ 1 S1 −V ∗ 1 S1 V1S∗ 1 −V1I∗ 1I2 V ∗ 1 I1I∗ 2  + max  2 −S∗ 2 S2 −S2I∗ 2I1 S∗ 2I2I∗ 1 , 3 −S∗ 2 S2 −V ∗ 2 S2 V2S∗ 2 −V2I∗ 2I1 V ∗ 2 I2I∗ 1  = max  4 −S∗ 1 S1 −S1I∗ 1I2 S∗ 1I1I∗ 2 −S∗ 2 S2 −S2I∗ 2I1 S∗ 2I2I∗ 1 , 5 −S∗ 1 S1 −S1I∗ 1I2 S∗ 1I1I∗ 2 −S∗ 2 S2 −V ∗ 2 S2 V2S∗ 2 −V2I∗ 2I1 V ∗ 2 I2I∗ 1 , 5 −S∗ 1 S1 −V ∗ 1 S1 V1S∗ 1 −V1I∗ 1I2 V ∗ 1 I1I∗ 2 −S∗ 2 S2 −S2I∗ 2I1 S∗ 2I2I∗ 1 , 6 −S∗ 1 S1 −V ∗ 1 S1 V1S∗ 1 −V1I∗ 1I2 V ∗ 1 I1I∗ 2 −S∗ 2 S2 −V ∗ 2 S2 V2S∗ 2 −V2I∗ 2I1 V ∗ 2 I2I∗ 1  . We see that all elements in the max in the last expression of the above formula are non positive because of the inequality of arithmetic and geometric means. Similarly, we can easily check that for all unicycles CG with at most n vertices, the second sum in the last expression of (27) are non-positive (see [10, Proof of Theorem 4.1]). Hence, L′ EE is non-positive and it is easy to check that the equality L′ EE = 0 holds if and only if (S1, V1, I1, · · · , Sn, Vn, In) = S∗ 1, V ∗ 1 , I∗ 1, · · · , S∗ n, V ∗ n , I∗ n . This implies, from the LaSalle’s invariance principle, that the endemic equilibrium E∗is globally asymptotically stable. g JW was supported by National Natural Science Foundation of China (nos. 11401182, 11471089), Science and Technology Innovation Team in Higher Education Institutions of Heilongjiang Province (No. 2014TD005). HT was supported by Grant-in-Aid for JSPS Fellows from the Ministry of Education, Culture, Sports, Science, and Technology in Japan. TK was supported by Grant-in-Aid for Young Scientists (B) of Japan Society for the Promotion of Science (No. 15K17585) and the program of the Japan Initiative for Global Research Network on Infectious Diseases (J-GRID); from Japan Agency for Acknowledgements ld l k h k We would like to thank the editor and anonymous reviewers for their helpful comments to the earlier version of this paper. We would like to thank Dr. Akihiro Ishii for helpful discussions regarding the serological test for HSV-2. Competing interests Competing interests The authors declare that they have no competing interests. Funding Page 19 of 20 Wang et al. Theoretical Biology and Medical Modelling (2017) 14:13 Medical Research and Development, AMED. RO was supported by Grant-in-Aid for Young Scientists (B) of Japan Society for the Promotion of Science (No. 15K19217) and Precursory Research for Embryonic Science and Technology (PRESTO) grant number JPMJPR15E1 from Japan Science and Technology Agency (JST). The authors were supported by JSPS Bilateral Joint Research Project (Open Partnership). Availability of data and materials h d h h f d f The data that support the findings of this study are available in the National Health and Nutrition Examination Survey, “http://www.cdc.gov/nchs/nhanes/”. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. References 1. World Health Organization. Media centre: Herpes simlex virus. 2017. Available from: http://www.who.int/. Accessed 25 Jan 2017. 2. Alsallaq RA, Schiffer JT, Longini IM, Wald A, Corey L, Abu-Raddad LJ. Population level impact of an imperfect prophylactic HSV-2 vaccine. Sex Transm Dis. 2010;37:290–7. 3. Blower S. Modelling the genital herpes epidemic. Herpes. 2004;3:138A–146A. 3. Blower S. Modelling the genital herpes epidemic. Herpes. 2 4. Lou Y, Qesmi R, Wang Q, Steben M, Wu J, Hefferman JM. E 4. Lou Y, Qesmi R, Wang Q, Steben M, Wu J, Hefferman JM. 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Attitude of health professionals towards COVID-19 vaccination and associated factors among health professionals, Western Ethiopia: A cross-sectional survey
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PLOS ONE PLOS ONE RESEARCH ARTICLE Tadesse TolossaID1*, Bizuneh Wakuma2, Ebisa Turi1, Diriba Mulisa2, Diriba Ayala3, Getahun Fetensa2,4, Belayneh Mengist5, Gebeyehu Abera6, Emiru Merdassa Atomssa1, Dejene Seyoum1, Tesfaye Shibiru7, Ayantu Getahun1 1 Department of Public Health, Institute of Health Science, Wollega University, Nekemte, Ethiopia, 2 Department of Nursing, Institute of Health Science, Wollega University, Nekemte, Ethiopia, 3 Department of Midwifery, Institute of Health Science, Wollega University, Nekemte, Ethiopia, 4 Department of Health Behavior and Society, Institute of Health, Jimma university, Jimma, Ethiopia, 5 Department of Public Health, College of Health Science, Debre Markos University, Debre Markos, Ethiopia, 6 Nekemte Health Center, Nekemte, Ethiopia, 7 School of Medicine, Institute of Health Sciences, Wollega University, Nekmete, Ethiopia Methods Received: June 30, 2021 Accepted: February 22, 2022 Published: March 9, 2022 An institution-based cross-sectional study was conducted among health care workers found in Nekemte town from April 14–21, 2021. A total of 439 health professionals present on duty during the study period was included in the study. The data were collected by using self- administered questionnaire. Epidata version 3.2 was used for data entry, and STATA ver- sion 14 was used for data analysis. The binary logistic regression model was employed to determine factors associated with the attitude towards COVID-19 vaccination. Adjusted Odds Ratio (AOR) with 95% confidence intervals was computed and statistical significance was declared at a 5% level (p-value < 0.05). Peer Review History: PLOS recognizes the benefits of transparency in the peer review process; therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. The editorial history of this article is available here: https://doi.org/10.1371/journal.pone.0265061 * yadanotolasa@gmail.com Introduction Citation: Tolossa T, Wakuma B, Turi E, Mulisa D, Ayala D, Fetensa G, et al. (2022) Attitude of health professionals towards COVID-19 vaccination and associated factors among health professionals, Western Ethiopia: A cross-sectional survey. PLoS ONE 17(3): e0265061. https://doi.org/10.1371/ journal.pone.0265061 Even though people of the world were eagerly waiting for the hope of vaccine development, vaccine hesitancy is becoming the top concern in both developed and developing countries. However, there is no adequate evidence regarding the attitude and perception of health pro- fessionals towards the COVID 19 vaccine in resource-limited settings like Ethiopia. The aim of this study was to assess health professionals’ attitudes and perceptions towards COVID 19 vaccine in Western Ethiopia. Editor: Syed Ghulam Sarwar Shah, Oxford University Hospitals NHS Foundation Trust, UNITED KINGDOM Editor: Syed Ghulam Sarwar Shah, Oxford University Hospitals NHS Foundation Trust, UNITED KINGDOM Editor: Syed Ghulam Sarwar Shah, Oxford University Hospitals NHS Foundation Trust, UNITED KINGDOM Attitude of health professionals towards COVID-19 vaccination and associated factors among health professionals, Western Ethiopia: A cross-sectional survey Tadesse TolossaID1*, Bizuneh Wakuma2, Ebisa Turi1, Diriba Mulisa2, Diriba Ayala3, Getahun Fetensa2,4, Belayneh Mengist5, Gebeyehu Abera6, Emiru Merdassa Atomssa1, Dejene Seyoum1, Tesfaye Shibiru7, Ayantu Getahun1 Tadesse TolossaID1*, Bizuneh Wakuma2, Ebisa Turi1, Diriba Mulisa2, Diriba Ayala3, Getahun Fetensa2,4, Belayneh Mengist5, Gebeyehu Abera6, Emiru Merdassa Atomssa1, Dejene Seyoum1, Tesfaye Shibiru7, Ayantu Getahun1 PLOS ONE PLOS ONE Attitude of health professionals towards COVID-19 vaccination Data Availability Statement: All relevant data are within the paper and its Supporting information files. Funding: The author(s) received no specific funding for this work. Competing interests: The authors have declared that no competing interests exist. Abbreviations: AOR, Adjusted Odds Ratio; COR, Crude Odds Ratio; HCW, Health Care Worker; MLS, Medical Laboratory Science; WURH, Wollega University Referral Hospital. Data Availability Statement: All relevant data are within the paper and its Supporting information files. associated with unfavorable attitude towards COVID-19 vaccine, whereas age less than 30 years (AOR = 2.14, 95%CI:1.25,3.67, P-value <0.001), working in a private clinic (AOR = 7.77, 95% CI: 2.19, 27.58, P-value <0.001) and health center (AOR = 2.45, 95%CI: 1.01, 5.92, P-value = 0.045) were positively associated with unfavorable attitude towards COVID- 19 vaccine. Funding: The author(s) received no specific funding for this work. Conclusion and recommendation Abbreviations: AOR, Adjusted Odds Ratio; COR, Crude Odds Ratio; HCW, Health Care Worker; MLS, Medical Laboratory Science; WURH, Wollega University Referral Hospital. In general, the attitude and perception of health care professionals toward the COVID-19 vaccine in the study area were unsatisfactory. Knowledge about the COVID-19 vaccine, age of health care workers, and place of work are the factors which affects attitude towards COVID-19 vaccine. Thus, we recommend the media outlets and concerned bodies to work to develop trust among the public by disseminating accurate and consistent information about the vaccine. Introduction Starting from the day it was declared a pandemic, COVID-19 remains the worst Global public health challenge. According to the worldometer report, COVID-19 affects about 220 countries and territories. More than 350 million cases, and 5.6 million deaths happened due to COVID- 19 as of January 24, 2022 [1,2]. The pandemic brought the double burden in developing coun- tries already overwhelmed by the health care system challenges [3]. Given that sub-Saharan Africans are not the highest shareholder by cases and death during the early phase [4], the direct effect of COVID-19 and the indirect effect of its mitigation, dis- rupted the health care services [5]. The serious preventive measures (movement restriction, physical distancing, lockdowns, hand washing and sanitizing) were practiced [6]. However, the counter effect of some mitigation brought significant change in health care settings espe- cially by task shifting and task sharing. Its effect on the economy is also evident. Though these mitigation procedures played a paramount role in averting the burden of COVID19, the whole world was hoping for vaccine development [7]. A few COVID-19 vaccines that are being used globally or locally [7]. As of June 10, 2021, from 287 candidate vaccines, 102 are in the clinical phase, 185 are in the pre-clinical phase [8]. From these, WHO has listed the Pfizer/BioNTech, Astrazeneca-SK Bio, Serum Institute of India, Janssen and Moderna vaccines for emergency use [6,7]. Believing Health Care Workers (HCWs) are explicitly exposed to increased risk of infection through direct contact with patients, they should be prioritized for vaccination [9]. The willingness of the general population to accept the vaccine ahead of COVID-19 vaccine development was relatively promising compared to today’s reality [10–12]. Even though peo- ple of the world were eagerly waiting for the vaccine development, vaccine hesitancy is becom- ing the top concern in both developed and developing countries [11,13–17]. For instance, the vaccine acceptance is 21% in Egypt [18], 54.6% in China[19], and 57.6% of the adult popula- tion in the USA [20] intended to be vaccinated. Studies conducted in different regions of Ethi- opia reported willingness to take COVID-19 vaccine were 46.1% in Southern Ethiopia [21],39.7 in Addis Ababa [22], and 48.6% in Southwestern Ethiopia [23]. Result Copyright: © 2022 Tolossa et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. A total of 431 health professionals participated in the study yielding a response rate of 98.1%. The results indicated that 51.28% (95%CI: 45.12%, 57.34%) of health professionals had a favorable attitude towards COVID-19 vaccination. Having good knowledge about the COVID-19 vaccine (AOR = 0.38, 95%CI: 0.22, 0.64, P-value <0.001) was negatively 1 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 Study design An Institutional based cross-sectional study design was employed. Study area and period This study was conducted in health institutions located in Nekemte town. Nekemte is the capi- tal city of East Wollega Zone, and it is located 330 KM from Addis Ababa, the capital city of Ethiopia. The study was conducted from April 15–21, 2021. Data from Nekemte Town Health Office showed that the town has one teaching referral hospital owned by Wollega University, one specialized hospital administered under Oromia Regional Health Bureau, two health cen- ters (Nekemte and Cheleleki Health center), and more than fifteen medium and above private clinics, and more than 800 health professionals are found in Nekemte town. Introduction The most common reason mentioned for hesitancy were concerns about the safety of a vaccine and wide-ranging lack of confidence, worries about the efficiency of the vaccine[17,18,24] 2 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination Several studies indicate that healthcare professionals (HCPs) play a paramount role and can significantly affect the general public’s decisions to receive the COVID- 19 vaccine [25,26]. In Ethiopia, there have been 169,640 confirmed cases of COVID-19, with 9651 deaths till May 30, 2021 [1]. The Ethiopian government and the Ethiopian Ministry of health exert great efforts to provide the COVID-19 vaccines and sort the vaccination as a priority for healthcare workers (HCWs) and older people, especially people with chronic diseases history [27]. To overcome the expected upcoming challenge of vaccination hesitancy, we have to measure and know the exact reasons. However, there is no adequate evidence regarding the attitude and perception of health professionals towards the COVID-19 vaccine in resource-limited settings like Ethiopia. Hence, this study aimed to assess health professionals’ attitudes and perceptions towards COVID 19 vaccine in West Ethiopia. PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 Variables The attitude of health professionals towards the COVID-19 vaccine was the dependent variable of this study. For attitude questions, the likert-scale method with a five points scale (strongly agree, agree, neutral, disagree, strongly disagree) responses were used to allow the study partic- ipants to express how much they agree or disagree with a particular question. Ten items were used to assess the attitude of health professionals towards COVID-19 vaccine. Participants’ response was from 10 to 50. Higher scores denoted a “favorable attitude” towards COVID-19 vaccine. “Favorable attitude” was when the scoring was  mean or 25 (50% and above) out of 50 items and < 25 (<50%) was rated as “unfavorable attitude”. Socio-demographic variables such as (age, sex, marital status, educational level, educational background, religion), medical history (chronic medical disease and previously infected with COVID-19), knowledge towards COVID-19 vaccine, and perception towards COVID-19 vac- cine) were independent variables of this study. For knowledge related items, the questions contained the category of (“Yes”/“No”). A cor- rect answer was assigned “1” point and an incorrect answer was assigned “0” points. The total score ranged from 0 to 5. “Good knowledge” was when the scoring was 2.5 (50% and above) out of 5 items and score below 2.5 indicated “poor knowledge” on COVID-19 vaccine. Finally, the perception of participants towards COVID-19 vaccine was assessed by using five items with "Yes"/No" category. The total score ranged from 0 to 5. Respondents who scored greater than or equal to the mean score ( 2.5 or  50%) were grouped to have "good perception" and participants who scored less than the mean score (<2.5 or <50%) were grouped to have "poor perception" towards COVID-19 vaccine (S3 File). Data collection techniques and data quality assurance A questionnaire was developed by reviewing previously published papers [28,29], and adapted to local context. The tool was designed and distributed to respondents in English language since the participants could read, write, and understand the language. The questionnaires comprised socio-demographic data, medical history, knowledge, attitude, and perception towards the COVID-19 vaccine. The data was collected by using self-administered question- naires. The questionnaire was given to all health professionals on duty and returned to data collectors after filling it. Cronbach’s alpha was used to assess the reliability of the tool, and the value was 0.78 (value more than 0.7 to 0.95 is acceptable) [30]. To ensure its quality, the questionnaire was pre-tested on 5% of participants. Then possible amendments were done based on the findings. The discussion was held between investigators and data collectors, based on the pre-test result, and accordingly, some amendments were made. The data collectors gave the one-day training about the tool and data collection proce- dure. Data were checked daily for completeness, accuracy, clarity, and consistency by the supervisors and principal investigator. Any error or ambiguity, and incompleteness were cor- rected accordingly. Population, sample size and sampling techniques All health professionals working in private and public health institutions of Nekemte town were a source population. Health professionals who were not on duty due to different reasons were excluded from the study. All health professionals on duty during data collection and will- ing to participate in the study were selected. The sample size was determined by single population proportion with the following assumptions: Since this study was the first of its type in Ethiopia, p = 50% was taken, with a 5% margin of error and a 95% confidence level. Accordingly, the calculated sample size was 384, and after adding a 15% allowance for a non-response rate, the final sample size was 442 health professionals. All health institutions found in Nekemte town were included in the study. There are two public hospitals in Nekemte town, two health centers, and 15 medium clinics. Then the sample size was proportionally allocated to hospitals, health centers and private clinics. Around 710 health professionals are working in two hospitals, 50 in two health centers and 60 health pro- fessionals in all private clinics. For hospitals, we have used the identification number of the health professionals, and the identification number was used as a sampling frame. Then com- puter-generated simple random sampling technique was used to select the sample. Health pro- fessionals who were not on duty during the study period were excluded from the sampling frame. For health centers and private clinics, all health professionals who were available during the study period were included in the study. Furthermore, health professionals working in more than one health facility were considered only in a single health facility to prevent any dis- tortion of information. 3 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination Socio demographic characteristics of the health professionals Four hundred thirty-one health professionals were filled the questionnaire and yielded a response rate of 98.1%. Two hundred sixty eight (62.28%) of participants were male. Regarding the age of the health professionals, nearly two-thirds of them, 274 (63.57%), belong to less than 30 years old age group. More than half 253(58.07%) of the participants were protestant religion followers. Greater than three fourth of the health professionals who participated in this study were from hospital institutions 350 (81.21%) (Table 1). The attitude of the health professionals towards COVID-19 vaccine Almost half 210 (48.72%) of the participants have poor attitude toward COVID-19 vaccina- tion. One-third of the participants strongly agreed that COVID-19 could not be controlled without vaccination. Moreover, nearly one-third of participants agreed that mass vaccination against COVID-19 helps overcome the pandemic (Table 2). Regarding the effectiveness of the newly discovered COVID-19 vaccination, less than a quarter of the participants strongly dis- agreed with 63 (14.62%) (Fig 1). Medical disorder related characteristics of the health professionals Thirty-three healthcare workers have a history of taking vaccination in their lives (7.66%). Nearly one fifth of the health care workers in this study had chronic medical diseases 19 (4.41%). Participants’ most commonly reported chronic disease was hypertension 6 (46.15%). Greater than half of the participants were vaccinated against coronavirus 240 (55.68%). Data management and analysis Epidata version 3.0 was used for data entry [31], and exported to STATA version 14.0 for fur- ther analysis [32]. Descriptive statistics, like frequencies, percentages, mean and standard devi- ation were computed. Before analysis, data were cleaned and edited by using simple frequencies and cross-tabulation. Re-categorization of categorical variables and categorization of continuous variables was done. The assumption of the logistic regression model was checked before fitting to the model. The binary logistic regression model was fitted to deter- mine factors associated with attitude towards COVID-19 vaccine. The multivariable logistic 4 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination regression analysis included factors associated with the outcome variable at 20% (p-value 0.20) significant level in the bivariable logistic regression analysis. Then crude and adjusted odds ratio and their corresponding 95% confidence intervals were presented in the final multi- variable logistic regression table. Finally, AOR with 95% confidence intervals was computed and statistical significance was declared when it was significant at a 5% level (p-value < 0.05). Correlation matrices checked multicollinearity (association between explanatory variables), and the model goodness of fit test was checked by Hosmer and Lemeshow test. Ethical considerations The study was approved, and ethical clearance letters were obtained from Wollega University, Institute of Health Science Research Ethics review board (Min. No. 07/2021). After approval, a permission letter was obtained from the administrative body of health facilities to respective clinics. Verbal consent was obtained from study participants, and the purpose of this study was stated to all participants. Everybody participated voluntarily in this study. PLOS ONE PLOS ONE Table 1. Socio demographic characteristics of the health professionals in Nekemte city, Western Ethiopia, 2021. Variables Option Frequency Percent Age <30years old 274 63.57 > = 30years old 157 36.43 Sex Male 268 62.18 Female 163 37.82 Marital status Never married 176 40.84 Married 243 56.38 Separated 8 1.86 Others 4 0.93 Religion Muslim 73 16.94 Protestant 253 58.70 Catholic 10 2.32 Orthodox 71 16.47 Others 24 5.57 Institution Hospitals 350 81.21 Health center 34 7.89 Private 47 10.90 Education level Diploma 38 8.82 First degree 362 83.99 Masters 24 5.57 Doctors 2 0.46 Specialty degree 5 1.16 Back ground Nurses 186 43.16 Midwifery 56 12.99 Pharmacy 32 7.42 Medical practitioner 47 10.90 Public health 41 9.51 Anesthetists 19 4.41 MLS 36 8.35 Psychiatrics 6 1.39 others 8 1.86 https://doi org/10 1371/journal pone 0265061 t001 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 Health care workers perception towards COVID-19 vaccine The distributions of each perception item about the COVID-19 vaccine are presented in Table 3. Concerning the question “Do you think the COVID-19 vaccine is effective”? Nearly one-third of them thought the vaccine against COVID-19 was effective. More than half of the participants responded unsure for the question “Do you think COVID-19 will be controlled only by preventive measures without vaccination”? (Table 3). Almost half of the participants accept that the newly developed COVID-19 vaccine has side effect 209 (48.49%) (Fig 2). 5 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 Attitude of health professionals towards COVID-19 vaccination PLOS ONE Table 2. Attitude of the health care workers towards COVID-19 vaccine in Nekemte health facilities, Western Ethiopia. Factors associated with attitude of health professionals towards COVID-19 vaccine In multivariable logistic regression, variables like age, sex, institution types, having chronic dis- eases and allergic reaction to previous medication have shown significant association with the outcome of interest. From those variables, two of them showed significant association with the attitude of health professionals toward a vaccine against COVID-19. The odd of developing poor attitude toward COVID-19 vaccine was 2.14 times higher among health professionals aged < 30 years than their counterparts (AOR = 2.14, 95%CI: 1.25, 3.67). The likelihood of having a poor attitude toward the COVID-19 vaccine was 2.45 times higher among health pro- fessionals working at health centers than those working at hospitals AOR = 2.45(95%CI 1.01,5.92). Similarly, the odds of having a poor attitude towards the COVID-19 vaccine was 7.77 times higher among health professionals working at private clinics and hospitals AOR = 7.77(95% CI 2.19,27.58). Moreover, the proportion of health professionals with unfa- vorable attitudes was 62% lower among professionals who have good knowledge of COVID-19 vaccination than their counterparts AOR = 0.38(95%CI: 0.22, 0.64) (Table 4). 6 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 Attitude of health professionals towards COVID-19 vaccination PLOS ONE Variables Option Frequency Percent The vaccine that is currently given in Ethiopia is the actual one that those innovative countries are taking Strongly disagree 114 26.45 Disagree 132 30.63 Neutral 81 18.79 Agree 79 18.33 Strongly agree 25 5.80 If one person takes COVID-19 vaccination, it has a great contribution for other people Strongly disagree 65 15.08 Disagree 86 19.95 Neutral 53 12.30 Agree 155 35.96 Strongly agree 72 16.71 I will take the vaccine if I get it without hesitation Strongly disagree 61 14.15 Disagree 183 42.46 Neutral 51 11.83 Agree 86 19.95 Strongly agree 50 11.60 I encourage my family and others to take the vaccination Strongly disagree 58 13.46 Disagree 135 31.32 Neutral 61 14.15 Agree 127 29.47 Strongly agree 50 11.60 COVID-19 cannot be controlled without vaccination Strongly disagree 85 19.72 Disagree 136 31.55 Neutral 65 15.08 Agree 111 25.75 Strongly agree 34 34 COVID-19 vaccine is fairly distributed for all Strongly disagree 67 15.55 Disagree 122 28.31 Neutral 84 19.49 Agree 99 22.97 Strongly agree 59 13.69 Mass vaccination can overcome the epidemic attack of the COVID-19 Strongly disagree 53 12.30 Disagree 90 20.88 Neutral 77 17.87 Agree 138 32.02 Strongly agree 73 16.94 The best prevention method is to take vaccine against COVID-19 Strongly disagree 54 12.53 Disagree 91 21.11 Neutral 92 21.35 Agree 134 31.09 Strongly agree 60 13.92 The COVID-19 vaccine is not tested adequately for its effectiveness Strongly disagree 28 6.50 Disagree 73 16.94 Neutral 67 15.55 Agree 129 29.93 Strongly agree 134 31.09 After vaccinated against COVID-19 other precaution can be avoided Strongly disagree 89 20.65 Disagree 131 30.39 Neutral 62 14.39 Agree 66 15.31 Strongly agree 83 19.26 The overall attitude towards COVID-19 vaccine Favorable 221 51.28 Unfavorable 210 48.72 https://doi.org/10.1371/journal.pone.0265061.t002 If one person takes COVID-19 vaccination, it has a great contribution for other people I will take the vaccine if I get it without hesitation I will take the vaccine if I get it without hesitation I encourage my family and others to take the vaccination COVID-19 cannot be controlled without vaccination COVID-19 vaccine is fairly distributed for all Mass vaccination can overcome the epidemic attack of the COVID-19 The best prevention method is to take vaccine against COVID-19 The COVID-19 vaccine is not tested adequately for its effectiveness After vaccinated against COVID-19 other precaution can be avoided The overall attitude towards COVID-19 vaccine https://doi.org/10.1371/journal.pone.0265061.t002 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 7 / 14 PLOS ONE Attitude of health professionals towards COVID-19 vaccination Fig 1. PLOS ONE Attitude of the health professionals regarding effectiveness of the Corona virus vaccine, 2021. https://doi.org/10.1371/journal.pone.0265061.g001 Fig 1. Attitude of the health professionals regarding effectiveness of the Corona virus vaccine, 2021. https://doi.org/10.1371/journal.pone.0265061.g001 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 Discussion Though the vaccine development against COVID-19 was promising for the world population, vaccine hesitancy has become a global challenge to the successful uptake of the vaccine [11,13– 17]. Literature shows that vaccine safety and efficacy are among the worries of the people and the reasons for vaccine hesitancy [17,18,24]. Health care professionals are at a particular con- cern to be vaccinated to influence the general population for vaccination positively. There was a dearth of information about the attitude and perception of health professionals toward COVID-19 vaccination and its associated factor in Ethiopia, particularly in the study area. Therefore, this study was intended to determine the attitude of health professionals toward COVID-19 vaccination and its associated factors in Nekemte town. Accordingly, 31.55% of the study participants had agreed to take the vaccine without hesita- tion if available in the present study. This is lower than the study findings from Southwestern Ethiopia (48.4%) [23], Eastern Ethiopia (61.4%) [33], Bangladesh (58.6%) [34], Canada (72.40) [35]. The possible explanation for this might be the variation in trust and reliability of the source of information about COVID-19 vaccine. Moreover, 41.07% of the study subjects in the present study have also agreed on encouraging families and others to take the vaccine while 65.5% of participants in Bangladesh agreed to do so. Furthermore, 59.75% of this study’s health professionals agreed that COVID-19 would not be controlled without vaccination. This echoes the finding from Bangladesh (63.4%) [34]. In addition, nearly half of the study participants in the current study have agreed on mass vaccination to overcome the pandemic. This is also congruent with study done in Libya [36]. Comparable to the study finding from Saudi Arabia (37%) [37], only one-third of participants agreed on the vaccine’s effectiveness in the present study. This depicts that there is still a need to provide reliable and accurate information about the vaccine’s effectiveness against COVID-19 to health care professionals and the public. 8 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination Table 3. Perception the health care professionals towards COVID-19 vaccine. Variables Option Frequency Percent Have you ever been infected with COVID-19 Yes 95 22.04 No 169 39.21 I don’t know 167 38.75 Do you think that the COVID-19 vaccine is effective? Discussion Yes 131 30.39 No 34 7.89 I don’t know 266 61.72 Do you think that COVID-19 vaccine is mandatory for health care workers? Yes 262 60.79 No 24 5.56 I don’t know 145 33.64 Do you think COVID-19 will be controlled only by preventive measures without vaccination? Yes 85 19.72 No 102 23.67 I don’t know 244 56.61 Do you think that various COVID-19 vaccines have been discovered? Yes 142 32.95 No 46 10.67 I don’t know 243 56.38 Do you think that the COVID-19 vaccine will be affordable and accessible by the common person! Yes 59 13.69 No 145 33.64 I don’t know 227 52.67 https://doi.org/10.1371/journal.pone.0265061.t003 PLOS ONE Table 4. Multivariable analysis of factors associated with attitude towards COVID-19 vaccine among health professionals in Nekemte city, Western Ethiopia. Characteristics Attitude COR(95%CI) AOR(95%CI) P-value Poor Good Age <30 149 125 1.87(1.25,2.79) 2.14(1.25,3.67) <0.01 > = 30 61 96 Ref Sex Male 125 143 Ref Female 85 78 0.80 (0.54,1.18) 0.93(0.54, 1.59) 0.795 Institution Hospital 195 155 Ref Health center 10 24 3.01(1.40, 6.50) 2.45(1.01,5.92) 0.045 Private clinic 5 42 10.56 (4.0,27.35) 7.77(2.19,27.58) <0.01 Chronic diseases Yes 9 10 Ref No 201 211 0.94(0.37,2.37) 0.76(0.25,2.29) 0.630 History of allergic reaction to previous medication Yes 21 20 Ref No 189 201 1.11(0.58,2.12) 1.04(0.46,2.33) 0.914 Knowledge about COVID-19 vaccination Poor knowledge 44 86 Ref Good knowledge 139 163 0.30(0.18,0.49) 0.38(0.22,0.64) <0.01 https://doi.org/10.1371/journal.pone.0265061.t004 of the general population had a favorable attitude toward COVID-19 vaccination [38]. The possible reason for the observed discrepancy might be due to the relative information differ- ence among the population of interest. Furthermore, it might be due to health care profession- als being at higher risk of infection with the virus that might result in a favorable attitude toward vaccination to minimize the risk of infection. This implies a need to assure the vac- cine’s effectiveness, safety, and efficacy to enhance its uptake by health professionals and the general public. Health professionals are the counselor and advocators of the general population that their decision to receive the vaccine can greatly influence the uptake by the general population. The factors affecting health care professionals’ attitude toward COVID-19 vaccination were knowledge towards COVID-19 vaccination, age of respondents, and type of health facility. Accordingly, the proportion of health professionals who have unfavorable attitudes was 62% lower among professionals with good knowledge of COVID-19 vaccination than their coun- terparts. This might be because knowing the importance of the COVID-19 vaccine can posi- tively influence someone to have a positive attitude toward it. Moreover, the odds of having unfavorable attitudes were much higher among health professionals working in private clinics and health centers than those in hospitals. This variation might be due to the relative number of client flow to the health center and private clinic being much lower than the hospital and, hence the professionals consider themselves at lower risk of exposure and infection to COVID-19. In addition, almost all COVID-19 patients have been admitted to hospitals than private clinics or health centers. https://doi.org/10.1371/journal.pone.0265061.t003 The current study revealed that half of the health care professionals who participated in this study have a favorable attitude toward COVID-19 vaccination. This is lower than the study done in Bangladesh reported that 78% of the general population had a favorable attitude [34]. However, it is higher than the online survey which was done in Ethiopia that reported 24.2% Fig 2. Perception the health care workers regarding Corona virus vaccine’s side effect, 2021. https://doi.org/10.1371/journal.pone.0265061.g002 Fig 2. Perception the health care workers regarding Corona virus vaccine’s side effect, 2021. https://doi.org/10.1371/journal.pone.0265061.g002 Fig 2. Perception the health care workers regarding Corona virus vaccine’s side effect, 2021. https://doi.org/10.1371/journal.pone.0265061.g002 Fig 2. Perception the health care workers regarding Corona virus vaccine’s side effect, 2021. PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 9 / 14 Attitude of health professionals towards COVID-19 vaccination PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 Limitation of the study The study did not provide qualitative perspectives on the attitude and perception of health professionals towards the COVID-19 vaccine and its associated factors, which, if available, could underpin the quantitative findings. Moreover, since it is a cross-sectional study, it did not address the cause and effect relationship between the factors and the outcome variables. Supporting information S3 File. Tool. (DOCX) PLOS ONE Therefore, professionals working at health centers and private clinics for known and obvious reasons consider themselves to have a lower risk of infection with COVID-19. As a result, they might have an unfavorable attitude toward the COVID-19 vaccine than professionals working in the hospital setting. In this study, age of HCWs were significantly associated with attitude towards COVID-19 vaccine, in which health professionals aged less than 30 years had negative attitude towards the vaccine. This is in line with study conducted in North Ethiopia which reported higher age pos- itively associated with positive attitude towards COVID-19 vaccine [39]. This might be due to the fact that, as age increase, the probability of developing comorbidity increase, and the chance of infecting with COVID-19 also high. Thus the HCWs intention to receive the vaccine would be high. 10 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination Declaration Ethical approval and consent to participate. The study was approved, and ethical clearance letters were obtained from Wollega University, Institute of Health Science Research Ethics review board. After approval, a permission letter was obtained from the administrative body of health facilities to respective clinics. Verbal consent was obtained from study participants, and the purpose of this study was stated to all participants. Everybody participated voluntarily in this study. Acknowledgments We want to thank all health facilities for their invaluable co-operation during data collection, and our deep acknowledgment also goes to the data collectors for their interest and commit- ment in carrying out the study. Conclusion In general, the attitude and perception of health care professionals toward the COVID-19 vac- cine in the study area were unsatisfactory. Having poor knowledge about the COVID-19 vac- cine, young age group, working in private clinics and health centers are the independent determinants of unfavorable attitudes towards the COVID-19 vaccine. Therefore, there is still a need to improve health professionals’ knowledge of the COVID-19 vaccine by providing reli- able information regarding vaccine safety, efficacy, and effectiveness. Furthermore, the media outlets need to work to develop trust among the public by disseminating accurate and consis- tent information about the vaccine. In addition, future researchers should also explore more about the attitude and perception of health care professionals toward the COVID-19 vaccine and its determinants using qualitative data. Author Contributions Conceptualization: Tadesse Tolossa, Diriba Mulisa, Getahun Fetensa, Belayneh Mengist, Gebeyehu Abera, Tesfaye Shibiru. Data curation: Diriba Ayala, Dejene Seyoum. Data curation: Diriba Ayala, Dejene Seyoum. 11 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination Formal analysis: Tadesse Tolossa, Bizuneh Wakuma, Ebisa Turi, Diriba Mulisa, Getahun Fetensa. Funding acquisition: Bizuneh Wakuma, Diriba Mulisa, Diriba Ayala, Gebeyehu Abera, Emiru Merdassa Atomssa, Dejene Seyoum. Investigation: Ebisa Turi, Getahun Fetensa, Belayneh Mengist, Gebeyehu Abera, Tesfaye Shibiru. Methodology: Tadesse Tolossa, Bizuneh Wakuma, Ebisa Turi, Diriba Ayala, Dejene Seyoum. Project administration: Getahun Fetensa, Belayneh Mengist, Gebeyehu Abera, Ayantu Getahun. Resources: Tadesse Tolossa, Ebisa Turi, Diriba Mulisa, Emiru Merdassa Atomssa. Software: Tadesse Tolossa, Bizuneh Wakuma, Belayneh Mengist, Tesfaye Shibiru. Supervision: Bizuneh Wakuma, Diriba Ayala, Getahun Fetensa, Tesfaye Shibiru, Ayantu Getahun. 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Dereje N., et al., COVID-19 Vaccine hesitancy in Addis Ababa, Ethiopia: A mixed-methods study. medRxiv, 2021. 25. Griffin DS, M G., Griffin DO., Adolescents trust physicians for vaccine information more than their parents or religious leaders. Heliyon, 2018. 4(12): p. e01006. https://doi.org/10.1016/j.heliyon.2018. e01006 PMID: 30619955 26. Karafillakis E, D I., Apfel F, et al., Vaccine hesitancy among healthcare workers in Europe: a qualitative study. Vaccines, 2016. 34(41): p. 5013–5020. https://doi.org/10.1016/j.vaccine.2016.08.029 PMID: 27576074 27. Reliefweb, Accelerating broad and equitable access to the COVID-19 vaccine in Ethiopia: https:// reliefweb.int/report/ethiopia/accelerating-broad-and-equitable-access-covid-19-vaccine-ethiopia. 2021. 28. Kumar H., et al., Knowledge and Perception of Health Professionals towards COVID-19. Age (years), 2020. 25(090): p. 11.5. 29. Verger P., et al., Online study of health professionals about their vaccination attitudes and behavior in the COVID-19 era: addressing participation bias. Human Vaccines & Immunotherapeutics, 2021: p. 1– 6. https://doi.org/10.1080/21645515.2021.1921523 PMID: 34047670 30. Tavakol M. and Dennick R., Making sense of Cronbach’s alpha. PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 39. Alle Y.F. and Oumer K.E., Attitude and associated factors of COVID-19 vaccine acceptance among health professionals in Debre Tabor Comprehensive Specialized Hospital, North Central Ethiopia; 2021: cross-sectional study. Virusdisease, 2021. 32(2): p. 272–278. https://doi.org/10.1007/s13337- 021-00708-0 PMID: 34222565 References International journal of medical educa- tion, 2011. 2: p. 53. https://doi.org/10.5116/ijme.4dfb.8dfd PMID: 28029643 31. Lauritsen J.M. and Bruus M., EpiData entry. A comprehensive tool for validated entry and documenta- tion of data. Odense Denmark: The EpiData Association, 2008. 32. Kohler U. and Kreuter F., Data analysis using Stata. 2005: Stata press. 33. Zewude B. and Belachew A., Intention to Receive the Second Round of COVID-19 Vaccine Among Healthcare Workers in Eastern Ethiopia. Infect Drug Resist, 2021. 14: p. 3071–3082. https://doi.org/10. 2147/IDR.S326055 PMID: 34408451 13 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0265061 March 9, 2022 PLOS ONE Attitude of health professionals towards COVID-19 vaccination 34. Islam M.S., et al., Knowledge, attitudes and perceptions towards COVID-19 vaccinations: a cross-sec- tional community survey in Bangladesh. medRxiv, 2021. https://doi.org/10.1186/s12889-021-11880-9 PMID: 34645399 35. Verger P., et al., Attitudes of healthcare workers towards COVID-19 vaccination: a survey in France and French-speaking parts of Belgium and Canada, 2020. Eurosurveillance, 2021. 26(3): p. 2002047. 36. Elhadi M., et al., Knowledge, attitude, and acceptance of healthcare workers and the public regarding the COVID-19 vaccine: a cross-sectional study. BMC public health, 2021. 21(1): p. 1–21. https://doi. org/10.1186/s12889-020-10013-y PMID: 33388037 37. Ahmed N.J., et al., Public knowledge and attitudes toward COVID-19 Vaccination: A cross-sectional study. Medical Science, 2021. 25(108): p. 279–284. 38. Mesesle M., Awareness and Attitude Towards COVID-19 Vaccination and Associated Factors in Ethio- pia: Cross-Sectional Study. Infection and Drug Resistance, 2021. 14: p. 2193–2199. https://doi.org/10. 2147/IDR.S316461 PMID: 34163184 39. Alle Y.F. and Oumer K.E., Attitude and associated factors of COVID-19 vaccine acceptance among health professionals in Debre Tabor Comprehensive Specialized Hospital, North Central Ethiopia; 2021: cross-sectional study. Virusdisease, 2021. 32(2): p. 272–278. https://doi.org/10.1007/s13337- 021-00708-0 PMID: 34222565 14 / 14
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The evaluation of a remote support program on quality of life and evolution of disease in COPD patients with frequent exacerbations
BMC pulmonary medicine
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Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 DOI 10.1186/s12890-016-0304-3 Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 DOI 10.1186/s12890-016-0304-3 RESEARCH ARTICLE Open Access The evaluation of a remote support program on quality of life and evolution of disease in COPD patients with frequent exacerbations Bernardino Alcazar1* , Pilar de Lucas2, Joan B. Soriano3, Alonso Fernández-Nistal4, Antonia Fuster5, Jose Miguel Rodríguez González-Moro2, Aurelio Arnedillo6, Patricia García Sidro7 and María José Espinosa de los Monteros8 Abstract Background: Chronic obstructive pulmonary disease (COPD) patients often present considerable individual medical burden in their symptoms, limitations, and well-being that complicate medical treatment. To improve their overall health status, while reducing the number of exacerbations, a multidisciplinary approach including different elements of care is needed. The aim of this study was to evaluate the effects of a remote support program on COPD patients at high risk of experiencing worsening of their disease and other health-related outcomes. Methods: An observational, multicenter, prospective study aimed at evaluating the impact of a 7-month remote support program on COPD patients in exacerbations control and changes in health status measured with the COPD assessment test (CAT). Factors associated with a clinically relevant decrease in CAT were assessed using a logistic regression analysis. Results: A total of 114 subjects started the program. The majority of the study population were males (81.6 %), retired (70.2 %), without academic qualifications or with a low level of education (68.4 %), and ex-smokers (79.8 %). The mean ± SD age was 69.6 ± 9.1 years and the BMI was 27.8 ± 5.5 Kg/m2. Overall, 41.9 % (95 % CI 31.9–52.0) patients, significantly improved health status (CAT decrease ≥2 points). Univariate analysis showed that significant improvement in CAT was associated with baseline CAT scores [high CAT score 19.2 (±7.5) vs. low CAT score 12.4 (±6.4); OR = 1.15, 95 % CI: 1.07–1.24; p < 0.001] and with being non-compliant [62.5 % (15/24) of non-compliant vs 34.7 % (24/69) of compliant patients significantly improved CAT scores; OR = 3.13, 95 % CI: 1.19–8.19; p = 0.021). After controlling for the effect of all variables in a multivariable logistic regression model, the only factor that remained significant was baseline CAT score. The proportion of smokers in the total population remained constant during the study. There was a significant reduction in the number of exacerbations after entering this remote support program with median -1 (IQR: -2, 0), (p < 0.001). The Morisky-Green questionnaire showed an increase of treatment compliance, namely at baseline, 25.8 % (24/93) of patients were noncompliant while in the end 66.7 % (16/24) of them became compliant) (p = 0.053). Conclusions: A remote support program for high-risk COPD patients results in an improvement of the patients’ health status, particularly in those with initially poor health status, and it helps to reduce COPD exacerbations. The evaluation of a remote support program on quality of life and evolution of disease in COPD patients with frequent exacerbations Bernardino Alcazar1* , Pilar de Lucas2, Joan B. Soriano3, Alonso Fernández-Nistal4, Antonia Fuster5, Jose Miguel Rodríguez González-Moro2, Aurelio Arnedillo6, Patricia García Sidro7 and María José Espinosa de los Monteros8 © The Author(s). 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. * Correspondence: balcazarnavarrete@gmail.com 1Hospital de Alta Resolución de Loja, Agencia Sanitaria H. de Poniente, Avda Tierno Galván s/n., CP 18300 Loja, Granada, Spain Full list of author information is available at the end of the article Study population Patients of both genders, aged 40 years or older, fulfilling the selection criteria who signed the informed consent were recruited. The inclusion criteria were: a) COPD confirmed by spirometry performed in stable state not more than 12 months prior to recruitment in the study with a post-bronchodilator ratio of FEV1/FVC < 0.7; b) smoker or former smoker of at least 10 pack-years; c) patients with 2 or more moderate/severe exacerbations reported in the 12 months prior to study entry; d) pa- tient clinically stable at the time of inclusion in the study and who was willing to participate in the Horizonte pa- tient support program. Disease-specific programs are an integral component of collaborative self-management. This approach is recog- nized to improve health outcomes in people with chronic conditions [10] and has also successfully improved the health related quality of life (HRQoL) of patients with chronic respiratory disease, such as asthma [11]. These programs provide information for patients to recognize and therefore to prevent, and decrease the severity and/or frequency of symptoms and to implement appropriate treatment for the episodes [11]. The exclusion criteria in the study were: (i) patients who had never smoked, (ii) those who suffered a moderate/ severe exacerbation in the previous 30 days (iii) other chronic respiratory disease (e.g. bronchial asthma, allergic rhinitis, severe bronchiectasis, cancer, restrictive lung disease, etc.) or pulmonary surgery, (iv) or who, in the opinion of the investigator, did not demonstrate sufficient cognitive capacity; presented sensory or psychiatric dis- ability or language barriers that might prevent or hinder participation in the study, (v) and participation in another study or clinical trial. A number of studies have evaluated the effect of differ- ent education programs for COPD and have concluded that participation in these programs was associated with an increase in the knowledge of COPD, an improvement in specific skills to manage the disease, an increased ad- herence to inhaled therapy, and a decrease in emer- gency room visits and hospital admissions due to COPD exacerbations; among other positive outcomes [12–15]. However, the available evidence is still inconclusive due to different study designs, different types of COPD patients included, methodological limitations, and a wide variation of reported outcome measures. An observation period of 12 months that included 7 months of allocation in the Horizonte remote support program and a follow-up period of 5 months was estab- lished. Abstract Keywords: Chronic obstructive pulmonary disease, Education, Management, Quality of life, Exacerbations Page 2 of 12 Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 2 of 12 Page 2 of 12 Background the disease (www.atlantishealthcare.com). It has been pre- viously used in Spain under controlled conditions, to as- sure its applicability in COPD patients, but has not been incorporated in to common clinical practice until just recently. Chronic obstructive pulmonary disease (COPD) is consid- ered a preventable, treatable, disabling respiratory disease characterized by an often progressive and mainly irre- versible airflow obstruction [1, 2]. COPD is currently the fourth leading cause of death worldwide, and is pro- jected to be the third cause of death in developed coun- tries by 2020 [3, 4]. Thus, the primary aim of the study was to assess the outcomes of the Horizonte remote support program for COPD patients at high risk, in terms of reduction in fre- quency and severity of exacerbations, and improvement in the patients’ health status measured with the COPD assessment test (CAT) when used as a part of the usual treatment. COPD is a paradigm of chronic disease, in which self- management and support are essential for a proper con- trol [5]. Primary medical management of COPD often focuses on improving airflow using bronchodilators and anti-inflammatory therapies; however, the airflow obstruc- tion associated with COPD is not completely reversible and often tends to progressively worsen over time [6]. Much of the deterioration and progression of the disease is related to the number and severity of exacerbations ex- perienced by patients [7] and, as the disease progresses, the patients experience a worsening in their quality of life [8]. Because complete recovery/cure from COPD is impossible, health professionals should focus on the improvement of patient-centered outcomes including health status and quality of life; which are important outcome measures for treatment and care in COPD pa- tients [9]. Design of the study and data collection Design of the study and data collection This was an observational, multicenter, prospective study where 24 pulmonologists, distributed throughout the Spanish national territory centres, recruited consecutive patients between November 2013 and October 2014. Each researcher aimed to recruit 9 consecutive patients. Sample size calculation For the sample size calculation, it was estimated that 171 completers were needed to detect a mean change in CAT of at least 2.5 (±10.0) points, with 90 % power and an alpha of 0.05. Assuming a dropout rate of 20 % from the start of the study, the number of patients recruited should total 214. Horizonte program “Moderate COPD exacerbations were defined as a sud- den increase in respiratory symptoms that required am- bulatory treatment with systemic corticosteroids and/or antibiotics, and exacerbations were considered severe when the patient required hospitalization”. The Horizonte program (developed by the company At- lantis Healthcare) (15) is based on the sending of text messages (SMS) and e-mails, in addition to calls made by skilled nurses, to patients who have given their con- sent. The program has been endorsed by the Spanish Pulmonology and Thoracic Surgery Society (SEPAR) and it is a support program for patients with COPD and was designed to help them understand their disease and treat- ment by changing their misconceptions, improving adher- ence to prescribed treatments and healthy habits (eg. reducing smoking), and consequently their quality of life. The program is available for both newly diagnosed COPD patients and those already diagnosed and treated. Initially, the risk of non-adherence is assessed in each patient by the completion of a questionnaire. According to these results, segments and risk levels are set (high or low risk of non-adherence), and different interventions are established: Telephone calls from nurses, notebooks in which the objectives are preset to guide the patient, magazines (5 issues for high risk and 2 issues for low risk), additional documentation focused on the specific problems of each patient (max. 4 per patient), and SMS and e-mails whose frequency varies depending on the patient’s risk (see a complete description at the end of the manuscript). Statistical analysis To describe the qualitative variables, absolute frequencies and percentages were used. For quantitative variables, those normally distributed used mean, standard deviation (SD), minimum and maximum figures, while median, interquartile range, minimum and maximum were used when they were not normally distributed. Variables of interest were compared between study groups using the Chi-squared or the Fisher’s exact test for categorical variables, and the Student’s “t” test for independent data (or the Mann-Whitney U test if the assumption of normality was not met), to compare quantitative variables. The Kolmogorov-Smirnov test or Shapiro-Wilk test were used to assess if the quantitative variables followed a normal distribution. Comparisons of quantitative variables between more than two groups were made using the Kruskal-Wallis test or analysis of variance (ANOVA), depending on data distribution. The program’s objective is to improve patient educa- tion with regard to the knowledge of their disease and to achieve better adherence. Patient coordination is led by the company Atlantis Healthcare and is funded by Takeda Pharmaceutical Spain SA. A more detailed description of the Horizonte program can be reviewed at Additional file 1. The pre and post-intervention comparisons of quantita- tive variables were performed using the t Student test or the Wilcoxon test, depending on the data distribution. The pre and post-intervention comparisons of qualitative variables of two categories were performed using the McNemar test. Study population An evaluation was carried out before and after a 2 and 5-month period posterior to the inclusion in the study, in which the effectiveness of the measures imple- mented in the support program were assessed. Each patient conducted their own self-monitoring, comparing their health status sequentially. For each patient included, We hypothesized that the implementation in a real clinical practice setting of a disease-specific remote sup- port program (Horizonte program) for COPD patients at high risk, would positively influence these patients’ health status. The Horizonte program basically consists of send- ing text messages, e-mails, and conducting regular calls by qualified nurses, to facilitate proper monitoring of Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 3 of 12 Page 3 of 12 from 0 to 5 (0 = no impairment). An overall score is calcu- lated by adding the score from each item with total scores ranging from 0 to 40; a higher score indicates a more se- vere health status impairment or a poorer control of COPD [17, 18]. The CAT’s minimal clinical important difference (MCID) has not yet been established, and has been estimated to be 2.0 or more points [19]. data was collected in an electronic data collection note- book (e-CDR) designed for this purpose. The information requested in this e-CDR conformed to usual clinical practice, and referred to in the standard management of patients with COPD. Subject characteristics The study flow-diagram and flow-chart are shown in Figs. 1 and 2. A total of 148 subjects were initially recruited in the study. Thirty-four were excluded because they did not meet all the inclusion criteria (n = 114), then 100 completed the intervention program, and finally 93 com- pleted all study procedures (62.8 %). Baseline demographic characteristics of the patients are shown in Table 1. Most participants were male (81.6 %) and were ex-smokers (79.8). Mean age was 69.6 years ± 9.1 and mean BMI was 27.8 ± 5.5 Kg/m2. Clinical characteristics and pulmonary Study variables Recruiting physicians collected information regarding demographic data, smoking, medical history, comorbidi- ties, physical examination (weight, height, BMI, abdom- inal circumference), pharmacological treatment, history of exacerbations in the past 7 months, number of hospi- talizations for COPD in the past 7 months, spirometry (lung function), Morisky-Green and Levine Tests, Battle test, exacerbations from baseline, and hospitalizations. The cardiovascular risk was assessed according to BMI, gender, and waist circumference [16]. Incidence rates of exacerbations were described by annu- alized incidence rates with their 95 % confidence interval (95 % CI). Annualization of the rates and their correspond- ing confidence intervals were performed by adjusting to a Poisson model incorporating the time (expressed in years) of each patient in the study as incidence rates with their corresponding 95 % CI, and p-values. The analysis of a clinically significant change in CAT was assessed by logistic regression analysis, and expressed by the odds ratio (OR) Patients were asked to fill in the CAT questionnaire at baseline (VB) and after 2 (V2), 7 (last Horizonte program visit – V3) and 12 months (FV) in its validated Spanish version. The CAT consists of 8 items with scores ranging Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 4 of 12 Fig. 1 Flow Diagram of the study with its 95 % confidence interval and p values. Changes in CAT scores throughout the study were analyzed using a generalized linear mixed model of repeated measures. Data analysis was performed using the Statistical package SAS version 9.4 and statistical significance was considered when p < 0.05. function parameters of the sample at baseline are shown in Tables 2 and 3, respectively. A total of 90 subjects (78.9 %) had been vaccinated against influenza. Mean FVC and FEV1 (%) at the baseline were 71.3 % (±19.4) and 48.7 % (17.4 %) %, respectively. Regarding COPD severity by spirometric GOLD stage, 5.3 % had mild COPD, 36.8 % moderate, 43.9 % severe and 14.0 % very severe COPD. At baseline, 98.2 % (112/114) of partici- pating patients were receiving treatment/s for COPD (Tables 1, 2 and 3) Changes in smoking status and pharmacological treatment During the study, most participants (93.6 %) did not change their smoking status. However, from baseline up to 2 months prior to inclusion (V2), 4.3 % (4/93) of participants changed their smoking status (2 gave up smoking, one significantly decreased the number of cigarettes/day, and another significantly increased the Fig. 2 Flow-chart of the study Alcazar et al. Chi-square test; FFisher’s exact test; UMann-Whitney U test COPD chronic obstructive pulmonary disease, S.D standard deviation, BMI body mass index C F U are test; FFisher’s exact test; UMann-Whitney U test Changes in smoking status and pharmacological treatment BMC Pulmonary Medicine (2016) 16:140 Page 5 of 12 Table 1 Socio-demographic characteristics of the study population Overall Treatment non-adherence based on Morisky-Green baseline score High-Risk Low-Risk p-value N = 114 27 (23.7) 87 (76.3) Gender Men n(%) 93 (81.6) 18 (66.7) 75 (86.2) 0.043F Women n(%) 21 (18.4) 9 (33.3) 12 (13.8) Missing n 0 0 0 Age (years) Mean (S.D.) 69.6 (9.1) 68.3 (10.0) 70.0 (8.8) 0.449U ≤65 years n(%) 44 (38.6) 11 (40.7) 33 (37.9) 0.793C > 65 years n(%) 70 (61.4) 16 (59.3) 54 (62.1) Missing n 0 0 0 Level of education No studies/Primary studies n(%) 78 (68.4) 17 (63.0) 61 (70.1) 0.485C Intermediate and higher education n(%) 36 (31.6) 10 (37.0) 26 (29.9) Missing n 0 0 0 Employment situation Retired n(%) 80 (70.2) 16 (59.3) 64 (73.6) 0.156C Other n(%) 34 (29.8) 11 (40.7) 23 (26.4) Missing n 0 0 0 BMI (kg/m2) Mean (S.D.) 27.8 (5.5) 27.8 (6.2) 27.8 (5.3) 0.931U Underweight (<18.5) n(%) 3 (2.6) 1 (3.7) 2 (2.3) 0.738F Normal weight (18.5–24.9) n(%) 36 (31.6) 10 (37.0) 26 (29.9) Overweight (25.0–29.9) n(%) 41 (36.0) 8 (29.6) 33 (37.9) Obesity (≥30.0) n(%) 34 (29.8) 8 (29.6) 26 (29.9) Missing n 0 0 0 Cardiovascular risk None n(%) 31 (27.2) 8 (29.6) 23 (26.4) 0.907C Increased n(%) 27 (23.7) 5 (18.5) 22 (25.3) High n(%) 29 (25.4) 7 (25.9) 22 (25.3) Very/Extremely high n(%) 27 (23.7) 7 (25.9) 20 (23.0) Missing n 0 0 0 Smoking status Ex-smoker n(%) 91 (79.8) 17 (63.0) 74 (86.1) 0.012C Smoker n(%) 23 (20.2) 10 (37.0) 13 (14.9) Missing n 0 0 0 COPD treatment (at baseline) n(%) 112 (98.2) 27 (100.0) 85 (97.7) 1.000C Long-acting B2 agonists n(%) 101 (90.2) 23 (85.2) 78 (91.8) 0.456F Long-acting anticholinergics n(%) 99 (88.4) 24 (88.9) 75 (88.2) 1.000F Phosphodiesterase-4 Inhibitors n(%) 30 (26.8) 6 (22.2) 24 (28.2) 0.539C Inhaled Corticosteroids n(%) 88 (78.6) 17 (63.0) 71 (83.5) 0.023C Oxygen therapy n(%) 32 (28.6) 4 (14.8) 28 (32.9) 0.069C non-invasive mechanical ventilation n(%) 12 (10.7) 4 (14.8) 8 (9.4) 0.479F Missing n 0 0 0 COPD chronic obstructive pulmonary disease, S.D standard deviation, BMI body mass index CChi-square test; FFisher’s exact test; UMann-Whitney U test Table 1 Socio-demographic characteristics of the study population Alcazar et al. Changes in smoking status and pharmacological treatment BMC Pulmonary Medicine (2016) 16:140 Page 6 of 12 Table 2 Clinical characteristics Overall Treatment non-adherence based on Morisky-Green baseline score High-Risk Low-Risk p-value N = 114 27 (23.7) 87 (76.3) Time of evolution of COPD (years) Mean (S.D.) 8.8 (6.8) 7.7 (6.2) 9.2 (7.0) 0.314U Missing 1 0 1 Number of moderate exacerbations in the last 12 months Mean (S.D.) 1.6 (1.1) 1.5 (0.8) 1.6 (1.2) 0.967U Missing 0 0 0 Number of severe exacerbations in the last 12 months Mean (S.D.) 1.2 (1.6) 0.7 (1.0) 1.4 (1.8) 0.049U Missing 0 0 0 Total number of exacerbations in the last 12 months Mean (S.D.) 2.8 (1.4) 2.2 (0.5) 3.0 (1.5) 0.003U 2–3 exacerbations n(%) 97 (85.1) 26 (96.3) 71 (81.6) 0.069F 4 or more exacerbations n(%) 17 (14.9) 1 (3.7) 16 (18.4) Missing 0 0 0 Comorbidities Cardiac comorbidities n(%) 41 (36.0) 8 (29.6) 33 (37.9) 0.432C Coronary heart disease (CHD) n(%) 22 (19.3) 4 (14.8) 18 (20.7) 0.499C Peripheral vascular disease n(%) 13 (11.4) 2 (7.4) 11 (12.6) 0.730F Missing n 0 0 0 COPD chronic obstructive pulmonary disease, S.D standard deviation CChi-square test; FFisher’s exact test; UMann-Whitney U test COPD chronic obstructive pulmonary disease, S.D standard deviation CChi-square test; FFisher’s exact test; UMann-Whitney U test mild stages respectively; p = 0.015), higher scores in the mMRC (6.2 points more in those with mMRC > 2) and BODEx (5.4 points more in BODEx >4; p < 0.001), and being a current smoker (2.3 increase compared with ex-smokers; p = 0.026); whereas a better health status measured by CAT was associated with higher FEV1(%) (0.09 decrease per % unit; p < 0.001), longer walking au- tonomy (2.9 and 5.2 points less than <30 min walkers among those walking 30–60 min and > 60 min respectively; p < 0.001) and higher compliance measured by the Morisky- Green questionnaire (2.6 points less in com- pliant patients; p = 0.005). number of cigarettes/daily). Between V2 and V3, 4.3 % (4/93) of patients changed their smoking status, (2 gave up smoking, one resumed smoking again, and one significantly reduced the number of cigarettes/day). Fi- nally, between the V3 and FV, 2.2 % (2/93) of patients significantly reduced the number of cigarettes/day. During the baseline visit, COPD treatment was chan- ged in 36.0 % (41/114) of patients. Changes in smoking status and pharmacological treatment At the first follow-up visit (V2), 99.1 % (111/112) of patients were receiving treatment for COPD and during the visit; the treatment was changed in 25.9 % (29/112) of them. At the last visit of the program (V3) and at the end of the study (FV), all patients were receiving treatment for COPD. Changes in adherence are stated at the end of this section. Significant Improvements in CAT Significant Improvements in CAT A total of 41.9 % (95 % CI 31.9–52.0) patients signifi- cantly improved their reported health status (CAT de- crease by 2 points or more). Univariate analysis showed that significant improvement in CAT was associated with baseline CAT scores [high CAT score 19.2 (±7.5) vs. low CAT score 12.4 (±6.4); OR = 1.15, 95 % CI: 1.07–1.24; p < 0.001] and being non-compliant as measured with the Morisky-Green questionnaire [62.5 % (15/24) of non-compliant vs 34.7 % (24/69) of compliant patients significantly improved CAT scores; OR = 3.13, 95 % CI: Changes in CAT At baseline, patients had relatively high CAT scores: [15.3 (SD = 7.6)]. Throughout the study period, CAT scores improved an average of -0.4 (95 % CI: -1.6; 0.8) points, although not statistically significant (p = 0.530, paired t-Student) (Fig. 3). Worse health status measured by CAT was associated with longer duration of COPD (0.14 increase of CAT per year; p = 0.018), severe and very severe GOLD stages (1.9 and 3.3 points more than Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 7 of 12 Table 3 Lung function at baseline 1.19–8.19; p = 0.021). After controlling for the effect of all variables in a multivariable logistic regression model, the only factor that remained associated with CAT change (“significant improvement” vs. Changes in CAT “no improvement”) was the baseline CAT score (Table 4) Change in the number of exacerbations The average duration of COPD in the sample was 8.8 6.8 years, while in the 12 months prior to the stud 85.1 % experienced 2 or 3 exacerbations and 14.9 % ex perienced 4 or more D ring the Horizonte program Table 3 Lung function at baseline Overall Treatment non-adherence based on Morisky-Green baseline score High-Risk Low-Risk p-value N = 114 27 (23.7) 87 (76.3) Spirometry No n(%) 0 (0.0) ——— ——— Yes, prior to the visit n(%) 75 (65.8) 13 (48.2) 62 (71.3) 0.027C Yes, during the visit n(%) 39 (34.2) 14 (51.8) 25 (28.7) Spirometry results FVC (ml) - Mean (S.D.) 2485.4 (844.0) 2546.7 (788.7) 2466.4 (864) 0.668T FVC (%) - Mean (S.D.) 71.3 (19.4) 75.7 (21.7) 69.9 (18.6) 0.142U FEV1 (ml) - Mean (S.D.) 1239.7 (521.8) 1456.3 (544.9) 1172.5 (498.7) 0.013T FEV1 (%) - Mean (S.D.) 48.7 (17.4) 56.7 (17.8) 46.2 (16.6) 0.007U FEV1/FVC (%) - Mean (S.D.) 50.8 (13.2) 57.3 (10) 48.8 (13.5) 0.004U Missing n 0 0 0 GOLD stage Stage I: Mild (80 ≤FEV1% ≤100) n(%) 6 (5.3) 2 (7.4) 4 (4.6) 0.074F Stage II: Moderate (50 ≤FEV1% ≤79) n(%) 42 (36.8) 15 (55.6) 27 (31.0) Stage III: Severe (30 ≤FEV1% ≤49) n(%) 50 (43.9) 7 (25.9) 43 (49.4) Stage IV: Very severe (FEV1% < 30) n(%) 16 (14.0) 3 (11.1) 13 (14.9) Missing n 0 0 0 O2 saturation (%) X (D.E.) 93.9 (3.0) 95.0 (2.7) 93.5 (3.0) 0.025U O2 saturation >90 % 98 (86.0) 25 (92.6) 73 (83.9) 0.351F Missing n 0 0 0 Minutes of walking per day < 30 n(%) 39 (34.2) 6 (22.2) 33 (37.9) 0.323C 30–60 n(%) 36 (31.6) 10 (37.0) 26 (29.9) > 60 n(%) 39 (34.2) 11 (40.7) 28 (32.2) Missing n 0 0 0 Emphysema No n(%) 56 (49.1) 18 (66.7) 38 (43.7) 0.037C Yes n(%) 58 (50.9) 9 (33.3) 49 (56.3) Missing n 0 0 0 BODEx index Quartile 1: 0–2 points n(%) 28 (24.6) 12 (44.4) 16 (18.4) 0.011C Quartile 2: 3–4 points n(%) 44 (38.6) 11 (40.7) 33 (37.9) Quartile 3: 5–6 points n(%) 31 (27.2) 4 (14.8) 27 (31.0) Quartile 4: 7–10 points n(%) 11 (9.6) 0 (0.0) 11 (12.6) Missing n 0 0 0 S.D standard deviation CChi-square test; FFisher’s exact test; TT-Test; UMann-Whitney U test Change in the number of exacerbations The average duration of COPD in the sample was 8.8 ± 6.8 years, while in the 12 months prior to the study, 85.1 % experienced 2 or 3 exacerbations and 14.9 % ex- perienced 4 or more. Discussion The objective of the present study was to examine the impact of a remote support program on the health status of moderate/severe COPD patients. Recommendations for the use of specific support programs for patients with COPD are based on experience with other chronic dis- eases such as diabetes [20], coronary artery disease [21], and asthma [22]. Studies investigating the utility of such programs for COPD reported heterogeneous conclusions, and meta-analyses have argued that more studies are needed [23, 24]. Changes in COPD exacerbations frequency 12 months before and after the study are presented in Fig. 4. During the 12 months before the study, median total exacerba- tions was 2 (IQR: 2-3), while during the study it decreased to 1 (IQR: 0-3). Median change (post-pre study) in the number of exacerbations was therefore -1 (IQR: -2, 0), (p < 0.001). For moderate exacerbations, patients expe- rienced a median of 2 (IQR 1-2) and, during the study, 1 (IQR 0-1). Median change (post-pre study) in the number of moderate exacerbations is -1 (IQR: -2, 0), (p < 0.001). Fi- nally for severe exacerbations, patients experienced a median previous exacerbations of 1 (IQR 0-2) and, dur- ing the study, 0 (IQR 0-1), with a median change (post- pre study) in the number of severe exacerbations of 0 (IQR: -1, 0), (p = 0.017). Reducing the burden of disease by improving patients’ symptoms, functional status, and quality of life are import- ant goals. There has been a substantial increase in the use of newly developed tools that measure health status and it is important for clinicians and researchers to assess these instruments’ strengths and weaknesses in provid- ing insight into a patient’s condition and experience. Relying only on mortality and physiological outcomes could blind the clinician to the potential benefits that patients may receive from a treatment. A growing body of research utilizes end-points assessed directly by pa- tients whose self-reported health status includes health- related quality of life and their functional status [25]. Changes in adherence (VB-V3), 45.0 % of patients experienced exacerbations [30.0 % moderate exacerbations, 24.0 % severe exacerba- tions (8.0 % exacerbations that led to emergency room visits, and 17.0 % hospitalization)]. The median number of exacerbations was 2 for total exacerbations (IQR 1-3) with a maximum of 8; 1 for moderate exacerbation (IQR: 1-2) with up to 6; 1 for severe exacerbation (IQR: 1-1) with up to 8; and 1 emergency exacerbation (IQR: 1-1) with a maximum of 5. After program completion, 57.0 % of patients had suffered exacerbations [35.5 % moderate exacerbations, 29.0 % severe exacerbations, (15.1 % emergency exacerbations, and 22.6 % exacerba- tions requiring hospitalization)). Changes in adherence were of borderline significance (p = 0.053). According to the Morisky-Green question- naire, at baseline 25.8 % (24/93) of patients were non- compliant. Of these patients, at the end of the study, 66.7 % (16/24) became compliant. Of the 74.2 % (69/93) of compliant patients at baseline, 91.3 % (63/69) did not change their adherence and 8.7 % (6/69) became non- compliant when the study finished. Changes in CAT During the Horizonte program Change in the number of exacerbations 1.19–8.19; p = 0.021). After controlling for the effect of all variables in a multivariable logistic regression model, the only factor that remained associated with CAT change (“significant improvement” vs. “no improvement”) was the baseline CAT score (Table 4). Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 8 of 12 Fig. 3 COPD assessment test (CAT) scores at baseline, at the first (V2) and second (V3) follow-up visits and at the end of the study (FV) Fig. 3 COPD assessment test (CAT) scores at baseline, at the first (V2) and second (V3) follow-up visits and at the end of ssment test (CAT) scores at baseline, at the first (V2) and second (V3) follow-up visits and at the end of the study (FV) Changes in pulmonary function No significant differences in pulmonary function were observed from baseline. Initial mean FVE1 was 49.5 % (16.9) and at the end of the study it was 49.0 % (18.2) not statistically significant (0.0 (IQR: -5.0; 4.0), p = 0.822). Page 9 of 12 Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Table 4 Main objective analysis: Decrease in at least two points in CAT between the baseline and the final visit. Subgroup analysis: univariate and multivariate models Variable Category Univariate analysis OR (CI 95 %) Multivariate analysis OR (CI 95 %) Gender Women —————— Men 0.50 (0.17–1.48) Age 0.97 (0.93–1.02) Age ≤65 years —————— >65 years 0.48 (0.20–1.11) BMI 1.00 (0.92–1.08) BMI classification Normal (18.5–24.9) —————— Overweight (25.0–29.9) 1.37 (0.49–3.82) Obesity (≥30.0) 0.87 (0.31–2.49) CAT 1.15 (1.07–1.24) 1.15 (1.07–1.24) Time of evolution COPD (years) 0.96 (0.91–1.03) Previous exacerbations 2–3 —————— ≥4 0.42 (0.11–1.65) FEV1(%) Postbronchodilation 1.01 (0.98–1.03) GOLD stage Mild-moderate —————— Severe-very severe 0.96 (0.42–2.21) Dyspnea ≤2 —————— >2 0.67 (0.27–1.63) BODEx index ≤4 —————— >4 0.88 (0.38–2.07) Minutes walking a day <30 —————— 30–60 1.48 (0.54–4.07) >60 1.00 (0.36–2.78) Morisky-Green questionnaire Compliant —————— Noncompliant 3.13 (1.19–8.19) Significant cardiac comorbidity No —————— Yes 0.47 (0.17–1.36) Cardiovascular risk None —————— Increased 0.92 (0.28–3.102) High 0.89 (0.27–2.89) Very/extremely high 1.05 (0.33–3.38) Smoking status Ex-smoker —————— Smoker 1.98 (0.70–5.61) COPD chronic obstructive pulmonary disease, BMI body mass index, CAT COPD Assessment Test Table 4 Main objective analysis: Decrease in at least two points in CAT between the baseline and the final visit. Subgroup analysis: univariate and multivariate models COPD chronic obstructive pulmonary disease, BMI body mass index, CAT COPD Assessment Test need for effective care plans to optimize the use of lim- ited resources. The main finding of this study is that high risk COPD patients; who received a remote support program based on disease-specific self-management principles showed an improvement in their health status in nearly half of the pa- tients analyzed assessed with the CAT questionnaire and a significant reduction in the occurrence of exacerbations. Changes in pulmonary function Although we cannot identify which component of the intervention had an effect, the results nevertheless re- main important, considering the limitations of current COPD treatments, the burden of the disease, and the To assess health status in COPD patients, the most widely used short questionnaires are CAT [18], the Clin- ical COPD Questionnaire (CCQ) [26], the Airways Ques- tionnaire 20 (AQ20) [27], and the COPD severity score (COPDSS) [28]. In particular, CAT, AQ20, and CCQ have been assessed on their predictive value for exacerbations and mortality [29, 30]. CAT covers a broad range of effects of COPD on patients’ health including cough, phlegm, Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 10 of 12 Fig. 4 Difference in the number of exacerbation (12 months before starting the study and during the 12-months follow-up of the study) Fig. 4 Difference in the number of exacerbation (12 months before starting the study and during the 12-months follow reduction in lung function [39], and about one-half of patients who seek treatment in an emergency depart- ment report having had characteristic symptoms for at least 4 days [40]. Early treatment of exacerbations has been shown to reduce morbidity and effect on quality of life [41] and the remote program implemented in the study seems to be very effective at reducing exacerba- tions, even in patients who are difficult to control and with a long duration of COPD disease. Moreover, the reduced number of exacerbation of the present study confirms previous reports [42, 43] of improvements in exacerbations with disease specific interventions. On the contrary, in the study carried out by Van Wetering et al., no reductions in the number of exacerbations were ob- tained [44]. This is probably associated with a less ad- vanced COPD in the patients included in that study. chest tightness, breathlessness going up hills/stairs, ac- tivity limitation at home, confidence leaving home, sleep, and energy. CAT has demonstrated to be the best predictive questionnaire for a series of outcomes (new ambulatory or emergency exacerbations, hospitalization, or death) in patients with moderate-to-severe COPD [31]. Some studies have shown that patients with severe COPD improve less with specific health programs com- pared with patients with less severe disease [32, 33]. Changes in pulmonary function Interestingly enough, our study suggests that non- compliant patients and COPD patients with higher CAT scores at baseline, which means a worse health status, are the patients who have benefited the most from this remote program. This could be explained, at least partially, by differences in the severity of COPD among these groups of patients which led to a better health status and by the different interventions adapted to each patient’s specific risk to non-adherence, with more intense interventions for those patients at higher risk. Duration of intervention has been demonstrated to be an important variable in a previous meta-analysis [14]. The health-related quality of life scores, COPD-related ED visits, and hospital admission rates were similar between groups during the initial 3- to 6-month follow-up. How- ever, all of these outcomes reached statistical significance when the program outcomes were compared after a 12-month follow-up. The 7-month duration of the Horizonte program could have limited the statistical significance of some outcomes. Adherence to treatment was obtained in 100 % of the sample at the end of the program and it was maintained until the end of the study, which could suggest an im- provement in the compliance of the patients. Moreover, the results of the Morisky-Green questionnaire showed a tendency to an increase in adherence. Regarding the impact of the program on smoking status, significant heterogeneity has been observed in previous studies assessing the impact of disease-specific education programs. Only one out of three trials [45–47] reported significant differences in the number of current smokers between groups following the implementation of a disease-specific education program, maybe due to the fact that COPD patients lose their motivation after be- ing discharged from the hospital, and supervised home- based care could be more effective [48]. Exacerbations are important determinants of prognosis in patients with COPD, and are associated with health status [34, 35], lung function [36], mortality [37], and economic costs [38]. Prodromal symptoms of an exacer- bation commonly occur up to a week before a discernible This approach of care through a continuum sup- port and favouring self-management does not require Alcazar et al. BMC Pulmonary Medicine (2016) 16:140 Page 11 of 12 Page 11 of 12 specialized resources and can be easily implemented. Conclusions 3. Eva OE, Birgitta K, Kjell L, Ehrenberg A, Fossum B. Communication and self-management education at nurse-led COPD clinics in primary healthcare. Patient Educ Couns. 2009;77:209–17. The implementation of a remote support program for high risk COPD patients results in improvements of patients’ health status, particularly those with an ini- tially poor health status, and it effectively reduces exacerbations. 4. Carone M, Bertolotti G, Cerveri I, De Benedetto F, Fogliani V, Nardini S, et al. EDU-CARE, a randomised, multicentre, parallel group study on education and quality of life in COPD. Monaldi Arch Chest Dis. 2002;57:25–9. 5. Bourbeau J, Van der Palen J. Promoting effective self-management programmes to improve COPD. Eur Respir J. 2009;33:461–3. 6. Monninkhof E, van der Valk P, van der Palen J, van Herwaarden C, Zielhuis G. Effects of a comprehensive self-management programme in patients with chronic obstructive pulmonary disease. Eur Respir J. 2003;22:815–20. 7. Wilkinson T, Wedzicha J, Strategies for improving outcomes of COPD exacerbations. International journal of chronic obstructive pulmonary 4. Carone M, Bertolotti G, Cerveri I, De Benedetto F, Fogliani V, Nardini S, et al. EDU-CARE, a randomised, multicentre, parallel group study on education and quality of life in COPD. Monaldi Arch Chest Dis. 2002;57:25–9. 5. Bourbeau J, Van der Palen J. Promoting effective self-management programmes to improve COPD. Eur Respir J. 2009;33:461–3. 5. Bourbeau J, Van der Palen J. Promoting effective self-management programmes to improve COPD. Eur Respir J. 2009;33:461–3. 6. Monninkhof E, van der Valk P, van der Palen J, van Herwaarden C, Zielhuis G. Effects of a comprehensive self-management programme in patients with chronic obstructive pulmonary disease. Eur Respir J. 2003;22:815–20. References b 1. Vestbo J, Hurd SS, Agusti AG, Jones PW, Vogelmeier C, Anzueto A, et al. Global strategy for the diagnosis, management, and prevention of chronic obstructive pulmonary disease: GOLD executive summary. Am J Respir Crit Care Med. 2013;187(4):347–65. 2. Chapman KR, Mannino DM, Soriano JB, Vermeire PA, Buist AS, Thun MJ, et al. Epidemiology and costs of chronic obstructive pulmonary disease. Eur Respir J. 2006;27(1):188–207. 2. Chapman KR, Mannino DM, Soriano JB, Vermeire PA, Buist AS, Thun MJ, et al. Epidemiology and costs of chronic obstructive pulmonary disease. Eur Respir J. 2006;27(1):188–207. Ethics approval and consent to participate The study was approved by the local ethics committees and the Agencia Española del Medicamento y Productos Sanitarios (AEMPS) and all participants provided a written informed consent. Additional file Additional file 1: Description and workflow of the Horizonte Program. (DOCX 92 kb) 7. Wilkinson T, Wedzicha J, Strategies for improving outcomes of COPD exacerbations. International journal of chronic obstructive pulmonary disease. Dove Med Press. 2006;1(3):335–42. 7. Wilkinson T, Wedzicha J, Strategies for improving outcomes of COPD exacerbations. International journal of chronic obstructive pulmonary disease. Dove Med Press. 2006;1(3):335–42. 8. Martín-Escudero JC. Quality of life and COPD Spanish Clinical Journal 2009; 209 (2):59–60 8. Martín-Escudero JC. Quality of life and COPD Spanish Clinical Journal 2009; 209 (2):59–60 Changes in pulmonary function The present study supports its use as an integral part of the long-term care of patients with moderate to advanced COPD, but further studies are needed to confirm their effectiveness. Authors’ contributions BA, JBS, PL and AFN designed the study and directed the data analysis. MM and AFN drafted the manuscript. AF, JRGM, AA, PGS, MEM participated in data collection and critical revision of the data analysis. All authors read and approved the final manuscript. 14. Hurst JR, Fitzgerald-Khan F, Goldring JJ, Quint JK, Dilworth JP, Mikelsons C, et al. Use and utility of a 24-hour Telephone Support Service for “high risk” With COPD patients. Prim Care RespirJ. 2010;19(3):260–5. Funding The ESOPO study was funded by Takeda Pharmaceutical Spain SA. 12. Moullec G, Lavoie KL, Rabhi K, Julien M, Favreau H. 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Received: 28 March 2016 Accepted: 1 November 2016 Received: 28 March 2016 Accepted: 1 November 2016 Received: 28 March 2016 Accepted: 1 November 2016 Acknowledgements We would like to thank Belen San Jose, Ivan Alcolea, Esther Artime, Lorenzo Dominguez, Ignacio Mendez, Ana Ortega and Ana Zabaljauregui who provided support for the design, setup, coordination, monitoring, statistical analyses and medical writing services on behalf of OXON Epidemiology which was sponsored by Takeda Pharmaceutical Spain SA. 9. Voll-Aanerud M, Eagan TML, Wentzel-Larsen T, Gulsvik A, Bakke PS. Respiratory symptoms, COPD severity, and health related quality of life in a general population sample. Resp Med. 2008;102:399–406. 10. Bodenheimer T, Lorig K, Holman H, Grumbach K. Patient self management of chronic disease in primary care. JAMA. 2002;288:2469–75. 9. Voll-Aanerud M, Eagan TML, Wentzel-Larsen T, Gulsvik A, Bakke PS. 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Author details 1 1Hospital de Alta Resolución de Loja, Agencia Sanitaria H. de Poniente, Avda Tierno Galván s/n., CP 18300 Loja, Granada, Spain. 2Hospital Universitario Gregorio Marañón, Madrid, Spain. 3Instituto de Investigación Hospital Universitario de la Princesa (IISP), Universidad Autónoma de Madrid, Madrid, Spain. 4Departamento médico Takeda Farmacéutica España S.A., Madrid, Spain. 5Hospital Son Llàtzer, Mallorca, Spain. 6Hospital Universitario Puerta del Mar, Cádiz, Spain. 7Hospital de la Plana, Castellón, Spain. 8Hospital Universitario Virgen de la Salud, Toledo, Spain. Study limitations include lack of completion of the a priori minimum sample size and those of any observa- tional study, like neither randomization of the sample nor reduced room for inferences. Additionally it would have been desirable to have a control group to indetify the effect of Horizonte program itself. Nevertheless, our a priori defined recruitment procedure to minimize sam- pling bias, systematic evaluation of consecutive COPD patients from different centres, and evaluation of patients’ health status using a standardized assessment instrument (CAT) strengthens our results. Our study characteristics are very similar to those in COPD patients with frequent exacerbations [14], so it is reasonable to assume that non- included cases would have had similar characteristics. Competing interests 15. Tan JY, Chen JX, Liu XL, Zhang Q, Zhang M, Mei LJ. A goal -analysis on the impact of disease-specific education programs on health outcomes for patients With chronic obstructive pulmonary disease. Geriatr Nurs. 2012;33(4):280–96. Bernardino Alcázar reports personal fees from Novartis AG, Boehringer Ingelheim, GSK, Almirall, AstraZeneca, Takeda and grants and personal fees from Menarini. Alonso Fernández-Nistal is a full-time employee of Takeda Farmaceútica España. 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BMC Pulmonary Medicine (2016) 16:140 Consent for publication Not applicable. Predictors of success and failure in pulmonary rehabilitation. Eur Respir J. 2006;27:788–94. 33. Wedzicha JA, Bestall JC, Garrod R, Garnham R, Paul EA, Jones PW. Randomized controlled trial of pulmonary rehabilitation in severe chronic obstructive pulmonary disease patients, stratified with the MRC dyspnoea scale. Eur Respir J. 1998;12:363–9. 34. Seemungal TA, Donaldson GC, Paul EA, Bestall JC, Jeffries DJ, Wedzicha JA. Effect of exacerbation on quality of life in patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 1998;157(5 Pt 1):1418–22. Submit your next manuscript to BioMed Central and we will help you at every step: Submit your next manuscript to BioMed Central and we will help you at every step: 35. Bourbeau J, Ford G, Zackon H, Pinsky N, Lee J, Ruberto G. Impact on patients’ health status following early identification of a COPD exacerbation. Eur Respir J. 2007;30(5):907–13. • We accept pre-submission inquiries • Our selector tool helps you to find the most relevant journal • We provide round the clock customer support • Convenient online submission • Thorough peer review • Inclusion in PubMed and all major indexing services • Maximum visibility for your research Submit your manuscript at www.biomedcentral.com/submit and we will help you at every step: 36. Donaldson GC, Seemungal TAR, Bhowmik A, Wedzicha JA. Relationship between exacerbation frequency and lung function decline in chronic obstructive pulmonary disease. Thorax. 2002;57(10):847–52. 37. Soler-Cataluña JJ, Martínez-García MA, Román Sánchez P, Salcedo E, Navarro M, Ochando R. Severe acute exacerbations and mortality in patients with chronic obstructive pulmonary disease. Thorax. 2005;60(11):925–31. 38. Andersson F, Borg S, Jansson SA, Jonsson AC, Ericsson A, Prütz C, et al. The costs of exacerbations in chronic obstructive pulmonary disease (COPD). Respir Med. 2002;96(9):700–8. 38. Andersson F, Borg S, Jansson SA, Jonsson AC, Ericsson A, Prütz C, et al. The costs of exacerbations in chronic obstructive pulmonary disease (COPD). Respir Med. 2002;96(9):700–8.
https://openalex.org/W4362729385
https://zenodo.org/records/7810468/files/5-12.pdf
Kirghiz, Kyrgyz
null
NUMERICAL SOLUTION OF THE CAUCHY PROBLEM FOR IDEAL PLASTICITY EQUATIONS WITH YIELD CONDITION DEPENDING ON THE AVERAGE STRESS
Zenodo (CERN European Organization for Nuclear Research)
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NUMERICAL SOLUTION OF THE CAUCHY PROBLEM FOR IDEAL PLASTICITY EQUATIONS WITH YIELD CONDITION DEPENDING ON THE AVERAGE STRESS Nguyen Minh Hue, Pham Thi Thuy, Faculty of Basic Science, Ho Chi Minh City University of Transport, Ho Chi Minh City, Vietnam Annotation: The Cauchy problem of the propagation of zones of a plastic state in an unbounded medium from the boundary of a convex surface, on which normal pressure, tangential forces, and given displacement velocities act, is considered. In the case of complete plasticity and linear dependence of the yield condition on the average stress, the system of quasi-static ideal plasticity equations describing the stress-strain state of the medium is hyperbolic. When solving this system numerically, a different scheme is used for hyperbolic systems of conservation laws. Keywords: stress, deformation, full plasticity, yield strength, ideal plasticity, hyperbolic system РАЗДЕЛ. ЕСТЕСТВЕННЫЕ НАУКИ https://doi.org/10.5281/zenodo.7810468 UDK 50 ЧИСЛЕННОЕ РЕШЕНИЕ ЗАДАЧИ КОШИ ДЛЯ УРАВНЕНИЙ ИДЕАЛЬНОЙ ПЛАСТИЧНОСТИ С УСЛОВИЕМ ТЕКУЧЕСТИ В ЗАВИСИМОСТИ ОТ СРЕДНЕГО НАПРЯЖЕНИЯ. Нгуен Минь Хюэ, Фам Тхи Туи, Факультет фундаментальных наук, Университет транспорта Хошимина, Хошимин, Вьетнам Нгуен Минь Хюэ, Фам Тхи Туи, Факультет фундаментальных наук, Университет транспорта Хошимина, Хошимин, Вьетнам Аннотация: Рассмотрена задача Коши о распространении зон пластического состояния в неограниченной среде от границы INNOVATIVE SCIENTIFIC RESEARCH выпуклой поверхности, на которую действуют нормальное давление, касательные силы и заданные скорости перемещений. В случае полной пластичности и линейной зависимости условия текучести от среднего напряжения система квазистатических уравнений идеальной пластичности, описывающая напряженно-деформированное состояние среды, является гиперболической. При численном решении этой системы для гиперболических систем законов сохранения используется другая схема. у ру Ключевые слова: напряжение, деформация, полная пластичность, предел текучести, идеальная пластичность, гиперболическая система Quasi-static equations of ideal plasticity for determining stresses and displacement rates in the case of complete plasticity have the form: (1) (2) 𝜎௜௝,௝= 0, (1) 𝑚𝑎𝑥(|𝜎ଵ−𝜎ଶ|, |𝜎ଶ−𝜎ଷ|, |𝜎ଵ−𝜎ଷ|) = 2(𝑘௦−𝑚𝜎), (2) 𝜎< 𝑘௦/𝑚, 𝜎ଶ= 𝜎ଷ, (3) 𝑒ଵଵ+ 𝑒ଶଶ+ 𝑒ଷଷ= 0, (4) ൥ 𝑒ଵଵ 𝑒ଵଶ 𝑒ଵଷ 𝑒ଶଵ 𝑒ଶଶ 𝑒ଶଷ 𝑒ଷଵ 𝑒ଷଶ 𝑒ଷଷ ൩⋅൥ 𝑛ଵ 𝑛ଶ 𝑛ଷ ൩= 𝜆൥ 𝑛ଵ 𝑛ଶ 𝑛ଷ ൩, 2𝑒௜௝= 𝑢௜,௝+ 𝑢௝,௜ (5) (2) (3) (4) (3) (4) (5) Here 𝜎௜௝ are the components of the symmetric stress tensor in the Cartesian coordinate system 𝑥ଵ, 𝑥ଶ, 𝑥ଷ; 𝜎= (ఙభభାఙమమାఙయయ) ଷ is the mean stress; 𝜎ଵ, 𝜎ଶ, 𝜎ଷ are principal stresses; 𝑘௦> 0, 𝑚> 0 are constants; 𝑒௜௝ are the strain rate tensor components; 𝑢௜ are the components of the displacement velocity vector; 𝑛௜ are the components of the unit eigenvector of the stress tensor corresponding to the non-multiple eigenvalue (principal stress) 𝜎ଵ. Equality (2) means a linear dependence of the maximum shear stress on the average pressure [1] (such a dependence (Fig. 1) is typical for some soils [2]). Equality (3) means the Haar–Karman completes plasticity condition [3], equality (4) is the incompressibility condition [4], and relation (5) is the isotropy condition [4]. ISSN 2713-0010 SCIENTIFIC NETWORK PUBLICATION ~ 6 ~ SCIENTIFIC NETWORK PUBLICATION ~ 6 ~ р Figure 1 – Physical and mechanical properties of sand under pressure System (1)–(3) is studied using D. D. Ivlev’s representation of the stress tensor in the form [4]: 𝜎ଵଵ= క ௔+ ௞ೞ ௠+ 𝜉𝑛ଵ ଶ, 𝜎ଵଶ= 𝜉𝑛ଵ𝑛ଶ, 𝜎ଶଶ= క ௔+ ௞ೞ ௠+ 𝜉𝑛ଶ ଶ, 𝜎ଵଷ= 𝜉𝑛ଵ𝑛ଷ, 𝜎ଷଷ= క ௔+ ௞ೞ ௠+ 𝜉𝑛ଷ ଶ, 𝜎ଶଷ= 𝜉𝑛ଶ𝑛ଷ, 𝜉= 2𝜀(𝑘௦−𝑚𝜎) = 2𝜀𝑒௔௣, 𝑎= ି଺௠ ଷఌାଶ௠, 𝜀= ±1. . (6) (6) 𝜉= 2𝜀(𝑘௦−𝑚𝜎) = 2𝜀𝑒௔௣, 𝑎= ି଺௠ ଷఌାଶ௠, 𝜀= ±1. ЧИСЛЕННОЕ РЕШЕНИЕ ЗАДАЧИ КОШИ ДЛЯ УРАВНЕНИЙ ИДЕАЛЬНОЙ ПЛАСТИЧНОСТИ С УСЛОВИЕМ ТЕКУЧЕСТИ В ЗАВИСИМОСТИ ОТ СРЕДНЕГО НАПРЯЖЕНИЯ. ଷఌାଶ௠ Substitution (6) identically satisfies relations (2), (3). In this case, the principal stresses are equal ସ ଶ 𝜎ଵ= ସ ଷ𝜀(𝑘௦−𝑚𝜎) + 𝜎, 𝜎ଶ= 𝜎ଷ= − ଶ ଷ𝜀(𝑘௦−𝑚𝜎) + 𝜎. 𝜎ଵ= ସ ଷ𝜀(𝑘௦−𝑚𝜎) + 𝜎, 𝜎ଶ= 𝜎ଷ= − ଶ ଷ𝜀(𝑘௦−𝑚𝜎) + 𝜎. The functions 𝑝, 𝑛ଵ, 𝑛ଶ, 𝑛ଷ depending on 𝑥ଵ, 𝑥ଶ, 𝑥ଷ are determined from the quasilinear system of first-order equations obtained from (1), (6), and the finite relation 𝑛ଵ ଶ+ 𝑛ଶ ଶ+ 𝑛ଷ ଶ= 1: 𝑝,௜+ 𝑛௝𝑛௜, ௝+ 𝑘𝑛௜𝑛௦, 𝑠= 0, 𝑖, 𝑗, 𝑠= 1,2,3; 𝑘= (ଷఌାଶ௠) (ଷఌିସ௠). (7 (7) The particle velocity vector for a known stress tensor is determined from the conditions of incompressibility (4) and isotropy (5). p y ( ) py ( ) At 𝑚= 0, the parameter 𝑘= 1 and system (7) formally coincide with the system of equations of D. D. Ivlev [4] of the Tresca theory of plasticity under the condition of complete plasticity. In this case, the substitution that satisfies condition (2) and relation (3) for 𝑚= 0 differs from substitution (6). ~ 7 ~ ISSUE № 3-1(27) March 2023 Analysis of the structure of solutions to system (7) for 𝑘= 1 applies to the system (7) and for 𝑘≠1. If for 𝑘= 1 the normals to the characteristic surfaces form a cone with the half-angle 𝜑= 𝜋/4 and the axis oriented along the unit eigenvector 𝐧= (𝑛ଵ, 𝑛ଶ, 𝑛ଷ) of the stress tensor, then for 𝑘≠1 the half-angle 𝜑= arctg (1/√𝑘). The system for determining the velocity vector has a characteristic cone with a half-angle 𝜑= 𝜋/4. Submodels for system (7) with 𝑘≠1 are considered in [5]. System (4), (5), and (7) is hyperbolic. For this system, the problem of the propagation of plastic state zones in an unbounded medium from the boundary of a convex cavity, which is subjected to normal pressure, shear forces, and given displacement velocities, is considered. In [6, 7, 8], for systems (4), (5), (7) with 𝑚= 0, a numerical method was proposed for solving the Cauchy problem in an orthogonal curvilinear coordinate system (𝛼, 𝜃, 𝛾) formed by rotation around the vertical 𝑧 axis of a smooth convex curve 𝐿 with support function 𝐹(𝛾) (Fig. 2), where the coordinate surfaces 𝛼= const are equidistant. Taking into account (6), this method can be applied to the solution of the Cauchy problem for systems (4), (5), and (7) with 𝑚≠0. ИННОВАЦИОННЫЕ НАУЧНЫЕ ИССЛЕДОВАНИЯ ВЫПУСК №3-1(27) Март 2023 As an example, the problem of the propagation of zones of the plastic state from the boundary of an ellipsoidal cavity formed by rotation around the 𝑧 axis of a convex curve 𝐿 with the support function 𝐹(𝛾) = ඥ𝑎ଶsinଶ 𝛾+ 𝑏ଶcosଶ 𝛾, where 𝑎, 𝑏 are the semiaxes of the ellipse, were solved. The problem was solved in dimensionless variables. For 𝑚= 0, the stresses have the form: 𝜎ఈఈ= 𝑝+ 𝑛ఈଶ, 𝜎ఈఏ= 𝑛ఈ𝑛ఏ, 𝜎ఈఊ= 𝑛ఈ𝑛ఊ, 𝜎ఏఏ= 𝑝+ 𝑛ఏ ଶ, 𝜎ఊఊ= 𝑝+ 𝑛ఊଶ, 𝜎ఏఊ= 𝑛ఏ𝑛ఊ, 𝜎ఏఏ= 𝑝+ 𝑛ఏ ଶ, 𝜎ఊఊ= 𝑝+ 𝑛ఊଶ, 𝜎ఏఊ= 𝑛ఏ𝑛ఊ, where 𝜎ఈఈ, 𝜎ఈఏ, 𝜎ఈఊ, 𝜎ఏఏ, 𝜎ఊఊ, 𝜎ఏఊ are the stress components in the coordinate system (𝛼, 𝜃, 𝛾) divided by 2𝑘௦𝜀; 𝑝= 𝜎/(2𝑘௦𝜀) − 1/3; 𝑛ఈ, 𝑛ఏ, 𝑛ఊ are the components of the unit eigenvector corresponding to the principal stress 𝜎ଵ. At 𝑚≠0, the stresses were calculated by the formula (6), in which 𝑛ଵ= 𝑛ఈ, 𝑛ଶ= 𝑛ఏ, 𝑛ଷ= 𝑛ఊ should be put. where 𝜎ఈఈ, 𝜎ఈఏ, 𝜎ఈఊ, 𝜎ఏఏ, 𝜎ఊఊ, 𝜎ఏఊ are the stress components in the coordinate system (𝛼, 𝜃, 𝛾) divided by 2𝑘௦𝜀; 𝑝= 𝜎/(2𝑘௦𝜀) − 1/3; 𝑛ఈ, 𝑛ఏ, 𝑛ఊ are the components of the unit eigenvector corresponding to the principal stress 𝜎ଵ. At 𝑚≠0, the stresses were calculated by the formula (6), in which 𝑛ଵ= 𝑛ఈ, 𝑛ଶ= 𝑛ఏ, 𝑛ଷ= 𝑛ఊ should be put. ఊ In the numerical solution, the semiaxis of the ellipsoid is 𝑎= 2, and the semiaxis 𝑏= 1. At 𝑚= 0, the following initial conditions were set on the surface of the cavity (𝛼= 0): 𝑝(0) = 1, 𝑛ఈ(0) = 1, 𝑛ఏ(0) = 𝑛ఊ(0) = 0. To compare the solutions obtained at 𝑚= 0 and 𝑚≠0, the initial values for 𝜉(0) in formulas (6) were chosen so that the normal stresses 𝜎ఈఈ at 𝛼= 0 coincided. Figure 3 shows the dependences of the stresses 𝜎ఈఈ on the coordinate 𝛼 for the angles 𝛾= 0 and = 𝜋/2 at 𝑚= 0 and 𝑚= 0,5. ЧИСЛЕННОЕ РЕШЕНИЕ ЗАДАЧИ КОШИ ДЛЯ УРАВНЕНИЙ ИДЕАЛЬНОЙ ПЛАСТИЧНОСТИ С УСЛОВИЕМ ТЕКУЧЕСТИ В ЗАВИСИМОСТИ ОТ СРЕДНЕГО НАПРЯЖЕНИЯ. ISSN 2713-0010 SCIENTIFIC NETWORK PUBLICATION ~ 8 ~ Figure 2 – Orthogonal curvilinear coordinate system (𝛼, 𝜃, 𝛾): coordinate surface 𝑆(𝛼= 0), basis vectors 𝑘ఈ, 𝑘ఏ, 𝑘ఊ and generatrix 𝐿 of the coordinate surface 𝑆 Figure 2 – Orthogonal curvilinear coordinate system (𝛼, 𝜃, 𝛾): coordinate surface 𝑆(𝛼= 0), basis vectors 𝑘ఈ, 𝑘ఏ, 𝑘ఊ and generatrix 𝐿 of the coordinate surface 𝑆 ISSN 2713-0010 ~ 8 ~ ИННОВАЦИОННЫЕ НАУЧНЫЕ ИССЛЕДОВАНИЯ ВЫПУСК №3-1(27) Март 2023 ISSN 2713-0010 НАУЧНОЕ СЕТЕВОЕ ИЗДАНИЕ Figure 3 – Distribution of stresses 𝜎ఈఈ near an elliptical cavity for angles 𝛾= 0 and 𝛾= 𝜋/2 depending on the coordinate 𝛼: dotted lines – m = 0, solid lines – m = 0.5 Figure 3 – Distribution of stresses 𝜎ఈఈ near an elliptical cavity for angles 𝛾= 0 and 𝛾= 𝜋/2 depending on the coordinate 𝛼: dotted lines – m = 0, solid lines – m = 0.5 Figure 3 – Distribution of stresses 𝜎ఈఈ near an elliptical cavity for angles 𝛾= 0 and 𝛾= 𝜋/2 depending on the coordinate 𝛼: dotted lines – m = 0, solid lines – m = 0.5 Figure 3 – Distribution of stresses 𝜎ఈఈ near an elliptical cavity for angles 𝛾= 0 and 𝛾= 𝜋/2 depending on the coordinate 𝛼: dotted lines – m = 0, solid lines – m = 0.5 ~ 9 ~ INNOVATIVE SCIENTIFIC RESEARCH ISSUE № 3-1(27) March 202 Figure 4 – Distribution of stresses 𝜎ఈఈ, 𝜎ఊఊ and 𝜎ఏఏ near the elliptical cavity for the angle 𝛾= గ ସ depending on the coordinate 𝛼: dotted lines – 𝑚= 0, solid lines – 𝑚= 0,5 INNOVATIVE SCIENTIFIC RESEARCH ISSUE № 3-1(27) M Figure 4 – Distribution of stresses 𝜎ఈఈ, 𝜎ఊఊ and 𝜎ఏఏ near the elliptical cavity for the angle 𝛾= గ ସ depending on the coordinate 𝛼: dotted lines – 𝑚= 0, solid lines – 𝑚= 0,5 Figure 4 – Distribution of stresses 𝜎ఈఈ, 𝜎ఊఊ and 𝜎ఏఏ near the elliptical cavity for the angle 𝛾= గ ସ depending on the coordinate 𝛼: dotted lines – 𝑚= 0, solid lines – 𝑚= 0,5 Figure 4 shows the dependences of the stresses 𝜎ఈఈ, 𝜎ఏఏ, and 𝜎ఊఊ on 𝛼 for 𝛾= 𝜋/4 at 𝑚= 0 and 𝑚= 0,5. Figure 4 shows the dependences of the stresses 𝜎ఈఈ, 𝜎ఏఏ, and 𝜎ఊఊ on 𝛼 for 𝛾= 𝜋/4 at 𝑚= 0 and 𝑚= 0,5. Thus, under the linear dependence of the yield condition on the average stress for the case of complete plasticity, the Cauchy problem of the propagation of zones of the plastic state in an unbounded medium from the boundary of a convex surface on which normal pressure acts is numerically solved. ISSN 2713-0010 Bibliography Effect of hydrostatic pressure on the mechanical properties of polymeric materials / S.B. Ainbinder, M.G. Laka, I.Yu. Majors // Polymer Mechanics. – 1965. No. 1. 65-75 p. [8] Pisarenko G.S. Deformation and strength of materials under complex stress state / G.S. Pisarenko, A. A. Lebedev. – Kyiv, 1976. 416 p. [8] Pisarenko G.S. Deformation and strength of materials under complex stress state / G.S. Pisarenko, A. A. Lebedev. – Kyiv, 1976. 416 p. Bibliography [1] Lode V. Influence of the average principal stress on the fluidity of metals / V. 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Физико-механические свойства песка под давлением / Л.С. Казаченко, Ю. Кулинич В. // ФЦППИ. – 1972. № 1. 22-30 с. [3] Хаар А. К теории напряженных состояний в пластичных и рыхлых средах / А. Хаар, Т. Карман // Теория пластичности: Сб. Искусство. / изд. Ю. Н. Работнова. – М.: Гос. иностранное издательство лит., 1948. 41-56 с. [3] Хаар А. К теории напряженных состояний в пластичных и рыхлых средах / А. Хаар, Т. Карман // Теория пластичности: Сб. Искусство. / изд. Ю. Н. Работнова. – М.: Гос. иностранное издательство лит., 1948. 41-56 с. [4] Ишлинский А.Ю. Математическая теория пластичности / А.Ю. Ишлинский, Д.Д. Ивлев. – М.: Физматлит, 2001. 704 с. [4] Ишлинский А.Ю. Математическая теория пластичности / А.Ю. Ишлинский, Д.Д. Ивлев. – М.: Физматлит, 2001. 704 с. [5] Аннин Б.Д. Об уравнениях идеальной пластичности с условием текучести в зависимости от среднего напряжения / Б.Д. Аннин // Успехи механики сплошных сред: к 70-летию со дня рождения акад. В. А. 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Влияние гидростатического давления на механические свойства полимерных материалов / С.Б. Айнбиндер, М.Г. Лака, И.Ю. Направления // Механика полимеров. – 1965. № 1. 65- 75 с. [8] Писаренко Г. С. Деформация и прочность материалов при сложном напряженном состоянии / Г. С. Писаренко, А. А. Лебедев. – Киев, 1976. 416 с. [8] Писаренко Г. С. Деформация и прочность материалов при сложном напряженном состоянии / Г. С. Писаренко, А. А. Лебедев. – Киев, 1976. 416 с. © Nguyen Minh Hue, Pham Thi Thuy, 2023 Поступила в редакцию 02.03.2023 Принята к публикации 16.03.2023 © Nguyen Minh Hue, Pham Thi Thuy, 2023 Поступила в редакцию 02.03.2023 Принята к публикации 16.03.2023 Для цитирования: Nguyen Minh Hue, Pham Thi Thuy Numerical solution of the cauchy problem for ideal plasticity equations with yield condition depending on the average stress // Инновационные научные исследования. 2023. № 3- 1(27). C. 5-12. URL: https://ip-journal.ru/ ISSN 2713-0010 ~ 12 ~
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https://www.medrxiv.org/content/medrxiv/early/2021/09/16/2021.09.13.21263407.full.pdf
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Episodic future thinking and compassion reduce public health guideline noncompliance urges: A randomised controlled trial
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is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a 1 reprint reports new research that has not been certified by peer review and should not be used to guide clinical practice Background During the COVID-19 pandemic, public health departments have issued guidelines to limit viral transmission. In this environment, people will feel urges to engage in activities that violate these guidelines, but research on guideline adherence has been reliant on surveys asking people to self- report their typical behaviour, which may fail to capture these urges as they unfold. Guideline adherence could be improved through behaviour change interventions, but considering the wide range of behaviours that COVID-19 guidelines prescribe, there are few methods that allow observing changes of aggregate guideline adherence in the ‘wild’. Episodic future thinking and compassion reduce public health guideline noncompliance urges: A randomised controlled trial is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a Methods In order to administer interventions and to obtain contemporaneous data on a wide range of behaviours, we use ecological momentary assessment. In this preregistered parallel randomised trial, 95 participants aged 18-65 from the UK were assigned to three conditions using blinded block randomisation, and engage in episodic future thinking (n = 33), compassion exercises (n = 31), or a sham procedure (n = 31) and report regularly on the intensity of their occurrent urges (min. 1, max. 10) and their ability to control them. We investigate whether state impulsivity and vaccine attitudes predict guideline adherence, while assessing through which mechanism these predictors affect behaviour. Findings We found that episodic future thinking (b = -1.60) and compassion exercises (b = -1.40) reduce the intensity of urges. State impulsivity is associated with stronger urges, but we found no evidence that vaccine hesitancy predicts lesser self-control. Introduction Enhancing adherence to national COVID-19 health guidelines is essential for saving lives and preventing serious illness. However, studying predictors and methods for improving COVID-19 guideline adherence is challenging because this behaviour is not readily observed in laboratory settings, nor easy to reveal with self-report cross sectional surveys. The focus of this study is, using ecological momentary assessment rather than one-shot surveys, to find whether episodic future thinking and compassion exercises could contribute to increasing adherence to public health guidelines for preventing Covid-19 spread. We also investigate whether state impulsivity and vaccine attitudes predict guideline adherence, while assessing through which mechanism these predictors affect behaviour. A wealth of research has focused on best-practice for public health communication in order to achieve optimal guideline adherence of the public (1). Adhering to guidelines such as staying home during a lockdown can have immediate personal adverse impact on one’s financial situation (2), mental health (3-5), and physical health (6, 7). In contrast, the effects of non-adherence are often less immediate: when an individual contracts COVID-19 it may take time before symptoms and accompanying negative consequences are experienced; and those consequences may often affect others, such as infecting loved ones, or causing outbreaks in the community. Decisions on guideline adherence therefore constitute a dilemma between choosing the long-term greater good, over the short-term individual gain. Here, we therefore test if increasing people’s future-orientedness, and willingness to make decisions for others’ benefit has potential for increasing adherence. Episodic future thinking (EFT) refers to imagining or simulating experiences that might occur in one's personal future, and is known to decrease delay discounting (8, 9). The effects of EFT on delay discounting imply that the valuation of immediate rewards is diminished relative to future rewards. This means that EFT likely affects the intensity of urges, but the effects of EFT in various domains suggest that EFT might also impact self-control (10, 11). Accordingly, this study investigates whether engaging in EFT exercises can change the intensity of urges and self-control. Adherence to guidelines is ultimately also prosocial, and prosocial behaviour can be enhanced by stimulating compassion, the feeling that arises in witnessing another’s suffering and that motivates a subsequent desire to help (12). Compassion training has a valuation element in addition to a behavioural element, which means compassion training could affect both the intensity of urges and self-control (13, 14); which this study will investigate. Interpretation We conclude that episodic future thinking exercises and compassion training may be used to stimulate compliance of individuals who are a risk for the community, such as those in voluntary self-isolation. Keywords: impulsivity, episodic future thinking, compassion, inhibition, pandemic 2 2 is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a Introduction Vaccine hesitancy, attitudes on the effectiveness of these vaccines, and predictions about how soon the pandemic will end could factor into people’s behaviour. These attitudes are usually linked to other attitudes and behaviours relevant to pandemic behaviour such as lesser social distancing and mask wearing (15, 16). We therefore also test how such predictors of guideline adherence influence moment-to-moment behaviour. Impulsivity, the tendency to make rapid responses for short-term gratification and with insufficient regard for negative consequences (17), is negatively correlated to public health guidelines adherence (18, 19). The excessive future discounting characteristic of impulsivity can be influenced by fluctuations in internal states (20). To understand how impulsivity affects moment-to-moment behaviour, it is important to attain information on people’s mental state when behaviours occur (21, 22). Thus, we study these behaviours in an ecologically valid manner, where proximal information on state impulsivity is obtained. This study seeks to avoid the distortions that often afflict self-report measures about typical behaviour (23). In order to gain insights into moment-to-moment preventative behaviour in the ‘wild’ and real- time changes following behaviour change interventions, we employ an ecological momentary 3 3 . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. eer review) The copyright holder for this this version posted September 16, 2021. ; 0.1101/2021.09.13.21263407 . CC-BY 4.0 International license It is made available under a assessment (EMA; or experience sampling) paradigm. Participants are asked on multiple occasions each day about their urges pertaining to non-adherence of COVID-19 guidelines, and whether they were able to control them. assessment (EMA; or experience sampling) paradigm. Participants are asked on multiple occasions each day about their urges pertaining to non-adherence of COVID-19 guidelines, and whether they were able to control them. Introduction In this experiment, the main variables of interest are the perceived intensity of urges, and the probability of controlling urges, operationalised as self-control. In our preregistered analyses we predicted that both the compassion intervention and the episodic future thinking intervention would increase the likelihood of controlling urges, where we analyse their effect on self-control and on the intensity of urges. Furthermore, we predicted that state impulsivity is associated with stronger urges and fewer attempts to resist urges, and that vaccine hesitancy and shorter predicted back-to-normal time frames are negatively correlated with the likelihood of controlling an urge through diminishing self-control. In brief, we find that Compassion and EFT interventions reduce the intensity of urges, but we find no evidence that self-control is affected. State impulsivity is significantly related to the intensity of urges. Randomisation and Masking Randomisation and Masking Participants were randomly assigned a condition according to block randomisation (8 strata, 3 treatments, sequence obtained from sealedenvelope.com), see Figure A1 for the distribution of age and sex per condition. Participants were unaware of their condition assignment, and were either assigned to the EFT condition, the compassion condition, or the control condition. Participants The final sample contained 95 participants residing in the UK obtained through volunteer sampling using the Prolific participant recruitment platform. Participants were required to be between 18-65 years of age, and within that age group we created a representative sample, based on sex and age (2x4). Further details on the sample in Appendix A. In the final sample, there were 40 (42.1%) males, with a mean age of 41.4 (SD = 14.1), and 55 females (57.9%) with a mean age of 41.0 (SD = 12.5). 40 (42.1%) participants reported they had received a COVID-19 vaccine, and 5 reported that they had been diagnosed with COVID-19 at some point, with one participant reporting they had experienced both of these events. Even though the individual risk of COVID-19 is mitigated for vaccinated individuals and those who previously contracted COVID-19, they were still required to comply with public health guidelines. Therefore, vaccinated individuals were not excluded. To determine sample size, we estimated an effect size of a 5-percentage point increase in the probability to control an urge in the EFT and Compassion treatments, and assumed that participants would indicate they had an urge 3 times a day. We identified that 95% power could be achieved by collecting data from 90 participants. Code is available here. Procedure Participants were asked whether they, or one of their family members, were part of a group that is vulnerable to COVID-19. Participants also answered questions on their willingness to take a COVID- 19 vaccine and their beliefs about vaccine efficacy. We also elicited predictions of when people would be able to resume on-site work (insofar as that will ultimately be the case), when people would be able to go on holiday, and when life would go back to ‘normal’. These predictions and vaccination attitudes were then combined into three scores, varying from 0 to 10. 4 . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) print The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. eer review) The copyright holder for this this version posted September 16, 2021. ; 0.1101/2021.09.13.21263407 . CC-BY 4.0 International license It is made available under a Each morning at 7.30am (expiry time 10am), participants would be asked to do either an EFT exercise, a compassion (i.e., mentalising + affect-matching) exercise, or reflect on a recent news story related to COVID-19 (respectively). All prompts are included in Table A1. After each condition- dependent prompt, participants would be prompted with “Remember that your behaviour has an effect on the COVID-19 situation”. Videos of the user interface can be accessed here. Throughout each day, participants would receive 5 surveys that were available for 1 hour. Procedure In randomised order, they were asked whether since the last survey they had felt an urge to not wash their hands, not cover their mouths when coughing or sneezing, not socially distance (e.g. to hug, shake hands), not leave details for contact tracing, or whether they had felt an urge to leave their house, touch their face, or avoid getting tested when it would have been better to do the opposite - from a COVID-19 standpoint. Participants responded using a slider [0,10], where 0 indicated no urge, 1 indicated a very weak urge, and 10 indicated a very strong urge. We then administered the Momentary Impulsivity Scale (24). The experiment took place from 29 March to 4 April 2021. The UK was in a state of lockdown at that point in time, but most regions in the UK were in the early phase of reopening. Notably, the UK government announced on 29 March that 6 people from 6 different households would be allowed to meet outside. This, together with Easter weekend, produced a situation wherein people were likely to have non-adherence urges. See Figure 1 for a visualisation of urge intensities per day during the experiment. Figure 1. The perceived urge intensity (y-axis), partitioned by day (x-axis). The experiment was partially conducted over a public holiday, at which time stronger urges of non-adherence would be expected. 2 April (third line from the right) was Good Friday, and 4 April (the right-most line) was Easter Sunday. The coloured points represent the estimated marginal means, and the error bars are 95% CIs. The grey data points each represent the aggregated data of one participant. Figure 1. The perceived urge intensity (y-axis), partitioned by day (x-axis). The experiment was partially conducted over a public holiday, at which time stronger urges of non-adherence would be expected. 2 April (third line from the right) was Good Friday, and 4 April (the right-most line) was Easter Sunday. The coloured points represent the estimated marginal means, and the error bars are 95% CIs. The grey data points each represent the aggregated data of one participant. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a Analysis Our analyses were preregistered, and can be accessed here, data and code can be found here. The effects of impulsivity on the strength of an urge was analysed using a Linear Mixed Model (LMM), with predictors: condition, the type of urge (and interaction between those), state impulsivity, with the time of day and the day as control variables, and the participant as the random intercept. The type of urge was not included as a predictor in the main preregistered model, but it was specified in the exploratory analyses section and because the effects of the intervention might differ across domains, we decided to include it in the main analyses. The analysis, conducted with the afex package (25) used F-tests of fixed effects terms with Kenward-Roger approximation of degrees of freedom to calculate p-values. We used a binomial generalised mixed model (GLMM) to conduct the self-control analysis. In addition to the variables in the model above, vaccine hesitancy, vaccine effectiveness beliefs, back-to- normal timeline predictions, and whether participants attempted to resist the urge were included. In order to calculate p-values, likelihood ratio tests were used. In both analyses, we decided to deviate from the preregistration by including interaction terms with the intervention because we deemed it likely that the intervention might affect some urges more than others. The standard p<.05 criterion was used for determining whether the effects based on the Linear Mixed Model (LMM), or on the Generalised Linear Mixed Model (GLMM) were significantly different from those expected if the null hypothesis were correct. Reported effect sizes are model coefficients for numerical variables, and post-hoc tests were conducted for factors with the emmeans package, which calculates estimated marginal means of the outcome variable for factor levels. We corrected for multiple comparisons using false discovery rate adjusted p-values in our post-hoc tests. Predictors for Urge Intensity Predictors for Urge Intensity Predictors for Urge Intensity Main Variables of Interest Results Different types of urges occurred at different rates, which matters for interpreting the results. Over the one-week-long experiment, 83 out of the 95 participants reported the urge to leave the house at least once, and did so 6.80 times on average (SD = 6.09), 79 reported the urge to touch their face (M = 7.91, SD = 8.14), while 60 reported the urge to not wash their hands (M = 5.03, SD = 6.11). Only 21 participants reported the urge to not leave their contact details (M = 3.86, SD = 7.18), and 17 participants reported the urge to avoid getting tested (M = 4.82, SD = 7.77). 73 Participants reported the urge to disregard social distancing guidelines (M = 4.66, SD = 4.37), and 33 participants reported the urge to not cover their mouth (M = 2.82, SD = 4.39). There was high variance in the number of urges people experienced, and the average number of urges experienced was similar over the different conditions: in the EFT condition, people had 20.0 urges on average (SD = 30.2) in the Compassion condition, people had 23.1 urges on average (SD = 16.3) and in the Control condition 23.1 (SD = 26.7). Main Variables of Interest In accordance with our predictions, the condition factor (EFT, Compassion, Control) had a significant effect on how strong they perceived urges to be, F(2, 110) = 7.59, p < .001. Post-hoc tests show that participants experienced weaker urges in the EFT condition (estimated marginal mean (EMM) = 3.11, 95% CI [2.33, 3.89], t(111) = -3.571, p < .01), and in the Compassion condition (EMM = 3.30, 95% CI [2.51, 4.09], t(105) = -3.113, p < .01), than in the Control condition (EMM = 4.71, 95% CI [3.94, 6 . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a 5.48]). Urge intensity was not significantly different in the EFT condition from the Compassion condition (t(113) = .192, p = .67). See Figure 2. 5.48]). Urge intensity was not significantly different in the EFT condition from the Compassion condition (t(113) = .192, p = .67). See Figure 2. Figure 2. The effects of the between-participants conditions: Episodic Future Thinking (EFT; left, in purple) manipulation, the Compassion manipulation (middle, in blue), as compared to the Control condition (right, in green), on the perceived intensity of urges (y-axis [1,10]). The points are estimated marginal means, and the error bars are 95% CIs. The grey dots each represent the aggregated data of a participant in one of the conditions. Figure 2. The effects of the between-participants conditions: Episodic Future Thinking (EFT; left, in purple) manipulation, the Compassion manipulation (middle, in blue), as compared to the Control condition (right, in green), on the perceived intensity of urges (y-axis [1,10]). The points are estimated marginal means, and the error bars are 95% CIs. The grey dots each represent the aggregated data of a participant in one of the conditions. The type of urge had a significant effect on the perceived strength of urges, F(6, 2000) = 27.60, p < .001. Main Variables of Interest CC-BY 4.0 International license It is made available under a State impulsivity had a significant effect on the perceived strength of urges, b = .429, 95% CI [0.262, .597], F(1, 2030) = 25.25, p < .001. See Figure 3 for a depiction of the relationship between state impulsivity and the intensity of urges. Figure 3. The relationship between state impulsivity as measured by the MIS (x-axis) and the intensity of urges [1,10] (y-axis). The black lines at the bottom represent participants’ MIS scores per filled out survey, and the blue band shows the 95% CI. Figure 3. The relationship between state impulsivity as measured by the MIS (x-axis) and the intensity of urges [1,10] (y-axis). The black lines at the bottom represent participants’ MIS scores per filled out survey, and the blue band shows the 95% CI. Figure 3. The relationship between state impulsivity as measured by the MIS (x-axis) and the intensity of urges [1,10] (y-axis). The black lines at the bottom represent participants’ MIS scores per filled out survey, and the blue band shows the 95% CI. Main Variables of Interest People reported the strongest urges for leaving the house (EMM = 4.80, 95% CI [4.42, 5.18]), joint second strongest were urges to avoid getting tested (EMM = 3.94, 95% CI [3.34, 4.54]) and urges to not socially distance (EMM = 3.94, 95% CI [3.54, 4.35]), fourth were urges to not leave details for contact tracing (EMM = 3.78, 95% CI [3.15, 4.40]), fifth were urges to touch one’s face (EMM = 3.62, 95% CI [3.24, 4.00]), sixth were urges to avoid washing hands (EMM = 3.12, 95% CI [2.70, 3.55]), and the weakest urges pertained to covering mouth and nose when coughing/sneezing (EMM = 2.74, 95% CI [2.19, 3.30]). The effect of the condition factor on urge intensity also significantly interacted with the type of urge F(10, 1999) = 14.36, p < .001. Post-hoc tests revealed that urges to avoid leaving details for contact tracing were weaker in the EFT condition (EMM = 1.85, 95% CI [.44, 3.26]; t(678) = 7.025, p < .001), and in the Compassion condition (EMM = 2.47, 95% CI [1.00, 3.87]; t(644), = 6.161, p < .001), than in the Control condition (EMM = 7.04, 95% CI [5.96, 8.12]), but were not significantly different from each other, t(926) = .695, p = .49. Further, urges to avoid getting tested were also weaker in the EFT condition (EMM = 1.77, 95% CI [.48, 3.06]; t(635) = 7.768, p < .001), and in the Compassion condition (EMM = 2.68, 95% CI [1.33, 4.02]; t(618) = 7.768, p < .001), than in the Control condition (EMM = 7.38, 95% CI [6.21, 8.55]), but were not different from each other, t(744) = 1.170, p = .24. 7 . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) reprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . Predictors for Self-Control Predictors for Self-Control The condition factor did not have a significant effect on self-control, χ2(2) = 4.56, p = .10. The type of urge had a significant effect on self-control, χ2(6) = 219.89, p < .001. The estimated marginal means show that people were most likely to control an urge to not cover their mouths (EMM (Probability) = .690, 95% CI [.498, .833]; they were second most likely to control to not wash their hands (EMM = .637, 95% CI [.519, .741]); third were urges to not socially distance (EMM = .517, 95% CI [.407, .625]); fourth were urges to leave the house (EMM = .405, 95% CI [.318, .498]); fifth were urges to touch one’s face (EMM = .154, 95% CI [.109, .213]), sixth were urges to not leave contact details for contact tracing purposes (EMM = .086, 95% CI [.036, .193]); the most difficult urges to control were those that pertain to not get tested (EMM = .009, 95% CI [.003, .031]). It is important to note that these probabilities must be judged together with the relative frequencies of each urge. For instance, the probability of controlling an urge that pertains to avoiding getting tested is extremely low, but only 21 participants ever got one of these urges, for a total of 82 urges. See Figure 4 for a depiction of the probability to control various urges. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to (which was not certified by peer review) preprint this version posted September 16, 202 ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. eer review) The copyright holder for this this version posted September 16, 2021. ; 0.1101/2021.09.13.21263407 . CC-BY 4.0 International license It is made available under a Figure 4. The estimated marginal means for controlling various urges. Predictors for Self-Control Each point represents the probability of controlling an urge pertaining to a certain type of behaviour, from left to right: the probability of controlling an urge to not cover one’s mouth and nose when coughing or sneezing, to not wash hands, to not socially distance, to not stay home, to avoid providing contact details when entering an establishment, and to avoid getting tested. The error bars are 95% confidence intervals. The condition participants were assigned to significantly interacted with the type of urge in predicting Figure 4. The estimated marginal means for controlling various urges. Each point represents the probability of controlling an urge pertaining to a certain type of behaviour, from left to right: the probability of controlling an urge to not cover one’s mouth and nose when coughing or sneezing, to not wash hands, to not socially distance, to not stay home, to avoid providing contact details when entering an establishment, and to avoid getting tested. The error bars are 95% confidence intervals. The condition participants were assigned to significantly interacted with the type of urge in predicting self-control, χ2(12) = 29.45, p < .01. State impulsivity did not have a significant effect on self-control, b = .054, 95% CI [-.224, .332], χ2(1) = .16, p = .69. Furthermore, state impulsivity did not have a significant effect on the probability of attempting to resist an urge b = -.108, 95% CI. Vaccine hesitancy did not have a significant effect on self-control, b = -.103, 95% CI [-.270, .063], χ2(1) = 1.37, p < .24. Judgements about vaccine hesitancy did not have a significant effect on self- control (b = .038, 95% CI [-.177, .253]; χ2(1) = .09, p = .77), and neither did predictions about when life would go back to ‘normal’ after the pandemic (b = -.141, 95% CI [-.786, .505]; χ2(1) = .20, p = .66). Discussion These mechanisms both likely promote the salience of the potential negative consequences to people’s actions, which may be the reason for their effectiveness in this context. Alternative explanations include that compassion exercises can lead to increased positive affect and motivation (26), and can be helpful to deal with daily stressors (27), which may also decrease the perceived intensity of urges. We found no evidence that vaccine attitudes or predictions of back-to-normal timelines were associated with self-control. Other studies show that vaccine hesitancy is correlated with lesser social distancing and mask wearing (16), but most studies reporting these relationships rely on judgements about typical behaviour, or intentions to comply with guidelines. The lack of a significant relationship between vaccine attitudes and guideline adherence in this study suggests that more research is needed to understand how these attitudes affect moment-to-moment behaviour. We find that different urges occur at varying rates within and between participants, which is an important consideration when assessing the relative impact of these urges. If an urge is relatively rare, but difficult to control, then it may not be as relevant for policymakers and other key stakeholders to see if the motivation to control this urge can be increased. Urges to avoid getting tested, or to not leave contact details were relatively infrequent, but the fact that around 20% of the sample reported one of these urges at least once is worrying given their importance to pandemic management (28). State impulsivity was related to stronger urges, but not to diminished self-control. This evidence suggests that state fluctuations in impulsivity play an important, but poorly understood role in determining public health guideline adherence during pandemics. A recent study has found this ‘bottom-up’ effect of state impulsivity for a different, more general domain of urges (29). It also suggests that interventions targeting the internal state of the individual, and impulsivity in particular, might be effective at ameliorating their guideline adherence. Future research could investigate whether state impulsivity, as well as other internal states, can be targeted to improve public health guideline adherence. The main limitations of this study were that the heterogeneity of the experience of certain types of urges rendered the sample size too small to draw accurate inferences in some domains. Discussion Our findings show that episodic future thinking and compassion exercises reduced the intensity of certain urges, but did not affect self-control. This finding broadly aligns with the evidence that EFT can enhance future-oriented decision making in various contexts (10, 11). Given that urges usually pertain to immediate rewards, this reduction in the strength of urges after an EFT exercise is most likely because EFT reduces the relative value of immediate rewards compared to future rewards (8, 9). This finding suggests that an invitation to engage in EFT and compassion-inducing talking points could be incorporated into press conferences and some public announcements to decrease urges of . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) rint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. eer review) The copyright holder for this this version posted September 16, 2021. ; 0.1101/2021.09.13.21263407 . CC-BY 4.0 International license It is made available under a noncompliance during public health crises. People who pose a specific risk to the community (e.g., those in voluntary self-isolation after travelling abroad) could be invited to periodically perform such a task. noncompliance during public health crises. People who pose a specific risk to the community (e.g., those in voluntary self-isolation after travelling abroad) could be invited to periodically perform such a task. The mechanisms through which EFT and compassion exercises affect behaviour differ: EFT is known to enhance future-oriented decision making by decreasing delay discounting (8), whereas compassion exercises can increase altruism (12). Discussion Only around 20 individuals reported having urges to avoid to getting tested or to avoid leaving details for contact tracing at least once, and these 20 individuals were spread over the 3 conditions. This speaks to the strengths and weaknesses of our ecological momentary assessment paradigm because, on the one hand, it is a powerful paradigm for events that occur often and to a wide range of people (such as the urge to abandon social distancing), and it can provide insight into behaviour ‘in the wild’. On the other hand, for events that only happen for a narrow subset of people, or that happen infrequently, ecological momentary assessment needs to be applied to that particular subset, or another approach should be considered. The other limitation is that it is unclear to what extent the findings apply to different populations. Future research could focus on the role of behavioural science interventions, including, but not limited to, episodic future thinking and compassion-inducing exercises, in producing desired behaviour during public health crises. We also deem it important that more research is devoted to uncovering the factors predicting moment-to-moment decision making in people’s daily lives, where ecological momentary assessment and GPS data (30) could play a critical role. These methods can provide a more comprehensive understanding of the effects of behavioural interventions, shedding light on their 10 . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. eer review) The copyright holder for this this version posted September 16, 2021. ; 0.1101/2021.09.13.21263407 . CC-BY 4.0 International license It is made available under a . CC-BY 4.0 International license It is made available under a longevity and externalities. For proper understanding of behavioural drivers during the pandemic, there needs to be more emphasis on the proximal predictors to guideline compliance. Funding This research is supported by a Monash-Warwick Alliance Accelerator grant and by Martin and Loreto Hosking’s Three Springs Foundation. The funding sources had no involvement in the research conducted. Authors declare no competing interests. Authors declare no competing interests. Discussion longevity and externalities. For proper understanding of behavioural drivers during the pandemic, there needs to be more emphasis on the proximal predictors to guideline compliance. Acknowledgements References 1. Bavel JJV, Baicker K, Boggio PS, Capraro V, Cichocka A, Cikara M, et al. Using social and behavioural science to support COVID-19 pandemic response. Nature Human Behaviour. 2020;4(5):460 pp p p 2. Employment Situation Summary [press release]. U.S. Bureau of Labor Statistics, May 7 2021. p y y [p ] , y 3. Barari S, Caria S, Davola A, Falco P, Fetzer T, Fiorin S, et al. Evaluating COVID-19 public health messaging in Italy: Self-reported compliance and growing mental health concerns. MedRxiv. 2020. 4. Niedzwiedz CL, Green MJ, Benzeval M, Campbell D, Craig P, Demou E, et al. Mental health and health behaviours before and during the initial phase of the COVID-19 lockdown: longitudinal analyses of the UK Household Longitudinal Study. J Epidemiol Community Health. 2021;75(3):224-31. 4. Niedzwiedz CL, Green MJ, Benzeval M, Campbell D, Craig P, Demou E, et al. Mental health and health behaviours before and during the initial phase of the COVID-19 lockdown: longitudinal analyses of the UK Household Longitudinal Study. J Epidemiol Community Health. 2021;75(3):224-31. g y p y 5. Pieh C, Budimir S, Delgadillo J, Barkham M, Fontaine JR, Probst T. Mental health during COVID-19 lockdown in the United Kingdom. Psychosomatic medicine. 2021;83(4):328-37. g y p y 5. Pieh C, Budimir S, Delgadillo J, Barkham M, Fontaine JR, Probst T. Mental health during COVID-19 lockdown in the United Kingdom. Psychosomatic medicine. 2021;83(4):328-37. 6. Constandt B, Thibaut E, De Bosscher V, Scheerder J, Ricour M, Willem A. Exercising in times of lockdown: an analysis of the impact of COVID-19 on levels and patterns of exercise among adults in Belgium. International journal of environmental research and public health. 2020;17(11):4144. 6. Constandt B, Thibaut E, De Bosscher V, Scheerder J, Ricour M, Willem A. Exercising in times of lockdown: an analysis of the impact of COVID-19 on levels and patterns of exercise among adults in Belgium. International journal of environmental research and public health. 2020;17(11):4144. j p ( ) 7. Robinson E, Boyland E, Chisholm A, Harrold J, Maloney NG, Marty L, et al. Obesity, eating behavior and physical activity during COVID-19 lockdown: A study of UK adults. Appetite. 2021;156:104853. 8. Benoit RG, Gilbert SJ, Burgess PW. A neural mechanism mediating the impact of episodic prospection 7. Robinson E, Boyland E, Chisholm A, Harrold J, Maloney NG, Marty L, et al. Obesity, eating b and physical activity during COVID-19 lockdown: A study of UK adults. Appetite. 2021;156:104853. Acknowledgements The authors would like to thank Dr. Peter Koval for the use of the SEMA3 platform. Availability of data and materials All data and analysis code are available, links are provided in the manuscript. We also provide videos of the data collection procedure. References and physical activity during COVID-19 lockdown: A study of UK adults. Appetite. 2021;156:104853. 8. Benoit RG, Gilbert SJ, Burgess PW. A neural mechanism mediating the impact of episodic prospection on farsighted decisions. Journal of Neuroscience. 2011;31(18):6771-9. 9 Peters J Büchel C Episodic future thinking reduces reward delay discounting through an enhancement p y y g y pp ; 8. Benoit RG, Gilbert SJ, Burgess PW. A neural mechanism mediating the impact of episodic prospection on farsighted decisions. Journal of Neuroscience. 2011;31(18):6771-9. 9 P t J Bü h l C E i di f t thi ki d d d l di ti th h h t Peters J, Büchel C. Episodic future thinking reduces reward delay discounting through an enhance f prefrontal-mediotemporal interactions. Neuron. 2010;66(1):138-48. 10. Snider SE, LaConte SM, Bickel WK. Episodic future thinking: Expansion of the temporal window in individuals with alcohol dependence. Alcoholism: clinical and experimental research. 2016;40(7):1558-66. 11. Stein JS, Wilson AG, Koffarnus MN, Daniel TO, Epstein LH, Bickel WK. Unstuck in time: episodic future thinking reduces delay discounting and cigarette smoking. Psychopharmacology. 2016;233(21):3771-8. 12. Goetz JL, Keltner D, Simon-Thomas E. Compassion: an evolutionary analysis and empirical review. Psychological bulletin. 2010;136(3):351. 13. Omoto AM, Malsch AM, Barraza JA. Compassionate acts: Motivations for and correlates of volunteerism among older adults. The science of compassionate love: Theory, research, and applications. 2009:257-82. 14. Weng HY, Fox AS, Shackman AJ, Stodola DE, Caldwell JZ, Olson MC, et al. Compassion training alters altruism and neural responses to suffering. Psychological science. 2013;24(7):1171-80. 15. Romer D, Jamieson KH. Conspiracy theories as barriers to controlling the spread of COVID-19 in the US. Social Science & Medicine. 2020;263:113356. 11 is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. eer review) The copyright holder for this this version posted September 16, 2021. ; 0.1101/2021.09.13.21263407 . CC-BY 4.0 International license It is made available under a 6. Latkin CA, Dayton L, Yi G, Colon B, Kong X. Mask usage, social distancing, racial, and gender orrelates of COVID-19 vaccine intentions among adults in the US. PloS one. 2021;16(2):e0246970. 17. Moeller FG, Barratt ES, Dougherty DM, Schmitz JM, Swann AC. Psychiatric aspects of impulsivity. References ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a . CC-BY 4.0 International license It is made available under a References American journal of psychiatry. 2001;158(11):1783-93. 18. Kooistra EB, van Rooij B. Pandemic Compliance: A systematic review of influences on social distancing behaviour during the first wave of the COVID-19 outbreak. Available at SSRN 3738047. 2020. 19. Wismans A, Letina S, Wennberg K, Thurik R, Baptista R, Burke A, et al. The role of impulsivity and delay discounting in student compliance with COVID-19 protective measures. Personality and Individual Differences. 2021:110925. 20. Odum AL, Baumann AA. Delay discounting: State and trait variable. Impulsivity: The behavioral and neurological science of discounting: American Psychological Association; 2010. p. 39-65. 21. Curran PJ, Bauer DJ. The disaggregation of within-person and between-person effects in longitudinal models of change. Annual review of psychology. 2011;62:583-619. 1. Curran PJ, Bauer DJ. The disaggregation of within-person and between-person effects in longitudi odels of change. Annual review of psychology. 2011;62:583-619. 22. Fisher AJ, Medaglia JD, Jeronimus BF. Lack of group-to-individual generalizability is a threat to human subjects research. Proceedings of the National Academy of Sciences. 2018;115(27):E6106-E15. 23. Althubaiti A. Information bias in health research: definition, pitfalls, and adjustment methods. Journal of multidisciplinary healthcare. 2016;9:211. p y Tomko RL, Solhan MB, Carpenter RW, Brown WC, Jahng S, Wood PK, et al. Measuring impulsivity ily life: the momentary impulsivity scale. Psychological assessment. 2014;26(2):339. 25. Singmann H, Bolker B, Westfall J, Aust F, Ben-Shachar MS. afex: Analysis of factorial experiments. R package version 013–145. 2015. 26. Dahl CJ, Lutz A, Davidson RJ. Cognitive processes are central in compassion meditation. Trends in Cognitive Sciences. 2016;20(3):161-2. 27. Reddy SD, Negi LT, Dodson-Lavelle B, Ozawa-de Silva B, Pace TW, Cole SP, et al. Cognitive-based compassion training: A promising prevention strategy for at-risk adolescents. Journal of Child and Family Studies. 2013;22(2):219-30. 28. Stuart RM, Abeysuriya RG, Kerr CC, Mistry D, Klein DJ, Gray RT, et al. Role of masks, testing and contact tracing in preventing COVID-19 resurgences: a case study from New South Wales, Australia. BMJ open. 2021;11(4):e045941. p 29. van Baal S, Moskovsky N, Hohwy J, Verdejo-Garcia A. State impulsivity amplifies urges without diminishing self-control. 2021. g 30. Gollwitzer A, Martel C, Marshall J, Höhs JM, Bargh JA. Connecting self-reported social distancing to real-world behavior at the individual and us state level. 2020. 12 is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. Please imagine yourself after lockdowns and restrictions are over. You are doing your favourite activity that became possible after lockdowns lifted. Imagine how you feel, and picture your surroundings (think about smell and sound too). Please reflect on the fact that on 5 March, COVID-19 infections were rising in Europe again. Please reflect on the reporting from 14 March that many people in Lincolnshire are not turning up for their vaccinations. Appendix A To become eligible for the study, participants (n = 293) completed an eligibility survey prior to the experiment, which was used to create a representative sample. Participants were added to the EMA software in two rounds in order to cope with varying drop-out across the eight groups, since there was more dropout than anticipated during the EMA app download-phase. In total, 200 participants were added to the EMA software, 112 of whom downloaded the app, and 97 of those completed more than 50% of the surveys. As indicated in our preregistration, participants who completed less than 50% of surveys were excluded, the average survey completion rate for the rest was 83.7%. Finally, two participants never reported having urges of non-adherence, and thus these were included from the final sample, given that there was no variation in the data. Differing dropout across groups after the second round of participant entries led to an imbalance in the female/male sample division. Given that this study is the first of its kind, we cannot assume that these responses are missing at random. In order to address this issue, we analysed whether age and sex influence urges and self-control. Figure A1. The age and sex distribution of the sample. Figure A1. The age and sex distribution of the sample. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a . CC-BY 4.0 International license It is made available under a Please imagine yourself as a healthcare worker in the emergency room. You have not been able to get proper sleep and have had to keep families separated because it was too dangerous to see their loved ones. Try to feel the emotions that might be going through you. Table A1. The instructional prompts participants received each morning in their 7.30am survey. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 16, 2021. ; https://doi.org/10.1101/2021.09.13.21263407 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. eer review) The copyright holder for this this version posted September 16, 2021. ; 0.1101/2021.09.13.21263407 Episodic future thinking Control Compassion Please reflect on the news that shutdowns of the Ferguson shipyard during the Covid pandemic have added an extra £4.3m to the cost of two over-budget and delayed CalMac ferries. Please imagine yourself as a vulnerable person. You have severe asthma and will have significant trouble breathing if you catch COVID-19. Try to feel the emotions that might be going through you. Please imagine yourself after lockdowns and restrictions are over. You are on holiday, at your favourite destination. Try to imagine how you feel, and picture your surroundings (think about smell and sounds too). Please imagine yourself as a family member of a person in hospital due to COVID-19. You want to be with them, but you are not allowed to because you might catch it yourself. Try to feel the emotions that might be going through you. Please reflect on the news that the COVID-19 restrictions in Scotland were relaxed on 13 March. Up to four people from two different households can now gather outside. Please imagine yourself in the future when lockdowns and restrictions are over. You are travelling to a place you always wanted to go. Imagine how you feel and picture your surroundings (think about smells and sound too). Please imagine yourself in the future when lockdowns and restrictions are over, and picture that you are doing something you love. Imagine how you feel and picture your surroundings (think about smell and sound too). Please imagine yourself as a vulnerable person. You are an elderly person in a retirement home. You have not been able to receive any visitors for months, and your interactions with the other residents are restricted. Try to feel the emotions that might be going through you. Please reflect on the reporting from 14 March that many people in Lincolnshire are not turning up for their vaccinations. Please reflect on the news that on 14 March people were fined 800 pounds each for having a party in Gloucester. Please reflect on the news that 28% of people in need of social care have seen their health decline during COVID-19. Table A1. The instructional prompts participants received each morning in their 7.30am survey. 14 14
https://openalex.org/W4225269822
https://epub.uni-regensburg.de/52243/1/Radeck2022_Article_RhegmatogenousRetinalDetachmen.pdf
English
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Rhegmatogenous retinal detachment repair—does age, sex, and lens status make a difference?
Graefe's archive for clinical and experimental ophthalmology
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Key Messages In individuals operated for RRD over 40 years of age there were significantly more male patie In individuals operated for RRD over 40 years of age there were significantly more male patients. The male predominance in RRD was stronger in pseudophakic than in phakic eyes. The proportion of pseudophakic RRD has increased over the 15 years observation period. Graefe's Archive for Clinical and Experimental Ophthalmology https://doi.org/10.1007/s00417-022-05674-x Graefe's Archive for Clinical and Experimental Ophthalmology https://doi.org/10.1007/s00417-022-05674-x Graefe's Archive for Clinical and Experimental Ophthalmology https://doi.org/10.1007/s00417-022-05674-x RETINAL DISORDERS Rhegmatogenous retinal detachment repair—does age, sex, and lens status make a difference? Received: 21 October 2021 / Revised: 28 January 2022 / Accepted: 15 April 2022 © The Author(s) 2022 1 Department of Ophthalmology, University Hospital of Regensburg, Franz‑Josef‑Strauss‑Allee 11, D‑93042 Regensburg, Germany * Viola Radeck viola.radeck@ukr.de Abstract Purpose  To analyze the correlation between lens status, age, and sex in the epidemiology and success rates of rhegmatog‑ enous retinal detachment (RRD) surgery.i Methods  The files of all consecutive patients undergoing vitreoretinal surgery for uncomplicated RRD between Jan 2005 und Dec 2020 were retrospectively reviewed. Successful outcome was defined as no retinal redetachment occurring within 3 months after surgery. Results  5502 eyes with uncomplicated primary RRD were included. Mean age of the patients was 61.1 years (± 13.6 SD). In the age group over 40 years, a male predominance was found. The percentage of pseudophakic RRD increased from 25 to 40% during the 15 years observation period. In the age group 50 to 69 years, patients with pseudophakic detachments were male in 786 out of 1079 cases (72.9%). In the same age group, 1285 of 2110 (60.9%) patients with phakic RRD were male. Overall, primary success rate after one procedure was 91.2% (5018 of 5502). In the phakic eyes, the primary success rate was higher in those eyes that underwent combined phacovitrectomy (93.0%), compared to those without simultaneous cataract surgery (88.7%; p = 0.002). Conclusion  The ratio of male and female patients with RRD varies between age groups. The proportion of pseudophakic RRD has increased within 15 years. The male predominance in RRD is stronger in pseudophakic than in phakic eyes. In phakic eyes with RRD, a combined phacovitrectomy yielded better anatomical results. Keywords  Age · Cataract surgery · Sex · Pseudophakia · Retinal detachment surgery · Vitrectomy Keywords  Age · Cataract surgery · Sex · Pseudophakia · Retinal detachment surgery · Vitrectomy Key Messages In individuals operated for RRD over 40 years of age there were significantly more male patients. The male predominance in RRD was stronger in pseudophakic than in phakic eyes. The proportion of pseudophakic RRD has increased over the 15 years observation period. Success rates of primary vitrectomy for phakic RD was higher if a combined phacovitrectomy was performed. Key Messages In individuals operated for RRD over 40 years of age there were significantly more male patients. The male predominance in RRD was stronger in pseudophakic than in phakic eyes. The proportion of pseudophakic RRD has increased over the 15 years observation period. Success rates of primary vitrectomy for phakic RD was higher if a combined phacovitrectomy was performed Procedures A total of 810 (14.7%) eyes were treated with buckle sur‑ gery, 4692 (85.3%) with vitrectomy. In the vitrectomy cases, 95% received gas as a tamponade and 5% liquid silicone. The decision for buckle surgery or vitrectomy was left to the respective surgeon. In young patients with attached vitreous and atrophic holes or oral dialysis buckle surgery was preferred, most pseudophakic eyes were vitrectomized. Preferences however changed over the observation period, with an increasing proportion of eyes being treated with vitrectomy [3]. Materials and methods The files of all patients undergoing primary RRD surgery between January 2005 and December 2020 in our depart‑ ment were reviewed. Included were all eyes with uncom‑ plicated RRD undergoing buckle surgery or vitrectomy. Excluded were eyes with PVR grade C or more, eyes with a history of penetrating injury to the posterior segment of the eye, or a history of other vitreoretinal procedures in the past. Complicated cases such as malformations or retinopathy of prematurity (ROP) were also excluded from the analysis. High myopic eyes (> 6 Dpt) were included, but pathological myopia with RRD arising from macular holes in posterior staphylomata was excluded.i From the 2614 phakic eyes treated with vitrectomy, 2163 (82.7%) were operated combined with phacoemulsification and posterior chamber intraocular lens implantation. While in the early years only a minority of the phakic eyes was treated with combination surgery, at the end of the observa‑ tion period, about 90% were operated as phakovitrectomy (Fig. 2). In 2008 to 2010, there was a paradigm shift to com‑ bining cataract surgery with vitrectomy. This was based on reports of good results with combined surgery, sufficient experience of the surgeons in both techniques, and the aim to avoid a second (cataract) surgery for the patient. Failure was defined as diagnosis of redetachment docu‑ mented in the patient file within 3 months after primary sur‑ gery. In eyes with silicone oil tamponade, the silicone was removed usually 3 to 6 months after primary surgery, which may lead to an underestimation of redetachments since those occurring after silicone removal were not included. Age distribution Overall, 5502 eyes with uncomplicated primary RRD had VR surgery between January 2005 and December 2020 operated by 13 VR surgeons with different levels of surgical experience. Mean age of the patients was 61.1 years (± 13.6 SD). The age distribution is shown in Fig. 1. The youngest patient was 4, and the oldest was 98 years old. In the present study, we have analyzed the impact of lens status, age, and sex on epidemiology and success rates of RRD surgery. We investigated whether RRD occurring in different age groups would also differ in other features such as sex distribution and success rates. We have also analyzed if the increasing number of cataract operations leads to a distinct increase of pseudophakic RRD during the duration of this study from 2005 to 2020 and how pseudophakia may affect the sex distribution of RRD. Finally, we have com‑ pared success rates of combined phacovitrectomy with those of vitrectomy alone. Introduction increasing number of cataract surgeries and refractive lens exchanges, higher prevalence of myopia, and increasing life expectancy [1].f Rhegmatogenous retinal detachment (RRD) is a common surgical emergency in ophthalmology. Several factors con‑ tribute to an increasing occurrence of RRD, namely an RRD is not a homogenous entity. It can affect all age groups, but with different clinical features. The most com‑ mon presentation is an RRD caused by retinal tears asso‑ ciated with a posterior vitreous detachment (PVD). Other presentations include RRD with atrophic round holes in individuals without PVD and vitreoretinal degeneration/ dystrophies. Most studies show a male predominance in (0121 3456789) 3 Graefe's Archive for Clinical and Experimental Ophthalmology already recorded in our own files, indicating that the overall number of overlooked redetachments would not be signifi‑ cant [3, 4]. RRD patients, and the reason for the observed sex ratio is however unclear. Another factor that characterizes different subgroups of RRD is the lens status [2]. With the rising number of cataract operations, an increasing proportion of pseu‑ dophakic RRD can be expected. In phakic RRD on the other hand, vitrectomy is becoming increasingly common. Lens management during surgery is discussed controver‑ sially. Until today, there is no clear indication whether vitrectomy should be performed primarily without lens surgery or whether combined phacovitrectomy may be the better strategy. The study was approved by the local ethic board (Ethik‑ kommission der Universität Regensburg) and adheres to the principles of the declaration of Helsinki. 3 Graefe's Archive for Clinical and Experimental Ophthalmology Graefe's Archive for Clinical and Experimental Ophthalmology Graefe's Archive for Clinical and Experimental Ophthalmology Fig. 1   Number of eyes of patients with RRD in various age groups Fig. 2   Proportion of phakic eyes with RRD treated with vitrectomy alone or combined phacovitrectomy umber of eyes of with RRD in various ps Fig. 2   Proportion of phakic eyes with RRD treated with vitrectomy alone or combined phacovitrectomy Fig. 2   Proportion of phakic eyes with RRD treated with vitrectomy alone or combined phacovitrectomy Sex distribution in different age groups Overall, 3360 of 5502 eyes (61.1%) with RRD occurred in male patients. The proportion of male patients with RRD in various age groups is shown in Fig. 3. In the age group with RRD below 20 years, the proportion of boys was 56%. Between 20 and 39 years, 55% of the patients were female. Between 50 and 79 years, a majority of 64% was male. In the oldest group over 80 years, no gender predominance was observed (49.3% male). Our hospital is the only center for vitreoretinal emer‑ gencies in an area serving a population of about 2–3 mil‑ lion people. We assume that almost all redetachments were referred to us. In order to investigate, if we had been missing failures, in a subgroup of 1290 patients operated between 2007 and 2012, a more intense follow-up was conducted by contacting patients and their ophthalmologists. No addi‑ tional redetachments were detected in addition to those 1 3 Graefe's Archive for Clinical and Experimental Ophthalmology Lens status and sex Overall, primary success rate after one surgery was 91.2% (5018 of 5502). Figure 4 shows the rate of rede‑ tachments in different age groups. The primary success rate was lower for the youngest (age 0–19: success rate 84.4%; 38 out of 45) and oldest patients (age 80 + : success rate 84.1%; 292 out of 347) compared to the middle-aged group (age 20–79: success rate 91.7%; 4688 out of 5110). Primary failure rate of RDD surgery was 305/3360 (9.1%) in male patients and 179/2142 (8.4%) in female patients, which was not statistically significantly different (p = 0.4, Pearson chi-square test). 3398 (61.7%) eyes were phakic, 27 (0.5%) aphakic, and 2077 (37.7%) had an artificial intraocular lens. The percentage of pseudophakic RRD has increased over the observation period from 25 to about 40%. The increase in pseudophakic RRD occurred mainly between 2005 and 2014. Thereafter, it remained relatively stable (Fig. 5). Of the pseudophakic RRDs, 67.3% occurred in male patients, while the proportion of male patients was only 57.3% in the phakic RRDs. Since the sex ratio varied between age groups (see Fig. 3), we separately analyzed the age group 50–69  years of age. In this subset, the 1 Graefe's Archive for Clinical and Experimental Ophthalmology Graefe's Archive for Clinical and Experimental Ophthalmology pseudophakic detachments were male in 786 out of 1079 cases (72.9%), while from the phakic eyes in the same age group, 1285 out of 2110 (60.9%) were male. (n = 451; 88.7%). This difference was statistically significant (p = 0.002; Pearson chi-square test). Fig. 3   Sex distribution of eyes of patients with RRD in various age groups. For the age group 40–49, the sex distribution was significantly different from equal with p = 0.01, for the age groups 50–59, 60–69, and 70–79 with p < 0.0001. The other age groups were not sig‑ nificantly different from equal distribution. (Chi-square tests for one-dimensional tables) Fig. 4   Redetachment rates of eyes of patients in various age groups Fig. 4   Redetachment rates of eyes of patients in various age groups (n = 451; 88.7%). This difference was statistically significant (p = 0.002; Pearson chi-square test). pseudophakic detachments were male in 786 out of 1079 cases (72.9%), while from the phakic eyes in the same age group, 1285 out of 2110 (60.9%) were male. Fig. 3   Sex distribution of eyes of patients with RRD in various age groups. For the age group 40–49, the sex distribution was significantly different from equal with p = 0.01, for the age groups 50–59, 60–69, and 70–79 with p < 0.0001. The other age groups were not sig‑ nificantly different from equal distribution. (Chi-square tests for one-dimensional tables) Fig. 4   Redetachment rates of eyes of patients in various age groups 3 Lens status and success rates complicated RD cases were excluded, and some of them (trauma, Coats disease) are more commonly found in boys, the male predominance in children was less pronounced compared to other publications [5]. RRD has been consistently shown to be more com‑ mon in male patients. This fact persisted after exclusion of pseudophakia and trauma. It has been speculated that males had a longer axial length and this could explain the male predominance in RRD [9]. However, this would also be a risk factor for atrophic round hole RRD with attached posterior vitreous in young adults, but here females are at higher risk. Males are more affected by PVD associ‑ ated RRD with tractional tears. Anatomical changes with a more posteriorly located vitreous base in males have also been described [10] and would provide a more convincing explanatory approach. For young adults, most cases of RRD are due to atrophic round holes with an attached vitreous. This type of RRD is usually slowly evolving in myopic patients. Ung et al. showed that the mean age lies between 25 and 35 years and scleral buckling procedures remained highly effective in this selected group of patient [6]. Interestingly, this type of RRD was found predominantly in females [6–8]. In the present study, we also found a trend (not statistically significant) of female predominance (55%) in the age group 20–39 years of age. The majority of RRD occurs in the age group over 50 in association with a PVD and traction-induced retinal tears. Between 50 and 79 years of age, 64% of the RRD patients in our study were males. In the age group over 80, we found both sexes were equally common affected, although the proportion of males is only 38% in the general popu‑ lation in Germany according to the “Federal Office for Stastistics.” Thus, if the sex distribution in the population in this age group is taken into account, men over 80 years The number of cataract surgeries has increased in the order of 10% per year over the last decades in industrialized countries [11]. Increasingly, eyes with less advanced lens opacities and better vision are operated. In particular, eyes with high refractive errors undergo more commonly clear lens extraction, with highly myopic eyes being at highest risk for RRD. Lens status and success rates In this study, we provide data from a retrospective analysis of over 5000 consecutive cases who underwent primary RRD repair at a single university hospital. Mean age (61 years) and male predominance (proportion of 61%) is in agreement with other series in the literature [2]. However, a more dif‑ ferentiated analysis shows that there is no homogeneous sex distribution over the whole age spectrum. Patients with pseudophakic RRD repair were on aver‑ age 67 ± 11 (mean ± SD, range) years old. The phakic patients who had combined surgery were 63 ± 9 years old. Patients without cataract surgery during RRD repair were 49 ± 13 years of age. Mean age of the patients and rede‑ tachment rates for various subgroups are shown in Table 1. Notably, the primary success rate was higher in the phakic eyes that underwent phacovitrectomy (n = 2163; 93.0%), compared to those who were left phakic during vitrectomy For children, retinal detachment is found more often in boys [5]. RRD in small children is commonly associated with vitreoretinal degeneration/dysplasia. Since in our series 1 3 Graefe's Archive for Clinical and Experimental Ophthalmology Fig. 5   Proportion of pseudopha‑ kic lens status in eyes with RRD between 2005 and 2020 Table 1   Age and redetachment rates of various subgroups depending on lens status and surgical technique Number of eyes Redetachment rate, % Age, mean ± SD Treated with buckle surgery 810 10.9 49.2 ± 16.5 Pseudophakic, treated with vitrectomy 2051 9.2 66.7 ± 11.4 Aphakic, treated with vitrectomy 27 18.5 49.2 ± 15.2 Phakic, treated with vitrectomy, no lens surgery 451 11.3 49.4 ± 12.9 Phakic, treated with combined phacovitrectomy 2163 7.0 62.8 ± 9.4 Number of eyes Redetachment rate, % Age, mean ± SD Treated with buckle surgery 810 10.9 49.2 ± 16.5 Pseudophakic, treated with vitrectomy 2051 9.2 66.7 ± 11.4 Aphakic, treated with vitrectomy 27 18.5 49.2 ± 15.2 Phakic, treated with vitrectomy, no lens surgery 451 11.3 49.4 ± 12.9 Phakic, treated with combined phacovitrectomy 2163 7.0 62.8 ± 9.4 Table 1   Age and redetachment rates of various subgroups depending on lens status and surgical technique of age also have a higher individual risk for RRD than women (p = 0.003, chi-square test). Table 1   Age and redetachment rates of various subgroups depending on lens status and surgical technique Lens status and success rates Since cataract surgery is a major risk factor for RRD, it is inevitably that the proportion of pseudophakic RRD increases with time [1]. Here, we show an increase 1 Graefe's Archive for Clinical and Experimental Ophthalmology formation. Although not fully proven, it is assumed that increased oxygen diffusion to the lens may play a role [15]. Cataract formation after vitrectomy appears to be age dependent, with older patients developing lens opacifications earlier, often within a few months. Less expected, after buckle surgery also a high frequency of cataract surgery was observed [16]. Therefore, especially in patients beyond the age of accommodation, RRD may be operated primarily combined as phacovitrectomy. This saves the patient an additional surgery, is more cost effective, and reduces time of reduced vision [17]. Especially in times of pandemic, it can reduce the risk for nosocomial infection by avoiding additional hospital visits [18]. from 25 to 40% pseudophakia in RRD eyes over the obser‑ vation period. Notably, in the age group 50–69, a proportion of 73% of the patients with pseudophakic detachments was male, while in phakic eyes in the same age group, only 61% were male, although the majority (about 60%) of all cataract surgeries is performed in females in Europe [12] and the USA [13]. A similar phenomenon was observed in Scotland, where within the pseudophakic group, the overrepresentation of men was even more marked (M:F, 2.3:1), despite a higher rate of cataract surgery in women in the UK [14]. Although the present study was not designed to evaluate this question, a possible explanation for the data could be that males in this age group have a higher risk for RRD than females, which is further increased by cataract surgery. This effect appears less pronounced for women. Cataract surgery is believed to increase the RRD risk by accelerating vitreous degradation and PVD. Therefore, it would be plausible that sex differ‑ ences in the vitreous base anatomy [10] might play a role for the increased RRD risk for men. A major intraoperative advantage of combined sur‑ gery is uninhibited view and access to the most periph‑ eral retina and the vitreous base which allows a nearly complete removal of vitreous traction and identification of retinal tears. Lens status and success rates In a pseudophakic eye, the peripheral secondary cataract will obscure the view, and in phakic eyes, the complete release of traction to the vitreous base is hardly possible without risking to touch the lens. This may lead to better primary reattachment rates of phaco‑ vitrectomy. On the other hand, combined surgery requires broader surgical skills and has a higher potential to create intraocular inflammation which in turn may theoretically increase the risk for PVR development. In our study, the overall primary anatomic success rate was 91%, which is in accordance with other recently pub‑ lished studies for RRD surgery [2]. The high proportion of vitreous surgery follows a general trend from buckle to vit‑ rectomy [3]. No difference was observed in success rates of RD surgery between male and female patients. The redetachment rate in the very young and the very old age group was somewhat higher. For children, lower success rates have been previously observed [5]. This may be due to more atypical findings and a delayed diagnosis in children. In the very old, there is probably a higher rate of ocular and general comorbidities, leading to later diagnosis and more difficult ocular situations (e.g., PEX syndrome, cloudy cornea, and narrow pupil). A reduced capacity of the RPE to pump out subretinal fluid and reattach the retina may also play a role. A recent analysis of BEAVRS data also showed lower anatomical success rates in the age group over 80 with RRD [2]. Cataract surgery months or years after vitrectomy, when the lens is opaque, may be more challenging due to miss‑ ing vitreous support of the lens and hard lens nucleus, both leading to increased complications in cataract surgery. On the other hand, disadvantages of phacovitrectomy may be a reduced red light reflex due to vitreous hemorrhage or bul‑ lous detachment of the retina. Postoperative synechiae or anterior dislocation of the IOL due to gas pushing forward with iris capture may occur. In addition, calculation of the IOL may be more diffi‑ cult, especially if the macula is detached. Here the fellow eye may be used for measuring axial length. The number of eyes having undergone refractive surgery is increas‑ ing which also could complicate IOL calculation. Since RRD often occurs in highly myopic eyes, the selection of the intended refraction after lens surgery is difficult. References https://​doi.​org/​10.​1038/​sj.​ eye.​67016​18 7. Williams KM, Dogramaci M, Williamson TH (2012) Retrospec‑ tive study of rhegmatogenous retinal detachments secondary to round retinal holes. Eur J Ophthalmol 22:635–640. https://​doi.​ org/​10.​5301/​ejo.​50000​80f 7. Williams KM, Dogramaci M, Williamson TH (2012) Retrospec‑ tive study of rhegmatogenous retinal detachments secondary to round retinal holes. Eur J Ophthalmol 22:635–640. https://​doi.​ org/​10.​5301/​ejo.​50000​80f 8. Callaway NF, Vail D, Al-Moujahed A et al (2020) Sex differences in the repair of retinal detachments in the United States. Am J Ophthalmol 219:284–294. https://​doi.​org/​10.​1016/j.​ajo.​2020.​06.​ 039 8. Callaway NF, Vail D, Al-Moujahed A et al (2020) Sex differences in the repair of retinal detachments in the United States. Am J Ophthalmol 219:284–294. https://​doi.​org/​10.​1016/j.​ajo.​2020.​06.​ 039 9. Mitry D, Tuft S, McLeod D et al (2011) Laterality and gender imbalances in retinal detachment. Graefes Arch Clin Exp Ophthal‑ mol 249:1109–1110. https://​doi.​org/​10.​1007/​s00417-​010-​1529-0 10. Wang J, McLeod D, Henson DB et al (2003) Age-dependent changes in the basal retinovitreous adhesion. Invest Ophthalmol Vis Sci 44:1793–1800. https://​doi.​org/​10.​1167/​iovs.​02-​0802 Funding  Open Access funding enabled and organized by Projekt DEAL. 11. Erie JC (2014) Rising cataract surgery rates: demand and supply. Ophthalmology 121:2–4. https://​doi.​org/​10.​1016/j.​ophtha.​2013.​ 10.​002 Lens status and success rates Most studies however, including a small randomized trial [25] and a recent meta-analysis [26], found no difference in redetachment rates between the two approaches [22, 27]. Open Access  This article is licensed under a Creative Commons Attri‑ bution 4.0 International License, which permits use, sharing, adapta‑ tion, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. In the present study, we changed strategy in 2008 to 2010 and performed phacovitrectomy in most eyes over 50 years of age, even if the lens still was clear. When comparing the redetachment rates, we found better results in the group operated with combined surgery (7% vs 11% redetachment rate). One has to keep in mind however that the groups were not randomized and differed in several aspects. The phacovitrectomy patients were generally older and operated later in the observation period and the absolute differences were small. Lens status and success rates An intended emmetropia or low myopia will induce anisome‑ tropia, which necessitates contact lens correction or sub‑ sequent refractive lens surgery in the healthy fellow eye, which in turn will expose this eye to an even higher risk for RRD. Explaining this complex situation to a nervous patient in an emergency situation can be challenging. The success rates also showed some correlation with the lens status. In aphakic eyes, success rate was lower. In the present series, aphakic eyes were not generally considered to have complicated RRD and therefore were not excluded. They are only a small group of eyes, but may probably pre‑ sent with more confounding factors due to previous ante‑ rior segment trauma, narrow pupil, aphakia due to Marfan’s syndrome, or a congenital cataract. This may explain the higher redetachment rate. The small differences between buckle surgery, and vitrectomy in phakic and pseudophakic eyes are probably not relevant, considering that the groups differ in their initial situations. The literature does not consistently recommend to per‑ form cataract and vitreous surgery in one or two steps. Some studies report a lower success rate of combined surgery [19, 20]. In addition, combined surgery had less f A controversial question is whether cataract surgery should be performed simultaneously during vitreous sur‑ gery for RD. Vitrectomy leads to accelerated cataract 1 3 1 3 1 3 1 3 Graefe's Archive for Clinical and Experimental Ophthalmology favorable refractive outcome [20, 21] and there was a higher complication rate for inexperienced surgeons [22]. In a scenario-related survey of BEAVRS, most vitreoreti‑ nal surgeons would avoid combined surgery in RDD cases with a history of laser-assisted refractive surgery, even when faced with a visually significant cataract [23]. Other authors had better results with phacovitrectomy compared to vitrectomy alone [24]. Most studies however, including a small randomized trial [25] and a recent meta-analysis [26], found no difference in redetachment rates between the two approaches [22, 27]. Conflict of interest  The authors declare no competing interests. favorable refractive outcome [20, 21] and there was a higher complication rate for inexperienced surgeons [22]. In a scenario-related survey of BEAVRS, most vitreoreti‑ nal surgeons would avoid combined surgery in RDD cases with a history of laser-assisted refractive surgery, even when faced with a visually significant cataract [23]. Other authors had better results with phacovitrectomy compared to vitrectomy alone [24]. Funding  Open Access funding enabled and organized by Projekt DEAL. References 1. Nielsen BR, Alberti M, Bjerrum SS et al (2020) The incidence of rhegmatogenous retinal detachment is increasing. Acta Ophthal‑ mol 98:603–606. https://​doi.​org/​10.​1111/​aos.​14380 2. Ferrara M, Mehta A, Qureshi H et al (2021) Phenotype and out‑ comes of phakic versus pseudophakic primary rhegmatogenous retinal detachments: cataract or cataract surgery related? Am J Ophthalmol 222:318–327. https://​doi.​org/​10.​1016/j.​ajo.​2020.​09.​ 036 f Limitations of our study are its retrospective design, the lack of a stringent follow-up of the patients, the miss‑ ing information of preoperative PVD status, and missing information about visual acuity and functional outcome. However, we present a large number of RRD cases over a 15 years period from a single center and have focussed on data that can be obtained reliably in retrospective from the patients’ charts.l 3. Radeck V, Helbig H, Barth T et al (2021) Ablatiochirurgie: trends über 15 Jahre (Retinal detachment surgery: trends over 15 years). Ophthalmologe. https://​doi.​org/​10.​1007/​s00347-​021-​01430-4 4. Radeck V, Helbig H, Barth T et al (2021) The learning curve of retinal detachment surgery. Graefes Arch Clin Exp Ophthalmol. https://​doi.​org/​10.​1007/​s00417-​021-​05096-1 4. Radeck V, Helbig H, Barth T et al (2021) The learning curve of retinal detachment surgery. Graefes Arch Clin Exp Ophthalmol. https://​doi.​org/​10.​1007/​s00417-​021-​05096-1 5. Barth T, Zeman F, Helbig H et al (2017) Clinical features and outcome of paediatric retinal detachment. Ophthalmologica 237:63–72. https://​doi.​org/​10.​1159/​00045​5355 5. Barth T, Zeman F, Helbig H et al (2017) Clinical features and outcome of paediatric retinal detachment. Ophthalmologica 237:63–72. https://​doi.​org/​10.​1159/​00045​5355 In conclusion, our analysis of the influence of lens sta‑ tus, age, and sex in a large consecutive series of RD sur‑ gery revealed that the gender predominance in RD varies within different age groups. While in children, more boys were affected; in young adults, there were more females with RD; and in patients over 50 years of age, a strong male predominance was observed. The male predominance in RRD is stronger in pseudophakic than in phakic eyes. The proportion of pseudophakic RD has increased during the observation period from 25 to 40%. In phakic eyes with RRD combined phacovitrectomy yielded better anatomical results than vitectomy alone. 6. Ung T, Comer MB, Ang AJS et al (2005) Clinical features and surgical management of retinal detachment secondary to round retinal holes. Eye (Lond) 19:665–669. https://​doi.​org/​10.​1038/​sj.​ eye.​67016​18 6. Ung T, Comer MB, Ang AJS et al (2005) Clinical features and surgical management of retinal detachment secondary to round retinal holes. Eye (Lond) 19:665–669. Consent to participate  Informed consent was waived because of the retrospective design of the study. Declarations 12. Javaloy J, Druchkiv V, Beltrán J et al (2021) Retinal detach‑ ment after phacoemulsification in refractive surgery clinics: a large series analysis with variable follow-up during 16 years. Graefes Arch Clin Exp Ophthalmol. https://​doi.​org/​10.​1007/​ s00417-​021-​05160-w Ethics approval  All procedures performed in studies involving human participants were in accordance with the ethical standards of the ethical committee of the University of Regensburg and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. 13. Wu AM, Wu CM, Tseng VL et al (2018) Characteristics asso‑ ciated with receiving cataract surgery in the US Medicare and Consent to participate  Informed consent was waived because of the retrospective design of the study. 1 3 Graefe's Archive for Clinical and Experimental Ophthalmology Veterans Health Administration populations. JAMA Ophthalmol 136:738–745. https://​doi.​org/​10.​1001/​jamao​phtha​lmol.​2018.​1361 detachment. Can J Ophthalmol 50:360–366. https://​doi.​org/​10.​ 1016/j.​jcjo.​2015.​07.​003 p g j p 14. Mitry D, Charteris DG, Yorston D et al (2010) The epidemiology and socioeconomic associations of retinal detachment in Scotland: a two-year prospective population-based study. Invest Ophthalmol Vis Sci 51:4963–4968. https://​doi.​org/​10.​1167/​iovs.​10-​5400 22. Kim MS, Woo SJ, Park KH (2020) Phacovitrectomy versus lens- sparing vitrectomy for rhegmatogenous retinal detachment repair according to the surgical experience. Retina Publish Ahead of Print. https://​doi.​org/​10.​1097/​IAE.​00000​00000​003090i p g 15. Holekamp NM, Shui Y-B, Beebe DC (2005) Vitrectomy surgery increases oxygen exposure to the lens: a possible mechanism for nuclear cataract formation. Am J Ophthalmol 139:302–310. https://​doi.​org/​10.​1016/j.​ajo.​2004.​09.​046 23. Brent AJ, Bedi S, Wakefield M et al (2020) A comparative study of lens management in the United Kingdom and India with regard to rhegmatogenous retinal detachment surgery. Eur J Ophthalmol 30:1120–1126. https://​doi.​org/​10.​1177/​11206​72119​855209f p g j j 16. Feng H, Adelman RA (2014) Cataract formation following vit‑ reoretinal procedures. Clin Ophthalmol 8:1957–1965. https://​doi.​ org/​10.​2147/​OPTH.​S68661 24. Caiado RR, Magalhães O, Badaró E et al (2015) Effect of lens status in the surgical success of 23-gauge primary vitrectomy for the management of rhegmatogenous retinal detachment: the Pan American Collaborative Retina Study (PACORES) group results. Retina 35:326–333. https://​doi.​org/​10.​1097/​IAE.​00000​00000​ 000307 g 17. Port AD, Nolan JG, Siegel NH et al (2021) Combined phaco- vitrectomy provides lower costs and greater area under the curve vision gains than sequential vitrectomy and phacoemulsification. Graefes Arch Clin Exp Ophthalmol 259:45–52. https://​doi.​org/​10.​ 1007/​s00417-​020-​04877-4 25. Mora P, Favilla S, Calzetti G et al (2021) Parsplana vitrectomy alone versus parsplana vitrectomy combined with phacoemulsifi‑ cation for the treatment of rhegmatogenous retinal detachment: a randomized study. BMC Ophthalmol 21:196. Declarations https://​doi.​org/​10.​ 1186/​s12886-​021-​01954-y 18. Antaki F, Milad D, Javidi S et al (2020) Vitreoretinal surgery in the post-lockdown era: making the case for combined phacovit‑ rectomy. Clin Ophthalmol 14:2307–2309. https://​doi.​org/​10.​2147/​ OPTH.​S2709​34 26. Farahvash A, Popovic MM, Eshtiaghi A et al (2021) Combined versus sequential phacoemulsification and pars plana vitrectomy: a meta-analysis. Ophthalmol Retina. https://​doi.​org/​10.​1016/j.​oret.​ 2021.​01.​004 19. Loukovaara S, Haukka J (2018) Repair of primary RRD—compar‑ ing pars plana vitrectomy procedure with combined phacovitrec‑ tomy with standard foldable intraocular lens implantation. Clin Ophthalmol 12:1449–1457. https://​doi.​org/​10.​2147/​OPTH.​S1714​ 51 27. Guber J, Bentivoglio M, Sturm V et al (2019) Combined pars plana vitrectomy with phacoemulsification for rhegmatogenous retinal detachment repair. Clin Ophthalmol 13:1587–1591. https://​ doi.​org/​10.​2147/​OPTH.​S2153​52 20. Tan A, Bertrand-Boiché M, Angioi-Duprez K et al (2021) Out‑ comes of combined phacoemulsification and pars plana vitrec‑ tomy for rhegmatogenous retinal detachment: a comparative study. Retina 41:68–74. https://​doi.​org/​10.​1097/​IAE.​00000​00000​002803 Publisher's Note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. p g 21. Kim Y-K, Woo SJ, Hyon JY et al (2015) Refractive outcomes of combined phacovitrectomy and delayed cataract surgery in retinal 1 3
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A Metagenomic Approach to Evaluating Surface Water Quality in Haiti
International journal of environmental research and public health/International journal of environmental research and public health
2,018
cc-by
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Received: 8 August 2018; Accepted: 4 October 2018; Published: 10 October 2018 Abstract: The cholera epidemic that occurred in Haiti post-earthquake in 2010 has resulted in over 9000 deaths during the past eight years. Currently, morbidity and mortality rates for cholera have declined, but cholera cases still occur on a daily basis. One continuing issue is an inability to accurately predict and identify when cholera outbreaks might occur. To explore this surveillance gap, a metagenomic approach employing environmental samples was taken. In this study, surface water samples were collected at two time points from several sites near the original epicenter of the cholera outbreak in the Central Plateau of Haiti. These samples underwent whole genome sequencing and subsequent metagenomic analysis to characterize the microbial community of bacteria, fungi, protists, and viruses, and to identify antibiotic resistance and virulence associated genes. Replicates from sites were analyzed by principle components analysis, and distinct genomic profiles were obtained for each site. Cholera toxin converting phage was detected at one site, and Shiga toxin converting phages at several sites. Members of the Acinetobacter family were frequently detected in samples, including members implicated in waterborne diseases. These results indicate a metagenomic approach to evaluating water samples can be useful for source tracking and the surveillance of pathogens such as Vibrio cholerae over time, as well as for monitoring virulence factors such as cholera toxin. Keywords: cholera; metagenomic analysis; bioinformatics; whole genome sequencing; principle components analysis; water quality; environmental sampling; Haiti International Journal of Environmental Research and Public Health A Metagenomic Approach to Evaluating Surface Water Quality in Haiti Monika A. Roy 1,2, Jean M. Arnaud 1, Paul M. Jasmin 3, Steve Hamner 1, Nur A. Hasan 4,5, Rita R. Colwell 4,5 and Timothy E. Ford 1,* 1 Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA; monikaroy@umass.edu (M.A.R.); jarnaud@umass.edu (J.M.A.); shamner@montana.edu (S.H.) j 2 Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA 01003, USA 3 Equipes mobiles d’intervention rapide (EMIRA) du Ministère de la Santé Publique et de la Population (MSPP), Hinche HT 5111, Haiti; drpjasmin@gmail.com 2 Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA 01003, USA 3 Equipes mobiles d’intervention rapide (EMIRA) du Ministère de la Santé Publique et de la Population (MSPP), Hinche HT 5111, Haiti; drpjasmin@gmail.com pj g 4 CosmosID Inc., 1600 East Gude Drive, Rockville, MD 20850, USA; nur.hasan@cosmosid.com (N.A.H.); rcolwell@umiacs.umd.edu (R.R.C.) 4 CosmosID Inc., 1600 East Gude Drive, Rockville, MD 20850, USA; nur.hasan@cosmosid.com (N.A.H.); rcolwell@umiacs.umd.edu (R.R.C.) 5 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA * Correspondence: teford@umass.edu; Tel.: +1-413-545-3214 1. Introduction The emergence of cholera in Haiti, following the severe (7.0 Richter scale) earthquake south of Port-au-Prince in 2010, resulted in 817,000 cases of illness and more than 9749 deaths through 2016, according to the Haitian Ministry of Public Health and Population (MSPP) [1]. As a result of a coordinated response between the MSPP, the U.S. Centers for Disease Control and Prevention (CDC), the United Nations Children’s Fund (UNICEF), the Pan American Health Organization (PAHO), the World Health Organization (WHO), and other local and international health partners, external financial resources were raised to strengthen Haiti’s disease surveillance and response Int. J. Environ. Res. Public Health 2018, 15, 2211; doi:10.3390/ijerph15102211 www.mdpi.com/journal/ijerph www.mdpi.com/journal/ijerph Int. J. Environ. Res. Public Health 2018, 15, 2211 2 of 16 systems. While these efforts made tremendous strides in the country, the lack of continual funding for surveillance activities threatens progress towards eliminating diseases like cholera [2]. Cholera infection is caused by the bacterium Vibrio cholerae and is characterized by acute diarrhea and vomiting; the illness can range from subtle to severe, leading to death [3]. Cholera is a waterborne disease, with poor water and sanitation infrastructure a primary risk factor for transmission [4]. A significant correlation has also been found between rainfall and cholera incidence in Haiti, with a 4–7-day lag time [5]. Cholera has declined since its initial outbreak, with a total of 13,681 cases and 159 deaths in 2017 [1]. However, with declining surveillance funding, continued poor water quality, failing infrastructure, and future hurricane risks, a need exists for reliable and low-cost diagnostics for improving surveillance, prediction, and response to outbreaks using measurable environmental parameters [6,7]. Diagnostics tools for environmental sampling are being tested to shorten the time and reduce the number of expert personnel needed to determine cholera presence in a limited resource setting [8]. Several rapid diagnostic tests (RDTs) have been developed for cholera detection including the Crystal VC Dipstick, Artron V. cholerae O1 and O139 Combo Test, and the SD Bioline Cholera Ag O1/O139 RDT. These tests have significant performance variation, suggesting that they may be useful for initial surveillance in low resource settings, but that improvements are needed prior to their use in clinical settings [9]. A relatively inexpensive membrane filtration plate count technique has also been developed and tested that accurately quantifies V. 1. Introduction cholerae in a mixed-culture setting [10], however, this method requires 24 hours of incubation time in specific laboratory settings. q p y g PCR methods have provided useful information for detecting cholera at specific locations post-outbreak [11–13]. However, whole genome shotgun sequencing combined with advanced bioinformatic analysis offers a method to examine the genetic diversity of environmental samples and to characterize sites in terms of relative abundance of bacteria, fungi, protists, viruses, antimicrobial resistance (AMR), and virulence associated genes [14]. Metagenomic approaches are now being used to assess and characterize the microbiota and bacterial communities in diverse waters, ranging from Amazonian rivers to water sources in urban environments [15–17]. This method provides a way to not only identify factors related to cholera presence, but also provide characterization of factors related to other waterborne diseases present in Haiti. To our knowledge, only limited environmental monitoring of surface waters is currently conducted in Haiti. The University of Florida has established environmental monitoring sites in the Gressier/Leogane region of Haiti, west of Port-au-Prince, but the focus of sampling is only on monitoring environmental reservoirs of toxigenic V. cholerae 01 [11,13]. In the Artibonite region of the Central Plateau, focus has also been on the isolation of V. cholerae, where basic water quality parameters have been collected from the Artibonite River and tributaries. The results suggest high levels of E. coli, with a geometric mean of 500 CFU/100 mL (this included some samples taken from rivers outside the Artibonite region), with 74% of samples considered in the high risk category according to WHO guidelines [18]. Continuous water quality monitoring is needed in Haiti for public health purposes in assessing the epidemiology of waterborne diseases like cholera [19]. While still used on a point sampling basis, the use of metagenomics provides a powerful tool that yields more profiling information beyond V. cholerae presence, and has the potential to be used in a clinical setting. At present, hand-held sequencing technologies, such as the Oxford Nanopore Technologies handheld MinION, are expensive, at around $1000 per sample for reagents and a single flow cell. However, the potential for multiplexing up to 12 samples could bring the cost down to approximately $80 per sample [20]. Advances in barcoding chemistry [21], and the purchase of flow cells in bulk, also have the potential to further reduce per sample costs. 1. Introduction Although bioinformatics technologies are improving, further optimization is necessary before routine diagnostics for field use are possible. However, the advances made thus far make this technology comparable to the cost of bench-top instruments, but in a handheld, mobile device. With the 3 of 16 Int. J. Environ. Res. Public Health 2018, 15, 2211 development of handheld DNA sequencing technologies that make such sample analysis in remote locations and in as little as a few hours possible, this type of sample collection and metagenomic analysis could soon be conducted on a local scale in Haiti [22]. This paper explores the utility of using a metagenomic approach to evaluate surface water quality, and provides data on the relative abundance of pathogens from several sites in Haiti. 2.1. Water Sampling and Shipping Triplicate water samples were collected between 5–6 January 2018 from five surface water sites in the Central Plateau region of Haiti: Maïssade, Hinche, Thomonde, Mirebalais, and Lascahobas (Figure 1, Table 1). Information on elevation, average temperature, and average rainfall for January and July at largely populated communities close to these sampling sites is provided in Table 2. This reflects the significant seasonal differences in rainfall between these sampling dates. These sites were chosen based on ease of sampling, while at the same time targeting areas with the highest level of cholera incidence as reported by the MSPP. These sites are close to river crossings on roads linking the major towns in the Central Plateau region, including the Rivière La Thème in Mirebalais, close to the first reported cholera cases in 2010. Due to their proximity to river crossings, these sites are heavily used by communities for bathing, washing clothes and dishes, and other household activities where water could be inadvertently consumed. This may be a particular risk for young children and infants. Samples had also been collected the previous summer, between 24–28 July 2017, but were not replicated or collected from the exact same locations, though they were collected from the same region. They are included to provide a seasonal comparison. Figure 1. Sampling sites in the Central Plateau of Haiti (Mapdata©2018 Google). A blue star denotes the first cluster of cholera cases just south of Mirebalais [23]. Sites labelled 1 through 5a were sampled in triplicate in January 2018. Single samples were taken from sites labelled 6 and 7 in July 2017. Sites 1, 4 and 5b were also sampled in July 2017. Figure 1. Sampling sites in the Central Plateau of Haiti (Mapdata©2018 Google). A blue star denotes the first cluster of cholera cases just south of Mirebalais [23]. Sites labelled 1 through 5a were sampled in triplicate in January 2018. Single samples were taken from sites labelled 6 and 7 in July 2017. Sites 1, 4 and 5b were also sampled in July 2017. 4 of 16 Int. J. Environ. Res. Public Health 2018, 15, 2211 Table 1. Location and description of sampling sites. Site (Approximate Position on Map) Coordinates Description January 2018 1. Rio Frio, Maïssade 19.1703 N 72.1353 W Small tadpoles and fishes were visible in this water. Water depth was 2–3 feet and the water was very turbid. 2. 2.1. Water Sampling and Shipping Rivière Guayamouc, Hinche 19.1494 N 72.0092 W Trash piles and foraging pigs were present on the river banks. The water was extremely turbid. 3. Rivière de Thomonde, Thomonde 19.0082 N 71.9520 W Many people washed clothes and bathed at this site. The water was turbid and sediment a unique silver gray color. 4. Rivière La Thème, Mirebalais 18.8356 N 72.1071 W The water was turbid and served as irrigation for the sweet potato field nearby. Algae growth was present on the river banks. Trash bags and other plastics were floating on the sides of the river. 5a. Rivière Lascahobas, Lascahobas 18.8308 N 71.9451 W The water was clear with a visible rocky bed. The sample was easily filtered. However, the river bank contained numerous plastic waste products. July 2017 (samples collected during this time were not replicated) 1. Rio Frio, Maïssade 19.1703 N 72.1353 W People crossed their vehicles here, bathed, and washed clothes. 3. Rivière de Thomonde, Thomonde 19.0082 N 71.9520 W The water was clear and this site was upriver of considerable activity, but was also used for bathing and washing clothes. 4. Rivière La Thème, Mirebalais 18.8356 N 72.1071 W This site contained the most contaminated water comparatively. There was open defecation on the side of the river, trash piles, and many people washing clothes. 5b. Tributary of Rivière la Peigne, Lascahobas 18.8204 N 71.9464 W Water from this site came from a groundwater spring through a water pipe out of the side of a mountain. Many people were bathing near the pipe, with clothes washing below the sampling point. 6. Rivière Artibonite, below the Lac de Péligre 18.9026 N 72.0604 W Water was collected about a mile below the dam where it was released at the bottom of the reservoir. 7. Rivière Cabestor, Cabestor 18.8689 N 72.0011 W Water from the Rivière Cabestor mixed with water from a small creek near the MFH birthing center. At this sampling point, vehicles crossed the river, and people bathed and washed clothes. Table 1. Location and description of sampling sites. At each of the five sites for the January 2018 sampling, 250 mL water samples were collected and filtered directly on-site in triplicate using SterivexTM filters (0.22 µm pore size, polyethersulfone sterile membranes; Millipore® Sigma, St. Louis, MO, USA). These samples were collected approximately 10 m apart to minimize sediment disturbance. 2.2. Metagenomic Sequencing and Bioinformatics Analysis Metagenomic DNA was extracted from the filters using a DNeasy PowerWater Sterivex Kit (QIAGEN) following the manufacturer’s guidelines. Concentrations of the metagenomic DNA were measured using a Qubit Fluorometric Quantitation (Thermo Fisher Scientific, Waltham, MA, USA). Most samples yielded around 1–4 ng/µL genomic DNA (Table S1). Fragment libraries were constructed from 100 ng DNA (except for one sample with low yield where 15 ng DNA was used) using the Thermo Fisher IonXpress Plus Fragment Library kit (Thermo Fisher Scientific) according to the recommended manufacturer instructions. Genomic DNA libraries were quantified by qPCR and then sequenced on an Ion S5 XL Semiconductor Sequencer (Ion Torrent, Thermo Fisher Scientific) to generate 200 bp sequence reads. Each sample was sequenced with an average of 17M sequence read depth. General Sequencing Statistics of all samples, as well as Mean Sequence Quality distribution as measured by MultiQC [25] are illustrated by Figures S1 and S2, and Table S1. As the mean quality value across each base position in the read was always above quality score 17 for at least 80% of the read length (i.e., probability of correct base call ~98%), reads were not subjected to quality trimming. Raw genomic sequences were analyzed by CosmosID metagenomic software [26–31], including principle components analysis (PCA), to reveal microbial community composition, antibiotic resistance markers, and virulence gene pools. y p g p Briefly, the CosmosID platform utilizes high performance data mining algorithms and highly curated dynamic comparator databases (GenBook®) that rapidly disambiguate hundreds of millions of short reads of a metagenomic sequence into the discrete microbial genomes and genes engendering the identified sequences without the need for sequence assembly. Similarly, the community resistome and virulome, and the collection of antibiotic resistance and virulence associated genes, respectively, in the microbiome were also identified by querying the unassembled sequence reads against the CosmosID curated antibiotic resistance and virulence associated gene database. The GeneBook database is composed of over 150,000 microbial genomes and gene sequences representing bacterial, viruses, protists, and fungi, as well as antibiotic resistant and virulence associated genes. The curated databases provide extremely fine resolution in identification, discrimination of pathogens from ‘near neighbors’, and accurate measurement of relative abundance. Results are either reported as “filtered”—which is based on internal statistical scores that indicate the organism or gene is most likely present, or “unfiltered”—where further validation is recommended to confirm their presence (CosmosID documentation https://app.cosmosid.com/docs). 2.2. Metagenomic Sequencing and Bioinformatics Analysis Data are deposited in the NCBI Sequence Read Archive (SRA) database with accession number SRP158812. The resultant taxa abundance tables were used to calculate observed species richness, alpha diversity indices, and beta diversity distance matrices (data not shown for beta diversity). PCA was performed to cluster samples based on abundance using the covariance matrix of normalized data as the measure of similarity. 3.1. Environmental Sampling Sampling sites were selected as previously described, and are depicted in Figure 1. Sampling sites from January 2018 are labelled 1 through 5a, and sampling sites from the previous summer in July 2017 are labelled 1, 3, 4, 5b, 6, and 7. The location and description of each site are described in Table 1. Syringe cartridges were used to collect water samples to filter through Sterivex filters at all sites during both time points. 2.1. Water Sampling and Shipping Samples were placed on ice and transported directly to Port-au-Prince for shipping to the U.S. The shipping company, Deutsche Post DHL Group (DHL), required a letter from a Haitian organization before shipping the samples. This caused extensive delays until a letter was obtained from a local partner organization, Midwives for Haiti (MFH), based in Hinche, Haiti on 17 January 2018. The samples remained frozen during this waiting period. Regrettably, the samples were unable to be shipped with ice blocks. They arrived at CosmosID in a thawed state six days later, when they were immediately frozen prior to downstream processing and analysis. For samples collected the previous summer in July 2017, several ~100 mL samples were collected at a selection of sites, and these samples were transported over a 2-day period at room temperature to the U.S., whereby they were immediately frozen prior to downstream processing and analysis. Table 2. Elevation, average temperature, and average rainfall for January and July at largely populated communities close to the sampling sites [24]. Site Location Elevation (Meters) Average Temperature (◦C) Average Precipitation (mm) January 2018 July 2017 January 2018 July 2017 Maïssade 270 22.4 25.8 30.8 151 Hinche 238 21.6 25 28.1 155.2 Thomonde 284 Monthly data not available for this site, ~10 miles from Hinche Mirebalais 120 22.2 25.7 23.5 150.3 Lascahobas 219 20.3 23.7 29.5 136.3 Cabestor 300 Monthly data not available on this site, <10 miles from Lascahobas Lac de Péligre 175 Monthly data not available for these sites (both for above and below the Lac de Péligre) Table 2. Elevation, average temperature, and average rainfall for January and July at largely populated communities close to the sampling sites [24]. Int. J. Environ. Res. Public Health 2018, 15, 2211 5 of 16 2.2. Metagenomic Sequencing and Bioinformatics Analysis 3.2. Sequencing Analysis Sequence analysis of DNA extracted from the samples revealed a wide diversity of bacteria, with over a thousand strains of sequences at each site. Figure 2 depicts a Krona [32] visualization of all bacteria detected in January 2018 samples across the five sites. The predominant phylum of bacteria was the gram-negative Proteobacteria at 84% of total bacterial diversity. This phylum includes a wide variety of pathogens, and in this analysis Alphaproteobacteria comprised 41%, Betaproteobacteria Int. J. Environ. Res. Public Health 2018, 15, 2211 6 of 16 11%, and Gammaproteobacteria 44% of Proteobacteria. Within the Gammaproteobacteria class, the Pseudomonadales order comprised 81% (30% of total bacterial diversity), of which 92% was of the Acinetobacter genus (27% of total bacterial diversity). The Gammaproteobacteria class also includes Vibrio cholerae in the Vibrionales order. Among the five sampling sites from the January 2018 time point, mean species diversity was calculated to represent alpha diversity (Figure 3). All sites demonstrated similar levels of diversity, however, replicates from the Lascahobas River site showed the most variability. Figure 2. Krona visualization. Total bacterial diversity, representing gamma diversity, among all samples from the January 2018 time point. Figure 2. Krona visualization. Total bacterial diversity, representing gamma diversity, among all samples from the January 2018 time point. Figure 3. Choa1 alpha diversity. All three replicates of each site are represented by a box plot. Raw data used to generate the box plots are presented in Supplemental Table S2. Figure 3. Choa1 alpha diversity. All three replicates of each site are represented by a box plot. Raw data used to generate the box plots are presented in Supplemental Table S2. 7 of 16 Int. J. Environ. Res. Public Health 2018, 15, 2211 Each site also contained a relatively unique bacterial composition, or fingerprint, demonstrated by PCA performed on data gathered for all sites across the two sampling time points (Figure 4), and for the January 2018 sites alone (Figure 5). Supplemental Figure S3 shows dominant bacteria identified for all sites in the January 2018 sampling. Several Acinetobacter spp. appear in all sites, particularly the Lascahobas site where they comprise 10 of the top 12 bacterial genera detected in terms of relative abundance. In contrast, the other 4 sites had more bacterial diversity and Acinetobacter spp. comprised about 5 of the top 11–13 bacteria detected. Figure 4. 3.2. Sequencing Analysis Principle components analysis (PCA) of relative abundance of bacteria at all sites, including July 2017 samples, which were not replicated (* Site ~1 mile below Lac de Péligre dam). Figure 5. PCA of relative abundance of bacteria from replicate samples collected in January 2018. The relative abundance of the E. coli and V. cholerae bacteria, the V. cholerae Intl1 virule ne, and the Stx2-converting phage was quantified across replicates for each of the five sites J 2018 li i d d f h it i th J l 2017 li i d Th d Figure 4. Principle components analysis (PCA) of relative abundance of bacteria at all sites, including July 2017 samples, which were not replicated (* Site ~1 mile below Lac de Péligre dam). Figure 4. Principle components analysis (PCA) of relative abundance of bacteria at all sites, including July 2017 samples, which were not replicated (* Site ~1 mile below Lac de Péligre dam). Figure 5. PCA of relative abundance of bacteria from replicate samples collected in January 2018. Figure 5. PCA of relative abundance of bacteria from replicate samples collected in January 2018 The relative abundance of the E. coli and V. cholerae bacteria, the V. cholerae Intl1 virulence gene, and the Stx2-converting phage was quantified across replicates for each of the five sites in the January 2018 sampling period, and for each site in the July 2017 sampling period. These data are presented in Table 3. For both January 2018 and July 2017 sampling, E. coli was present in all replicates, although generally at low abundance. V. cholerae Intl1 was present in most replicates but with a wider range of abundance; of note, the relative abundance of Intl1 in Maïssade samples in July 2017 was much higher at 17.65% than samples collected in January 2018, all below 5.0%. Replicates for Mirebalais were all consistently higher for relative abundance of Intl1, above 7.0%, but one replicate The relative abundance of the E. coli and V. cholerae bacteria, the V. cholerae Intl1 virulence gene, and the Stx2-converting phage was quantified across replicates for each of the five sites in the January 2018 sampling period, and for each site in the July 2017 sampling period. These data are presented in Table 3. For both January 2018 and July 2017 sampling, E. coli was present in all replicates, although generally at low abundance. V. 3.2. Sequencing Analysis cholerae Intl1 was present in most replicates but with a wider range of abundance; of note, the relative abundance of Intl1 in Maïssade samples in July 2017 was much higher at 17.65% than samples collected in January 2018, all below 5.0%. Replicates for Mirebalais were all consistently higher for relative abundance of Intl1, above 7.0%, but one replicate Int. J. Environ. Res. Public Health 2018, 15, 2211 8 of 16 exhibited much higher abundance at 18.45%. V. cholerae was detected in some replicates across all sites and sampling periods, but at very low relative abundance, with the highest detection level of 0.02%. Stx2-converting phage was also detected in some replicates across all sites, but ranging from not detected to 9.82% relative abundance. Table 3. Relative abundance of sequences characterizing Escherichia coli, V. cholerae, V. cholerae Intl1 converting phage and Stx2 (Shiga toxin gene) converting phage. Site Replicate January 2018 E. coli V. cholerae V. cholerae Intl1 Stx2-converting phage Maïssade 1 0.12 ND 1.61 ND 2 0.01 <0.01 4.91 8.45 3 <0.01 ND ND 0.70 Hinche 1 0.04 ND 2.69 0.22 2 <0.01 <0.01 4.8 ND 3 <0.01 ND 0.11 ND Thomonde 1 0.03 <0.01 6.93 ND 2 0.01 <0.01 6.05 0.52 3 0.03 0.02 3.52 7.11 Mirebalais 1 <0.01 ND 7.59 4.31 2 <0.01 ND 18.45 9.82 3 0.01 <0.01 7.55 7.62 Lascahobas 1 0.19 <0.01 2.13 1.78 2 0.06 * ND 6.40 0.11 3 0.02 ND ND 0.36 July 2017 Maïssade 1 1.11 <0.01 ** 17.65 ND Mirebalais 1 0.16 <0.01 *** 7.18 ND Lascahobas 1 3.57 <0.01 *** 3.09 0.77 Below Péligre 1 0.14 ND ND ND Cabestor 1 0.34 ND ND ND Above Péligre 1 0.08 <0.01 *** 3.31 ND Notes: * E. coli O157:H7; ** V. cholerae RC385; *** V. cholerae HE-45; ND—not detected. All data are presented as percentages. Table 3. Relative abundance of sequences characterizing Escherichia coli, V. cholerae, V. cholerae Intl1 converting phage and Stx2 (Shiga toxin gene) converting phage. Supplemental Figures S4–S6 provide filtered sequence data on viruses, virulence factors and AMR genes for each site. Filtered data is used to allow these figures to be manageable. In the case of viruses, filtered data only detected viruses at 9 of the 15 sample sites, so a relative view is not possible (Figure S4). However, a large number of viruses were detected at lower confidence in the unfiltered data. 3.2. Sequencing Analysis Dominant fungi include Onygenales spp., Epichloe sylvatica, Puccinia arachidis, Clavaria fumosa, Lentinus polychrous, and at two of the Lascahobas sites Candida parapsilosis (1.92% and 2.39% abundance), Enterocytozoon bieneusi at one Hinche River site (2.52%) and two Lascahobas sites (1.98% and 2.85%), and Anncaliia algerae at two Hinche River sites (4.58% and 2.78%), one Mirebalais site (2.76%), and two Lascahobas sites (4.48% and 4.67%). Unfiltered results also identify Candida albicans, Alspergillus fumigates, and Pneumocystis jirovecii. Protist sequences are dominated by Paramecium biaurelia and Pseudoperonospora cubensis. However, Acanthamoeba polyphaga is present at one Hinche and one Mirebelais site (13.37 and 30.72%, respectively). Also present at almost all sites and highest at one Hinche River site (4.15%) is Plasmodium falciparum. Unfiltered data (not shown) also suggests sequence evidence for Entamoeba spp., Toxoplasma gondii, and Trypanosome congolense. Supplemental Figures S7 and S8 present information on fungi and protists. Dominant fungi include Onygenales spp., Epichloe sylvatica, Puccinia arachidis, Clavaria fumosa, Lentinus polychrous, and at two of the Lascahobas sites Candida parapsilosis (1.92% and 2.39% abundance), Enterocytozoon bieneusi at one Hinche River site (2.52%) and two Lascahobas sites (1.98% and 2.85%), and Anncaliia algerae at two Hinche River sites (4.58% and 2.78%), one Mirebalais site (2.76%), and two Lascahobas sites (4.48% and 4.67%). Unfiltered results also identify Candida albicans, Alspergillus fumigates, and Pneumocystis jirovecii. Protist sequences are dominated by Paramecium biaurelia and Pseudoperonospora cubensis. However, Acanthamoeba polyphaga is present at one Hinche and one Mirebelais site (13.37 and 30.72%, respectively). Also present at almost all sites and highest at one Hinche River site (4.15%) is Plasmodium falciparum. Unfiltered data (not shown) also suggests sequence evidence for Entamoeba spp., Toxoplasma gondii, and Trypanosome congolense. 4. Discussion The data presented in this study provide relative abundances of bacteria, fungi, protists, and viruses, as well as identify antibiotic resistance and virulence associated genes for several sites in samples collected in Haiti over two time points, using a metagenomic approach. 3.2. Sequencing Analysis Viruses were dominated by phages and associated with a wide range of potentially pathogenic bacteria. In the filtered sample set, Enterobacteria phages were dominant, with specific Escherichia and Salmonella phages present. In unfiltered data, additional phages were identified and associated with bacteria such as Aeromonas, Acetobacter, Arthrobacter, Bacillus, Bordatella, Burkholdaria, Clostridium, Cronobacter, Haemophilus, Mycobacteria, Pseudomonas, Shigella, Staphylococcus, Streptococcus, Vibrio, and Yersinia—all genera with important human pathogenic species. In addition, human mastadenovirus was detected. Due to the number of virulence factors detected, only the top factors representing 80% of total abundance are presented in Supplemental Figure S5. Virulence factors are dominated by those associated with the important pathogens, Klebsiella pneumonia, Proteus mirabilis, Pseudomonas aeruginosa, V. cholerae, and E. coli. Other pathogen-associated virulence factors are also present. Antimicrobial resistance genes are dominated by those conveying aminoglycoside, sulphonamide, beta-lactam, and in some cases tetracycline resistance (Figure S6). Int. J. Environ. Res. Public Health 2018, 15, 2211 9 of 16 Information on viruses, virulence factors, and AMR genes present in the most contaminated replicate of samples collected from the Thomonde site are described in Table 4. Notable is detection of Stx2-converting phage and Vibrio phage CTX. Table 4. Selection of some of the more dominant viruses and virulence factors detected in samples collected at the Thomonde site, replicate #3 from January 2018 sampling (filtered data, * indicates V. cholerae virulence factors from unfiltered data that require further confirmation). All classes of AMR genes detected in filtered data from this sample are also reported. Viruses and Bacteriophages Virulence Associated Genes Classes of AMR Genes Detected Enterobacteria phage HK630 Klebsiella pneumoniae: orf6, GI 42543951, tnpA Aminoglycosides: aadA, aadA5, aadA7, aadA16, aadA10, aac1, aac3 Ia, aph6 Id, aph, ant2” Ia Siphoviridae_u_s Enterobacter aerogenes: traM, tniB, ssb, korC Sulphonamide sul2 Escherichia virus P1 V. cholerae: intI1, GI 42567126 *, VCA0118 *, CARB-6 * Trimethoprim: dfrC Viruses_u_s Serratia marcescens: orfA, intI3 Beta-lactam: blaOXA, blaAIM Stx2-converting phage 1717 E. coli: qacEdelta1, aphA7 Macrolide: mphE, ermA Human mastadenovirus C Pseudomonas aeruginosa: intI1, accC1, aadA6 Phenicol: dha1 Enterobacteria phage BP-4795 Salmonella Infantis: tnpR G7cvirus_u_s Pseudomonas putida: qacEdelta1 Myoviridae_u_s Proteus mirabilis: sul1 Vibrio phage CTX Morganella morganii: oxa-2 Supplemental Figures S7 and S8 present information on fungi and protists. 4.3. Bacterial Diversity Of all replicates in the January 2018 sampling, the majority of bacteria detected originated from either the Alphaproteobacteria and Gammaproteobacteria classes (Figure 2). From the Gammaproteobacteria class, two bacterial genera of concern that were detected were Legionella and Acinetobacter. The total relative abundance of the family Legionellaceae was a low 1%. In contrast, the total relative abundance of Acinetobacter spp. was much higher, 27%, and Acinetobacter spp. were detected the most frequently in all five sites from the January 2018 samples, particularly from the Lascahobas samples (Figure S3), though this site also showed the largest variability among replicates (Figure 3). Acinetobacter spp. are nosocomial pathogens that survive for extended periods in water, including in drinking water [36], and are associated with multiple antibiotic resistance and a number of clinical outcomes, including pneumonia, wounds, and respiratory and GI tract infections [37–39]. Additionally, the species Acinetobacter baumannii is implicated in ~80% of hospital acquired Acinetobacter infections [40] and in this study comprised 5% of Acinetobacter species and 1% of total relative abundance (Figure 2). Again, it should be noted that these relative abundances may have been affected by the failure of the cold chain. In samples collected in July 2017, two non-toxigenic (environmental) strains of V. cholerae were detected (Table 3); the Haitian strain, HE-45, was detected at the La Thème, Lascahobas site and at the site above the Lac de Péligre, and the Chesapeake Bay environmental isolate, RC385, was detected at the Maïssade site. When virulence genes were examined, the V. cholerae intI1 gene was identified at these sites. The gene intI1 is included in a class of resistance integrons implicated in the spread of antibiotic resistance via horizontal gene transfer [41]. In the July 2017 sampling sites, intI1 was not detected in the absence of V. cholerae. In contrast, V. cholerae intl1 gene was detected in almost 90% of samples collected in January 2018, although V. cholerae was detected in less than 50% of the samples, and only at the species level. Although the focus of most prior studies has been on V. cholerae, one metagenomic study has been conducted to the southwest of Hinche, primarily in the region of the Rivière Hinquitte, a tributary of the Rivière Guayamouc [42]. This study examined bacterial diversity in source and point-of-use water. Consistent with our data, Acinetobacter was a dominant genus. 4.1. Limitations We are aware of the limitations of this study based on the failure of the cold chain due to the unanticipated refusal of the shipping company in Haiti to ship ice packs. For future studies, we are working with colleagues in Haiti for DNA extraction and preservation with DMSO-EDTA-salt (DESS) [33] prior to shipping. However, in this study the possibility of both growth and inhibition of select species call into question our measurements of relative abundance. In past work, members of the research team have had no problems recovering and isolating specific pathogens, including V. cholerae and enterohemorrhagic and enterotoxigenic E. coli (EHEC and EPEC) strains, from filters shipped wet from India [34]. So, even though our current work may not be quantitative, we believe the qualitative findings on specific pathogens are significant. Despite these limitations, several interesting trends are worth noting. The Mirebalais Rivière La Thème site showed greatest consistency in replicates, as demonstrated by PCA (Figures 4 and 5). This site is located near the epicenter of the 2010 cholera outbreak [23]. Other sites showed greater diversity among replicates, which may reflect the heterogeneity of the river samples collected at multi-use sites. Overall, PCA analysis was able to distinguish the five sites sampled in January 2018, Int. J. Environ. Res. Public Health 2018, 15, 2211 10 of 16 and demonstrated that it was possible to characterize the sites in terms of bacterial community structure. This finding is helpful for source tracking of groups of pathogens and determining potential sources of contamination for future studies. 4.2. Seasonal Differences As shown in Figure 4, there is a clear difference between results obtained in July 2017 and in January 2018, even though some samples were collected at the same sites. Samples collected in July 2017 demonstrated a different bacterial community composition compared to samples from any of the sites sampled in January 2018. This may be due to seasonal differences between those two time points, with a drier period occurring in January, compared to higher average temperatures and higher rainfall in July [35]. Sites sampled in July 2017 are closely clustered except for the site below the Lac de Péligre dam, which is an outlier. This was also the site with lowest diversity relative to other samples collected in July 2017. Since water is released from the bottom of the reservoir, it could be expected that this site would have a different microbial composition compared to the other sampling sites. 4.3. Bacterial Diversity Surprisingly, Klebsiella was the most dominant genus found in their study, yet was only present at low relative abundance in our study in unfiltered data (0.03%; 0.01% from the Rivière Guayamouc site). However, Klebsiella pneumoniae virulence genes were dominant at most of our sites. The majority of other dominant bacterial genera found in the two river water sources sampled in their study were also present at our sites, but also at low relative abundance (<0.2%). These findings could reflect the proximity of water sources used for drinking to the consumers, and hence to minimal sanitation, whereas our samples were taken at larger river sites with potentially greater input from agricultural and other sources. For example, Int. J. Environ. Res. Public Health 2018, 15, 2211 11 of 16 dominance of Sphingobium yanoikuyae (Figure S3), often associated with PAH-contaminated soils [43], at the Mirebalais Rivière La Thème site, as well as the presence of predatory Bacteriovorax spp. [44], will change the bacterial community structure in our study compared to the pathogen-dominated genera in the source and point-of-use study [42]. The finding of dominance of Klebsiella pneumoniae virulence genes in our samples, in the absence of much evidence for the bacterium itself, speaks to the importance of a complete metagenomic approach for potential health risk assessments from environmental samples. While there is evidence for environmental reservoirs of virulence factors in the absence of clinically important pathogens [45], the presence of these factors should not be ignored due to rapid dissemination through horizontal gene transfer, and further studies in this area are warranted [46]. 4.4. Phage and Virulence Factor Diversity Almost all the bacterial pathogens reflected by the presence of phages were detected at low relative abundance in the filtered data set with the exception of Cronobacter spp., Haemophilus spp. Shigella spp., and Vibrio spp. Cronobacter spp., Shigella spp., and Vibrio spp., were detected in the unfiltered dataset, but Haemophilus spp. was not detected, which is surprising given that the Haemophilus phage, HP1 was detected at almost all sites in unfiltered data, and as high as 9.1% relative abundance at one of the Hinche River sites. Important human pathogens reflected by identified virulence factors were also present in the filtered dataset, including Klebsiella pneumonia, Pseudomonas aeruginosa, and E. coli, and in the unfiltered dataset, V. cholerae. However, Proteus mirabilis was not detected, although this opportunistic pathogen is commonly found in soil and water [47]. 4.5. Fungal and Protozoan Diversity Fungi of greatest concern include Onygenales spp., which dominated most of the samples and includes a number of emerging human pathogens [48], Candida parapsilosis [49], Enterocytozoon bieneusi [50], and Anncaliia algerae [51]. Unfiltered results also suggest the presence of Candida albicans, Alspergillus fumigates and Pneumocystis jirovecii (the causative organism of Pneumocystis pneumonia). All of these pathogenic fungi are of concern, especially in Haiti where HIV infection rates remain very high, and have been shown to be a risk factor in susceptibility to cholera in Haiti [52]. Some pathogenic protozoan sequences are also of concern, including sequences representative of Acanthamoeba polyphaga at high relative abundance at two sites and the malaria parasite, Plasmodium falciparum at almost all sites. Presence of potentially pathogenic Entamoeba spp., and Toxoplasma gondii in unfiltered data is also of concern. Although not a human pathogen, the finding in unfiltered data of Trypanosome congolense, a major cause of African animal trypanosomosis, has implications for a subsistence agricultural economy [53]. 4.6. Cholera and EHEC Concerns The cholera toxin (CTX) converting phage is associated with cholera toxin production by V. cholerae and was detected in one sample collected at the Thomonde site (Table 4). Detection of the V. cholerae intI1 gene and the CTX converting phage are indicative of a potential risk for enhanced cholera toxin production by these strains. While waters sampled in this study were not sources used for drinking water, many of them are heavily used for bathing, washing clothes, and for other household activities where water could be inadvertently consumed. Shiga toxin converting phages were detected at most of the sites (~70%) sampled in January 2018 (Table 3). These phages are important in Shiga toxin production by EHEC, a pathogen that can cause disease with high mortality risk [54]. Although all sites were positive for E. coli at low relative abundance during the January 2018 sampling, only one was definitively identified as EHEC from the Lascahobas site at 0.06% relative abundance, where the Shiga toxin-producing EHEC serotype 0157:H7 was also detected. All sites sampled in July 2017 were positive for E. coli, at generally higher relative abundance than January samples, with the highest relative abundance of 3.48% at Int. J. Environ. Res. Public Health 2018, 15, 2211 12 of 16 the Lascahobas site, most likely reflecting the relatively higher temperatures and surface runoff from significant rainfall that had occurred over an extended period. Predictive models of disease events that combine both environmental parameters with knowledge of the presence of putative pathogens and virulence or antibiotic resistance genes in environmental samples, may be particularly useful in developing preventive strategies against a cholera outbreak. Surveillance efforts, in combination with simple interventions such as bio-sand filters [10] and development of an effective cholera vaccine [55–57] will aid in the elimination of this disease. Once optimized, hand-held sequencing technologies could then potentially be used as diagnostic tools and for source-tracking of pathogens. Overall, cholera surveillance requires multiple methods to gather accurate data in a timely manner for decision-making purposes, but this preliminary research provides an initial context for demonstrating the potential use of metagenomics to identify sources of cholera, track cholera-related genes and bacteriophages, and identify bacterial community fingerprints for different areas in Haiti. 5. Conclusions These preliminary results suggest that sequencing DNA from environmental water samples and subsequently applying metagenomic analysis offers a useful approach to characterize environmental samples collected from heavily used water bodies in Haiti. Toxigenic V. cholerae O1 and O139 strains were not detected in this analysis, consistent with the recent decline in cholera cases, although environmental V. cholerae strains and converting phages for both cholera and Shiga toxins were detected, indicating that a potential disease risk remains for nearby populations. While further sample collection and greater in-depth analysis are needed, the results of this preliminary study provide insight and offer a potential monitoring tool for detecting the re-emergence of toxigenic V. cholerae and other waterborne diseases in the aquatic environment in Haiti. Supplementary Materials: The following are available online at http://www.mdpi.com/1660-4601/15/10/2211/ s1, Figure S1. Mean Sequence Quality distribution representing the number of reads with average quality scores. Figure S2. Sequence Quality Histogram representing the mean quality value across each base position in the read. Figure S3. Top 11–13 most abundant (relative) bacteria for each replicate at the (a) Maïssade, (b) Hinche, (c) Thomonde, (d) Mirebalais, and (e) Lascahobas sites for January 2018 sampling. Figure S4. Filtered data for Viruses. Figure S5. Filtered data for top 80% virulence factors. Figure S6. Filtered data for top 50% AMR. Figure S7. Filtered data for Fungi. Figure S8. Filtered data for Protists. Table S1. DNA concentrations and general sequencing statistics of January 2018 samples measured by MultiQC. Table S2. Choa1 alpha diversity raw data used to generate the box plots for Figure 3. Author Contributions: Conceptualization, T.E.F.; Methodology, N.A.H., R.R.C., and T.E.F.; Software, N.A.H. and R.R.C.; Validation, M.A.R., J.M.A., N.A.H., R.R.C., S.H., P.M.J., and T.E.F.; Formal Analysis, M.A.R., J.M.A., N.A.H., R.R.C., and T.E.F.; Investigation, M.A.R., J.M.A., and P.M.J.; Resources, T.E.F.; Data Curation, N.A.H. and R.R.C.; Writing-Original Draft Preparation, T.E.F. and M.A.R.; Writing-Review & Editing, M.A.R., N.A.H., R.R.C., S.H., and T.E.F.; Visualization, M.A.R., J.M.A., N.A.H., R.R.C., and T.E.F..; Supervision, T.E.F.; Project Administration, T.E.F.; Funding Acquisition, T.E.F. Author Contributions: Conceptualization, T.E.F.; Methodology, N.A.H., R.R.C., and T.E.F.; Software, N.A.H. and R.R.C.; Validation, M.A.R., J.M.A., N.A.H., R.R.C., S.H., P.M.J., and T.E.F.; Formal Analysis, M.A.R., J.M.A., N.A.H., R.R.C., and T.E.F.; Investigation, M.A.R., J.M.A., and P.M.J.; Resources, T.E.F.; Data Curation, N.A.H. and R.R.C.; Writing-Original Draft Preparation, T.E.F. References 1. UN Office for the Coordination of Humanitarian Affairs. Haiti: Cholera figures, December 2017 (as of 29 January 2018). UN Office for the Coordination of Humanitarian Affairs: 2018. Available online: https: //reliefweb.int/report/haiti/haiti-cholera-figures-december-2017-29-january-2018 (accessed on 6 May 2018). 1. UN Office for the Coordination of Humanitarian Affairs. Haiti: Cholera figures, December 2017 (as of 29 January 2018). UN Office for the Coordination of Humanitarian Affairs: 2018. Available online: https: //reliefweb.int/report/haiti/haiti-cholera-figures-december-2017-29-january-2018 (accessed on 6 May 2018). 2. Juin, S.; Schaad, N.; Lafontant, D.; Joseph, G.A.; Barzilay, E.; Boncy, J.; Barrais, R.; Louis, F.J.; Jean Charles, N.L.; Corvil, S.; et al. Strengthening National Disease Surveillance and Response—Haiti, 2010–2015. Am. J. Trop. Med. Hyg. 2017, 97, 12–20. [CrossRef] [PubMed] 2. Juin, S.; Schaad, N.; Lafontant, D.; Joseph, G.A.; Barzilay, E.; Boncy, J.; Barrais, R.; Louis, F.J.; Jean Charles, N.L.; Corvil, S.; et al. Strengthening National Disease Surveillance and Response—Haiti, 2010–2015. Am. J. Trop. Med. Hyg. 2017, 97, 12–20. [CrossRef] [PubMed] . US Centers for Disease Control and Prevention. Cholera: Vibrio Cholerae Infection. Available on https://www.cdc.gov/cholera/general/index.html (accessed on 6 May 2018). 3. US Centers for Disease Control and Prevention. Cholera: Vibrio Cholerae Infection. 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Funding: This research was funded by Uniting for Health Innovation, an “independent, nonprofit organization that unites government, industry, and local communities in the Americas to advance innovation in public health.” Funding was also provided to M.A.R. through a training fellowship at UMass Amherst as part of the Biotechnology Training Program (National Research Service Award T32 GM108556). Acknowledgments: We would like to thank Midwives for Haiti (MFH) for providing housing and other in-country support to M.A.R. and J.M.A. during the two sampling collections. We would also like to thank Shah Manzur Rashed for his help in processing the water samples at Cosmos ID. Conflicts of Interest: The founding sponsor had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results. 13 of 16 13 of 16 Int. J. Environ. Res. 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Microbial community profiling of human saliva using shotgun metagenomic sequencing. PLoS ONE 2014, 9, e97699. [CrossRef] [PubMed] 31. Lax, S.; Smith, D.P.; Hampton-Marcell, J.; Owens, S.M.; Handley, K.M.; Scott, N.M.; Gibbons, S.M.; Larsen, P.; Shogan, B.D.; Weiss, S.; et al. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 2014, 345, 1048–1052. [CrossRef] [PubMed] 32. Ondov, B.D.; Bergman, N.H.; Phillippy, A.M. Interactive metagenomic visualization in a Web browser. BMC Bioinform. 2011, 12, 385. [CrossRef] [PubMed] 33. Gray, M.A.; Pratte, Z.A.; Kellogg, C.A. Comparison of DNA preservation methods for environmental bacterial community samples. FEMS Microbiol. Ecol. 2013, 83, 468–477. [CrossRef] [PubMed] 34. Hamner, S.; Broadaway, S.C.; Mishra, V.B.; Tripathi, A.; Mishra, R.K.; Pulcini, E.; Pyle, B.H.; Ford, T.E. Isolation of potentially pathogenic Escherichia coli O157:H7 from the Ganges River. Appl. Environ. Microbiol. 2007, 73, 2369–2372. [CrossRef] [PubMed] 35. Weatherbase. Hinche, Haiti. Available online: http://www.weatherbase.com/weather/weather.php3?s= 602189&cityname=Hinche-Centre-Haiti (accessed on 28 April 2018). 36. Pindi, P.K.; Yadav, P.R.; Shanker, A.S. Identification of opportunistic pathogenic bacteria in drinking water samples of different rural health centers and their clinical impacts on humans. Biomed. Res. Int. 2013, 2013, 348250. [CrossRef] [PubMed] 37. Fournier, P.E.; Richet, H. The epidemiology and control of Acinetobacter baumannii in health care facilities. Clin. Infect. Dis. 2006, 42, 692–699. [CrossRef] [PubMed] 38. Hung, Y.T.; Lee, Y.T.; Huang, L.J.; Chen, T.L.; Yu, K.W.; Fung, C.P.; Cho, W.L.; Liu, C.Y. Clinical characteristics of patients with Acinetobacter junii infection. J. Microbiol. Immunol. Infect. 2009, 42, 47–53. [PubMed] Int. J. Environ. Res. Public Health 2018, 15, 2211 15 of 16 15 of 16 39. Lolans, K.; Rice, T.W.; Munoz-Price, L.S.; Quinn, J.P. Multicity outbreak of carbapenem-resistant Acinetobacter baumannii isolates producing the carbapenemase OXA-40. Antimicrob. Agents Chemother. 2006, 50, 2941–2945. [CrossRef] [PubMed] 40. Centers for Disease Control and Prevention. Healthcare-Associated Infections. Available online //www.cdc.gov/hai/organisms/acinetobacter.html (accessed on 28 April 2018). 41. Deng, Y.; Bao, X.; Ji, L.; Chen, L.; Liu, J.; Miao, J.; Chen, D.; Bian, H.; Li, Y.; Yu, G. Resistance integrons: Class 1, 2 and 3 integrons. Ann. Clin. Microbiol. Antimicrob. 2015, 14, 45. [CrossRef] [PubMed] 42. Mukherjee, N.; Bartelli, D.; Patra, C.; Chauhan, B.V.; Dowd, S.E.; Banerjee, P. Microbial Diversity of Source and Point-of-Use Water in Rural Haiti—A Pyrosequencing-Based Metagenomic Survey. PLoS ONE 2016, 11, e0167353. References [CrossRef] [PubMed] 43. Cunliffe, M.; Kertesz, M.A. Effect of Sphingobium yanoikuyae B1 inoculation on bacterial community dynamics and polycyclic aromatic hydrocarbon degradation in aged and freshly PAH-contaminated soils. Environ. Pollut. 2006, 144, 228–237. [CrossRef] [PubMed] 44. Chen, H.; Young, S.; Berhane, T.K.; Williams, H.N. Predatory Bacteriovorax communities ordered by various prey species. PLoS ONE 2012, 7, e34174. [CrossRef] [PubMed] 45. Soborg, D.A.; Hendriksen, N.B.; Kilian, M.; Kroer, N. Widespread occurrence of bacterial human virulence determinants in soil and freshwater environments. Appl. Environ. Microbiol. 2013, 79, 5488–5497. [CrossRef] [PubMed] 46. Zhang, B.; Xia, Y.; Wen, X.; Wang, X.; Yang, Y.; Zhou, J.; Zhang, Y. The Composition and Spatial Patterns of Bacterial Virulence Factors and Antibiotic Resistance Genes in 19 Wastewater Treatment Plants. PLoS ONE 2016, 11, e0167422. [CrossRef] [PubMed] 47. Drzewiecka, D. Significance and Roles of Proteus spp. Bacteria in Natural Environments. Microb. Ecol. 2016, 72, 741–758. [CrossRef] [PubMed] 48. Dukik, K.; Munoz, J.F.; Jiang, Y.; Feng, P.; Sigler, L.; Stielow, J.B.; Freeke, J.; Jamalian, A.; Gerrits van den Ende, B.; McEwen, J.G.; et al. Novel taxa of thermally dimorphic systemic pathogens in the Ajellomycetaceae (Onygenales). Mycoses 2017, 60, 296–309. [CrossRef] [PubMed] 49. Trofa, D.; Gacser, A.; Nosanchuk, J.D. Candida parapsilosis, an emerging fungal pathogen. Clin. Microbiol. Rev. 2008, 21, 606–625. [CrossRef] [PubMed] 50. Matos, O.; Lobo, M.L.; Xiao, L. Epidemiology of Enterocytozoon bieneusi Infection in Humans. J. Parasitol. Res. 2012, 2012, 981424. [CrossRef] [PubMed] 51. Boileau, M.; Ferreira, J.; Ahmad, I.; Lavallee, C.; Qvarnstrom, Y.; Dufresne, S.F. Successful Treatment of Disseminated Anncaliia algerae Microsporidial Infection With Combination Fumagillin and Albendazole. Open Forum Infect. Dis. 2016, 3. [CrossRef] [PubMed] 52. Richterman, A.; Cheung, H.C.; Meiselbach, M.K.; Jerome, G.; Ternier, R.; Ivers, L.C. Risk Factors for Self-Reported Cholera within HIV-Affected Households in Rural Haiti. Open Forum Infect. Dis. 2018, 5. [CrossRef] [PubMed] 53. Faburay, B. The case for a ‘one health’ approach to combating vector-borne diseases. Infect. Ecol. Epidemiol. 2015, 5, 28132. [CrossRef] [PubMed] 54. Borriello, G.; Lucibelli, M.G.; De Carlo, E.; Auriemma, C.; Cozza, D.; Ascione, G.; Scognamiglio, F.; Iovane, G.; Galiero, G. Characterization of enterotoxigenic E. coli (ETEC), Shiga-toxin producing E. coli (STEC) and necrotoxigenic E. coli (NTEC) isolated from diarrhoeic Mediterranean water buffalo calves (Bubalus bubalis). Res. Vet. Sci. 2012, 93, 18–22. [CrossRef] [PubMed] 55. Routh, J.A.; Sreenivasan, N.; Adhikari, B.B.; Andrecy, L.L.; Bernateau, M.; Abimbola, T.; Njau, J.; Jackson, E.; Juin, S.; Francois, J.; et al. © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). References Cost Evaluation of a Government-Conducted Oral Cholera Vaccination Campaign-Haiti, 2013. Am. J. Trop. Med. Hyg. 2017, 97, 37–42. [CrossRef] [PubMed] Int. J. Environ. Res. Public Health 2018, 15, 2211 16 of 16 16 of 16 56. Ivers, L.C.; Hilaire, I.J.; Teng, J.E.; Almazor, C.P.; Jerome, J.G.; Ternier, R.; Boncy, J.; Buteau, J.; Murray, M.B.; Harris, J.B.; et al. Effectiveness of reactive oral cholera vaccination in rural Haiti: A case-control study and bias-indicator analysis. Lancet Glob. Health 2015, 3, e162–e168. [CrossRef] 56. Ivers, L.C.; Hilaire, I.J.; Teng, J.E.; Almazor, C.P.; Jerome, J.G.; Ternier, R.; Boncy, J.; Buteau, J.; Murray, M.B.; Harris, J.B.; et al. Effectiveness of reactive oral cholera vaccination in rural Haiti: A case-control study and bias-indicator analysis. Lancet Glob. Health 2015, 3, e162–e168. [CrossRef] 57. Franke, M.F.; Jerome, J.G.; Matias, W.R.; Ternier, R.; Hilaire, I.J.; Harris, J.B.; Ivers, L.C. Comparison of two control groups for estimation of oral cholera vaccine effectiveness using a case-control study design. Vaccine 2017, 35, 5819–5827. [CrossRef] [PubMed] © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
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Supplementary Data from Implication of &lt;i&gt;ZNF217&lt;/i&gt; in Accelerating Tumor Development and Therapeutically Targeting ZNF217-Induced PI3K–AKT Signaling for the Treatment of Metastatic Osteosarcoma
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Supplementary Figure 1 ZNF217 localization is additional TMA sections Supplementary Figure 1 ZNF217 localization is additional TMA sections Supplementary Figure 1 ZNF217 localization is additional TMA sections Additional images of positive TMA staining for ZNF217 in one representative site per section; magnification 40X, scale bars 25 µm. Black arrows depict examples of positive nuclear and cytoplasmic ZNF217 staining. Additional images of positive TMA staining for ZNF217 in one representative site per section; magnification 40X, scale bars 25 µm. Black arrows depict examples of positive nuclear and cytoplasmic ZNF217 staining. Supplementary Figure 2 Localization of ZNF217 in OSA cells (a) Western blot staining of cytoplasmic extract (CYTO) and nuclear chromatin- bound extract (NUC) using a ZNF217-specific antibody. (b) Confirmation of ZNF217 localization by immunofluorescence (IF) staining; magnification 40X, scale bars 100 µm. Red = ZNF217 staining and blue = DAPI counterstain. Supplementary Figure 2 Localization of ZNF217 in OSA cells (a) Western blot staining of cytoplasmic extract (CYTO) and nuclear chromatin- bound extract (NUC) using a ZNF217-specific antibody. (b) Confirmation of ZNF217 localization by immunofluorescence (IF) staining; magnification 40X, scale bars 100 µm. Red = ZNF217 staining and blue = DAPI counterstain. (a) Western blot staining of cytoplasmic extract (CYTO) and nuclear chromatin- bound extract (NUC) using a ZNF217-specific antibody. (b) Confirmation of ZNF217 localization by immunofluorescence (IF) staining; magnification 40X, scale bars 100 µm. Red = ZNF217 staining and blue = DAPI counterstain. Supplementary Figure 3 RNA-sequencing analysis of transient ZNF217 knockdown SJSA-1 cells Supplementary Figure 3 RNA-sequencing analysis of transient ZNF217 knockdown SJSA-1 cells (a) Heatmap of clustering in ZNF217 knockdown (KD) and control (CON) replicates by normalized raw read counts. (b) Functional gene network comprised of 440 DEGs identified using STRINGDB. (c) Functional GO analysis and (d) Reactome pathway enrichment of highly significant biological processes following transient ZNF217 knockdown. Supplementary Figure 4 PI3K blockade in OSA cells (a) PI3K inhibition with LY294002 reduces cell viability 48 hours post-treatment and (b) induces modest apoptosis. All data shown as mean ± SEM. Panel (a) One-way ANOVA with Bonferroni’s post hoc. Panel (b) Student’s T-test. **p < 0.01, ***p < 0.001, ****p < 0.0001. Supplementary Figure 4 PI3K blockade in OSA cells Supplementary Figure 4 PI3K blockade in OSA cells (a) PI3K inhibition with LY294002 reduces cell viability 48 hours post-treatment and (b) induces modest apoptosis. All data shown as mean ± SEM. Panel (a) One-way ANOVA with Bonferroni’s post hoc. Panel (b) Student’s T-test. Supplementary Figure 1 ZNF217 localization is additional TMA sections **p < 0.01, ***p < 0.001, ****p < 0.0001. Supplementary Figure 5 Flow plots of apoptosis in ZNF217 knockdown cells Flow plots of Annexin V+ staining in ZNF217 knockdown cells (si-ZNF217) compared to control (si-NS). entary Figure 5 Flow plots of apoptosis in ZNF217 knockdown cells plots of Annexin V+ staining in ZNF217 knockdown cells (si-ZNF217) Flow plots of Annexin V+ staining in ZNF217 knockdown cells (si-ZNF217) compared to control (si-NS). Supplementary Figure 6 Flow plots of apoptosis following treatment with TCN Flow plots of Annexin V+ staining in TCN-treated OSA cells (100 µM) compared to DMSO control. mentary Figure 6 Flow plots of apoptosis following treatment with TCN Flow plots of Annexin V+ staining in TCN-treated OSA cells (100 µM) compared to DMSO control plots of Annexin V+ staining in TCN-treated OSA cells (100 µM) compared to Flow plots of Annexin V+ staining in TCN-treated OSA cells (100 µM) compared to DMSO control. Supplementary Figure 7 ZNF217 expression in tumors from TCN-treated animals Representative IHC staining of ZNF217 in TCN- or control-treated animals; magnification 40X, scale bars 100 µm. Supplementary Figure 7 ZNF217 expression in tumors from TCN-treated animals Representative IHC staining of ZNF217 in TCN- or control-treated animals; magnification 40X, scale bars 100 µm. Supplementary Figure 7 ZNF217 expression in tumors from TCN-treated animals Supplementary Figure 7 ZNF217 expression in tumors from TCN-treated animals Representative IHC staining of ZNF217 in TCN- or control-treated animals; magnification 40X, scale bars 100 µm.
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STARD1 and NPC1 expression as pathological markers associated with astrogliosis in post-mortem brains from patients with Alzheimer's disease and Down syndrome
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Correspondence to: Jose C. Fernandez-Checa, Carmen Garcia-Ruiz; email: checa229@yahoo.com, cgrbam@iibb.csic.es Keywords: cholesterol, NPC1, StARD1, mitochondria, lysosomes Received: July 23, 2019 Accepted: December 23, 2019 Published: January 5, 2020 Correspondence to: Jose C. Fernandez-Checa, Carmen Garcia-Ruiz; email: checa229@yahoo.com, cgrbam@iibb.csic.es Keywords: cholesterol, NPC1, StARD1, mitochondria, lysosomes Received: July 23, 2019 Accepted: December 23, 2019 Published: January 5, 2020 Published: January 5, 2020 Copyright: Arenas et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Alzheimer´s disease (AD) is a progressive neurodegenerative disorder of complex etiology, while Down syndrome (DS) is considered a genetically determined form of AD. Alterations in cholesterol homeostasis have been linked to AD although the role in this association is not well understood. Increased expression of STARD1 and NPC1, which are involved in intracellular cholesterol trafficking, has been reported in experimental AD models but not in patients with AD. Here we analyzed endolysosomal/mitochondrial cholesterol homeostasis, expression of NPC1 and STARD1 and correlation with pathological markers of AD in cortex and hippocampus from post-mortem brains from patients with AD and DS. NPC1 expression was observed in hippocampus from patients with AD and DS. Moreover, STARD1 expression increased in hippocampus and cortex from patients with AD and DS, respectively, and its immunoreactivity discriminated controls from AD or DS with a better accuracy than Aβ42. Hippocampal areas stained with the recombinant GST-PFO probe showed increased mitochondrial cholesterol within astrocytes of brains from patients with AD and DS-brains compared to controls. Lysosomal cholesterol accumulation within hippocampal astrocytes was higher in DS than in AD. These data revealed increased intracellular cholesterol loading in hippocampus from patient with AD and DS and suggest that STARD1 could be a potential pre-clinical marker associated with early stages of AD pathology. AGING 2020, Vol. 12, Advance AGING 2020, Vol. 12, Advance www.aging-us.com Research Paper STARD1 and NPC1 expression as pathological markers associated with astrogliosis in post-mortem brains from patients with Alzheimer’s d d d p STARD1 and NPC1 expression as pathological markers associated with astrogliosis in post-mortem brains from patients with Alzheimer’s disease and Down syndrome Fabian Arenas1,2, Fernanda Castro1,2, Susana Nuñez1,2, Gemma Gay1, Carmen Garcia-Ruiz1,2,3,4, Jose C. Fernandez-Checa1,2,3,4 Fabian Arenas1,2, Fernanda Castro1,2, Susana Nuñez1,2, Gemma Gay1, Carmen Garcia-Ruiz1,2,3,4, Jose C. Fernandez-Checa1,2,3,4 1Department of Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), CSIC, Barcelona Spain 2Liver Unit, Hospital Clinic I Provincial de Barcelona, Instituto de Investigaciones Biomédicas August Pi i Sunyer (IDIBAPS), Barcelona, Spain 3Centro de Investigación Biomédica en Red (CIBEREHD), Barcelona, Spain 4Research Center for ALPD, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA 1Department of Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), CSIC, Barcelona, Spain 2Liver Unit, Hospital Clinic I Provincial de Barcelona, Instituto de Investigaciones Biomédicas August Pi i Sunyer (IDIBAPS), Barcelona, Spain 3 Intracellular cholesterol homeostasis in cortex from patients with AD and DS As alterations in cortex occur late in AD and reflect disease progression, we first examined the intracellular cholesterol homeostasis in the cortex of sporadic AD and DS using post-mortem cryopreserved cortex samples from patients with AD and DS (Table 1). Transcripts and protein expression of putative cholesterol carriers involved in intracellular cholesterol trafficking (NPC1, STARD3/MLN64, STARD4, and STARD1), as well as sensors/regulators of de novo cholesterol synthesis (INSIG-1 and SREBP2) were examined [2] and summarized in Supplementary Table 1. While the expression at mRNA or protein levels of STARD4, INSIG-1 and mature SREBP2 (mSREBP2) seems to be similar between AD, DS and control samples (Figure 1), cortex from patients with DS exhibited a significant overexpression of transcripts for the mitochondrial carrier STARD1 (Figure 1A), which translated at the protein levels (Figure 1B). Moreover, there was a trend for increased mRNA levels of NPC1 and STARD3/MLN64 in cortex from patients with DS (Figure 1A). In addition, cortex from AD-brains exhibited a small but significant increase in the NPC1 protein expression compared to control samples and a trend for increased STARD1 protein levels (Figure 1B). These findings indicate that cortex from patients with DS and AD exhibit increased expression of StARD1 and NPC1, respectively. Down syndrome (DS) is considered a genetically determined form of AD and individuals with DS invariably develop AD by their fourth decade [8]. Patients with DS exhibit cognitive markers of preclinical and prodromal AD [9]. The progression of AD pathology assessed by neuroimaging and/or cerebrospinal fluid levels of Aβ and tau (total and phosphorylated) revealed a similar pattern between normal population and individuals with DS, although these events in DS occur 10–20 years earlier than in normal population [10, 11]. Aging, obesity and ApoEε4-associated dyslipidaemia are important risk factors for development of AD dementia in normal and DS population [12]. Interestingly, hypercholesterolemic subjects with DS treated with statins exhibit a lower risk factor for AD development that correlates with slower amyloidogenic burden [13]. Besides the overlap between AD and DS, intracellular brain cholesterol homeostasis in patients with DS has not been reported. We hypothesized that alterations in intracellular cholesterol homeostasis in lysosomes and mitochondria in the brain could contribute to the molecular events involved in the AD continuum, emerging as a pathological event that could contribute to disease progression. Intracellular cholesterol homeostasis in cortex from patients with AD and DS Investigating the intracellular cholesterol homeostasis is critical to improve and expand the therapeutic armamentarium for AD, especially at preclinical stages, given that current clinical trials for AD have been disappointing. In contrast to the controversial role of changes in total brain cholesterol levels in AD [2, 14], our findings on the expression of putative intracellular cholesterol carriers (e.g. STARD1 and NPC1) in patients with AD and DS correlate with disease markers, such as Aβ42, and suggest that alterations in intracellular cholesterol homeostasis may be an early molecular event that favours the progression of the AD pathology. Moreover, the accuracy of STARD1 to discriminate controls from AD in the INTRODUCTION genesis, although other factors such as tau phosphorylation are also key for the progression of AD [1]. While alterations in cholesterol homeostasis have been linked to AD the role for this association is controversial. For instance, there has been evidence indicating that either increased or decreased total brain cholesterol levels are associated with AD-pathogenesis [2]. Whether intracellular cholesterol pools (e.g. Alzheimer’s disease (AD) is a progressive neuro- degenerative disorder of complex etiology and the most common form of dementia, which comprises early-onset AD (EOAD, ~5% of patients) and late-onset AD (LOAD, 95% of patients). The generation of toxic beta amyloid (Aβ) peptides is considered a central player in AD patho- AGING www.aging-us.com 1 endolysosomes and mitochondria) rather than total cholesterol levels are more relevant for AD pathology remains to be established. Indeed, hippocampus and frontal cortex of patients with AD and AD-Tg mice have been shown to exhibit increased expression of the lysosomal cholesterol transporter NPC1 [3], while increased steroidogenic acute regulatory protein (STARD1) expression, which regulates the mitochondrial cholesterol trafficking [4], has been reported in pyramidal hippocampal neurons of patients with AD [5]. Moreover, mitochondrial cholesterol accumulation in a hyper- cholesterolemic AD-Tg mouse model has been shown to impair mitochondrial antioxidant defense and stimulate oxidative stress, which results in the acceleration of AD- like neuropathology [6, 7]. However, the intracellular cholesterol homeostasis in human AD has not been explored. general population and in subjects with DS suggests that StARD1 could be a potential novel marker associated with early molecular events of AD pathology in both populations. STARD1 and NPC1 immunoreactivity in hippocampus from patients with AD and DS AD pathology is characterized by atrophy in hippocampus, temporal lobes and parietotemporal cortices where neuronal death correlates with amyloid plaques (largely composed of Aβ42) and neurofibrillary tangles (NFTs) [15]. Interestingly, an accelerated Aβ burden with greater plaques deposition and NFT have been described in the hippocampus of DS subjects exhibiting AD pathology [8]. Therefore, we examined the hippocampal expression of cholesterol carriers involved in lysosomal (i.e. NPC1) and mitochondrial (i.e. STARD1) trafficking and compared this outcome with the pathological markers Aβ42 and p-tau, summarized in Supplementary Table 1. Immuno- histochemical analysis of paraffin-fixed hippocampal sections showed increased Aβ42 and p-tau AGING 2 www.aging-us.com Table 1. Collected specimens from cases of AD, DS and controls. Subjects (males/females) Group Cryopreserved Cortex Paraffined hippocampus Cryopreserved hippocampus Total subjects Mean age ± SEM Anatomopatho- logic diagnosis Clinical diagnosis DS 5 (3/2) 7 (3/4) 4 (2/2) 7 (3/4) 56 ± 4.31 AD V-VI, CERAD C Dementia AD 5 (2/3) 7 (4/3) 5 (2/3) 7 (4/3) 80.7 ± 3.00 AD V-VI, CERAD B-C Dementia Control 6 (4/2) 7 (5/2) 5 (4/1) 7 (5/2) 69.7 ± 4.79 Without neurological lesions (5) Cognitively healthy Frontotemporal degeneration (1) FTD iLBD; incidental Lewy body disease (1) Cognitively healthy Note: For immunohistochemical and immunofluorescence analysis, 5 µm thin paraffin sections of hippocampus were available for all human brain samples, while 14 µm thin sections of frozen hippocampus were available for just 19 cases to analyse the intracellular cholesterol levels by immunofluorescence. On the other hand, cryopreserved human cortex of just 16 donors were available to assess gene expression and western blotting analysis. FTD, frontotemporal dementia. Table 1. Collected specimens from cases of AD, DS and controls. Note: For immunohistochemical and immunofluorescence analysis, 5 µm thin paraffin sections of hippocampus were available for all human brain samples, while 14 µm thin sections of frozen hippocampus were available for just 19 cases to analyse the intracellular cholesterol levels by immunofluorescence. On the other hand, cryopreserved human cortex of just 16 donors were available to assess gene expression and western blotting analysis. FTD, frontotemporal dementia. immunoreactivity in patients with AD and DS compared with control subjects (arrows in Figure 2A and 2B). These differences were significant for Aβ42 staining in CA1, CA2 and CA3 hippocampal regions from patients with DS, in agreement with the intrinsic overproduction of Aβ in this population [8]. STARD1 and NPC1 immunoreactivity in hippocampus from patients with AD and DS Moreover, there was a trend for increased Aβ42 in CA1 region from patients with AD. Interestingly, CA1, CA2 and CA3 hippocampal regions from patients with AD and DS showed a significant higher NPC1 protein expression than control samples (Figure 2A and 2B). In line with previous findings [5], the expression of StARD1 in hippocampal regions revealed a significant increase of STARD1 immunoreactivity in CA1 and CA3 areas from patients with AD compared with DS and controls (Figure 2A and 2B). Moreover, when STARD1 and Aβ42 immunoreactivity were compared among all samples, the hippocampal region-specific pattern of STARD1 expression significantly correlated with Aβ42 deposition in CA1 and CA3 (Figure 2C). Thus, although AD and DS are two related diseases, each exhibit specific changes regarding the expression of intracellular cholesterol carriers STARD1 and NPC1, with STARD1 overexpression in hippocampus being specific for AD while in cortex the increase seems to be characteristic of DS. In contrast, the increase in expression of NPC1 occurs in both diseases. In addition, the differential turnover between proteins and their corresponding mRNA likely contribute to the specific pattern of expression of STARD1 and NPC1 at the mRNA and protein levels in the cortex between AD and DS samples. Further research will be required to understand the full impact of these changes in AD pathology and its genetically related form DS. Discrimination capacity of NPC1 and STARD1 immunoreactivity in hippocampus from patients with AD and DS In analogy with Aβ42, we searched for expression of both NPC1 and STARD1 in the paraffin-fixed hippocampal samples as potential discrimination factors between AD and/or DS from normal controls. For each hippocampal region we analyzed the relative area immunolabeled with Aβ42, NPC1, and STARD1 and performed ROC curves analysis between controls subjects and patients with AD, DS, or the sum of both AD+DS groups (Figure 3). As expected, Aβ42 deposition revealed a highly significant AUC with a high accuracy not only to identify AD and/or DS samples as positive (sensitivity), particularly in CA1 hippocampal areas, but also to identify the control subjects (specificity) in all hippocampal regions from DS-brains (Figure 3). Similarly, in hippocampal CA1 and CA3 regions, NPC1 immunolabeling properly discriminated AD individuals, but not DS subjects, from controls (Figure 3). Unexpectedly, STARD1 dis- criminated AD and/or DS samples from control individuals in all hippocampal regions (Figure 3), suggesting that STARD1 immunolabeling exhibits a greater discrimination capacity than Aβ42. Moreover, multivariate data analysis of the cohort by principal components analysis (PCA) showed an efficient AGING 3 www.aging-us.com e 1. Cortical expression profile of intracellular cholesterol carriers and sensors/regulators. (A) Relative mRNA leve StARD3, StARD4, and StARD1 in human cortex from AD (n=5), DS (n=5), and control (n=6) subjects. Transcripts levels were norma espect to controls using β-actin. (*) p<0.05; (**) p<0.01. (B) Immunoblotting of NPC1, StARD1, StARD3/MLN64, mSREBP2 and INS al protein extracts (90 µg/lane) from human cortex from AD (n=5), DS (n=5), and control (n=6) donors. (C) Protein levels quantifie ometry and normalized using β−actin as housekeeping followed by normalization with control group. (*) p<0.05; (**) p<0.01. Figure 1. Cortical expression profile of intracellular cholesterol carriers and sensors/regulators. (A) Relative mRNA levels of NPC1, StARD3, StARD4, and StARD1 in human cortex from AD (n=5), DS (n=5), and control (n=6) subjects. Transcripts levels were normalized with respect to controls using β-actin. (*) p<0.05; (**) p<0.01. (B) Immunoblotting of NPC1, StARD1, StARD3/MLN64, mSREBP2 and INSIG-1 of total protein extracts (90 µg/lane) from human cortex from AD (n=5), DS (n=5), and control (n=6) donors. (C) Protein levels quantified by densitometry and normalized using β−actin as housekeeping followed by normalization with control group. (*) p<0.05; (**) p<0.01. AGING 4 www.aging-us.com confocal immunofluorescence imaging to explore the pattern distribution of the intracellular cholesterol transporters NPC1 and STARD1 within the astrocytes surrounding amyloid deposition in the different hippocampal regions (Figure 4). Discrimination capacity of NPC1 and STARD1 immunoreactivity in hippocampus from patients with AD and DS In agreement with previous observations in post-mortem human AD tissues as well as in animal models [16, 17], reactive astrocytes surrounding Aβ42 deposition were observed in hippocampus from patients with AD and DS (Figure 4A). Moreover, the colocalization analysis of ten representative images per sample revealed that astro- cytes in hippocampus from patients with DS visualization of the data for CA1 and CA3, capturing more than 97.6% and 85% of the markers variability, respectively, with a clear separation between control subjects from AD and DS patients (Supplementary Figure 1). Amyloid-related hippocampal astrogliosis associated with increased lysosomal and mitochondrial choles- terol content in patients with AD and DS To investigate whether disruption of intracellular cholesterol homeostasis correlate with AD, we used gure 2. Hippocampal expression of AD biomarkers and lysosomal/mitochondrial cholesterol carriers. (A) Representative ages of immunohistochemistry of paraffin sections (5 µm) against Aβ42, p-tau, StARD1 and NPC1 for CA1, CA2 and CA3 hippocampa gions from AD (n=7), DS (n=7), and control (n=7) subjects. Positive immunoreactivity is shown by black arrows. Scale bar: 100 µm. (B antitation of IHC shown in A using Image J software as described in Supplementary methods. For each hippocampal region, the % of munolabeled area was normalized to control group. (*) p<0.05; (**) p<0.01; (***) p<0.001. (C) Spearman’s correlation values between IHC munolabeling for Aβ42 and StARD1 in each hippocampal region. Figure 2. Hippocampal expression of AD biomarkers and lysosomal/mitochondrial cholesterol carriers. (A) Representative images of immunohistochemistry of paraffin sections (5 µm) against Aβ42, p-tau, StARD1 and NPC1 for CA1, CA2 and CA3 hippocampal regions from AD (n=7), DS (n=7), and control (n=7) subjects. Positive immunoreactivity is shown by black arrows. Scale bar: 100 µm. (B) Quantitation of IHC shown in A using Image J software as described in Supplementary methods. For each hippocampal region, the % of immunolabeled area was normalized to control group. (*) p<0.05; (**) p<0.01; (***) p<0.001. (C) Spearman’s correlation values between IHC- immunolabeling for Aβ42 and StARD1 in each hippocampal region. AGING 5 www.aging-us.com astrocytes indicated a region-specific significant increase of STARD1/GFAP colocalization index in CA1 and CA3 areas for patients with AD and DS, respectively, compared to controls (Figure 4B). Moreover, pilot observations following the staining of exhibit higher NPC1 expression than in AD and control samples, particularly in CA3 region (Figure 4B), suggesting increased lysosomal cholesterol levels in astrocytes from patients with DS. In addition, the analysis of the STARD1 content in hippocampal sis of the STARD1 content in hippocampal Moreover, pilot observations following the stainin e 3. Discrimination capacity of amyloid accumulation and lysosomal/mitochondrial cholesterol carriers. ROC curv nolabel for Aβ42, NPC1, and StARD1 in each hippocampal region with the significantly highest AUC resulted in the comparison bet ol and AD, DS, or AD+DS groups (Lower panel). Red dots show the cutoff for the corresponding IHC-immunolabel that b minate AD and/or DS condition from normal controls in each hippocampal region. (*) p<0.05; (**) p<0.01; (***) p<0.001. Figure 3. Discrimination capacity of amyloid accumulation and lysosomal/mitochondrial cholesterol carriers. Amyloid-related hippocampal astrogliosis associated with increased lysosomal and mitochondrial choles- terol content in patients with AD and DS ROC curv immunolabel for Aβ42, NPC1, and StARD1 in each hippocampal region with the significantly highest AUC resulted in the comparison bet control and AD, DS, or AD+DS groups (Lower panel). Red dots show the cutoff for the corresponding IHC-immunolabel that b Figure 3. Discrimination capacity of amyloid accumulation and lysosomal/mitochondrial cholesterol carriers. ROC curves of immunolabel for Aβ42, NPC1, and StARD1 in each hippocampal region with the significantly highest AUC resulted in the comparison between control and AD, DS, or AD+DS groups (Lower panel). Red dots show the cutoff for the corresponding IHC-immunolabel that better discriminate AD and/or DS condition from normal controls in each hippocampal region. (*) p<0.05; (**) p<0.01; (***) p<0.001. Figure 3. Discrimination capacity of amyloid accumulation and lysosomal/mitochondrial cholesterol carriers. ROC curves of immunolabel for Aβ42, NPC1, and StARD1 in each hippocampal region with the significantly highest AUC resulted in the comparison between control and AD, DS, or AD+DS groups (Lower panel). Red dots show the cutoff for the corresponding IHC-immunolabel that better discriminate AD and/or DS condition from normal controls in each hippocampal region. (*) p<0.05; (**) p<0.01; (***) p<0.001. Figure 3. Discrimination capacity of amyloid accumulation and lysosomal/mitochondrial cholesterol carriers. ROC curves of immunolabel for Aβ42, NPC1, and StARD1 in each hippocampal region with the significantly highest AUC resulted in the comparison between control and AD, DS, or AD+DS groups (Lower panel). Red dots show the cutoff for the corresponding IHC-immunolabel that better discriminate AD and/or DS condition from normal controls in each hippocampal region. (*) p<0.05; (**) p<0.01; (***) p<0.001. AGING 6 www.aging-us.com strocytes-expressing lysosomal and mitochondrial cholesterol carriers in hippocampal regions. (A) Rep ges of paraffined hippocampal regions (5 µm) from AD (n=7), DS (n=7), and control (n=7) subjects immunolabeled a yellow), and NPC1 or StARD1 (both green). Nuclei are stained with Hoechst 33342 (blue). Lower panels show the co en GFAP and NPC1 or StARD1 (white) highlighted in the squared areas. Scale bar: 10 µm. (B) Astrocyte colocalization and StARD1 (mitochondrial) cholesterol carriers into hippocampal regions from AD, DS, and control subjects. 10 region and per sample were analysed with Image J to assess the index of astrocyte (GFAP+) colocalization with NPC1 **) p<0.01; (***) p<0.001. Figure 4. Astrocytes-expressing lysosomal and mitochondrial cholesterol carriers in hippocampal regions. Amyloid-related hippocampal astrogliosis associated with increased lysosomal and mitochondrial choles- terol content in patients with AD and DS (A) Representative confocal images of paraffined hippocampal regions (5 µm) from AD (n=7), DS (n=7), and control (n=7) subjects immunolabeled against Aβ42 (red), GFAP (yellow), and NPC1 or StARD1 (both green). Nuclei are stained with Hoechst 33342 (blue). Lower panels show the colocalization mask between GFAP and NPC1 or StARD1 (white) highlighted in the squared areas. Scale bar: 10 µm. (B) Astrocyte colocalization with NPC1 (lysosomal) and StARD1 (mitochondrial) cholesterol carriers into hippocampal regions from AD, DS, and control subjects. 10 images per hippocampal region and per sample were analysed with Image J to assess the index of astrocyte (GFAP+) colocalization with NPC1 or StARD1. (*) p<0.05; (**) p<0.01; (***) p<0.001. AGING 7 7 www.aging-us.com astroglial lysosomal cholesterol accumulation (PFO/Lamp1 in GFAP+) significantly increased in hippocampus from AD and DS patients compared to controls (Figure 5B), an outcome that was more pronounced in DS (14.41±1.322 fold) than in AD brains (3.43±0.502 fold). Interestingly, these findings cor- related with the increased Aβ42 accumulation in the CA1, CA2 and CA3 hippocampal regions of DS-brains (Figure 2B). Furthermore, PCA analysis revealed that the levels of astroglial NPC1 and STARD1 content as well as the intraorganelle-cholesterol levels are able to separate each group (Supplementary Figure 2). paraffined hippocampal sections of brains from AD, DS and control groups with NeuN and IBA1 antibodies as neuronal and glial markers, respectively, indicated that STARD1 and NPC1 expression increased in hippo- campal neurons from AD and DA brains with respect to control, without changes in glia (not shown). To assess the intracellular cholesterol distribution within hippocampal astrocytes (i.e. GFAP+), cryo- preserved hippocampal samples of patients with AD and DS were analysed for the colocalization between GST-PFO probe, which detects cholesterol in membranes, with Lamp1 or Tom20 immunoreactivity to stain lysosome or mitochondria, respectively (Figure 5; and Supplementary Table 2). In line with the STARD1/GFAP colocalization, we found that the mitochondrial cholesterol content into hippocampal astroglia from patients with AD and DS was >2.5-fold higher than control donors (Figure 5B). Moreover, DISCUSSION We have analyzed the intracellular cholesterol trafficking in post-mortem samples from patients with DS and AD and assessed whether this event correlated with AD markers. An intriguing finding was that Aβ42 Figure 5. Lysosomal and mitochondrial cholesterol homeostasis in hippocampal astrocytes. (A) Representative confocal representative images of 4 µm thin-stacked cryopreserved hippocampus from AD (n=5), DS (n=4), and control (n=5) subjects immunolabeled with GST-PFO (red), GFAP (yellow), and Tom20 or Lamp1 (both green). Nuclei are stained with Dapi (blue). Lower panels show colocalization mask (white) between GST-PFO and Tom20 or Lamp1, respectively, highlighted in the squared areas. Scale bar: 10 µm. (B) Cholesterol (PFO+) colocalization with mitochondria (Tom20+) or lysosome (Lamp1+) into hippocampal astrocytes (GFAP+) from AD, DS, and control donors. 10 images per sample were analysed with Image J to assess the index of astrocytic cholesterol colocalization with Tom20 or Lamp1. Values are relativized with control to show differences as n-fold. (*) p<0.05; (**) p<0.01. Figure 5. Lysosomal and mitochondrial cholesterol homeostasis in hippocampal astrocytes. (A) Representative confocal representative images of 4 µm thin-stacked cryopreserved hippocampus from AD (n=5), DS (n=4), and control (n=5) subjects immunolabeled with GST-PFO (red), GFAP (yellow), and Tom20 or Lamp1 (both green). Nuclei are stained with Dapi (blue). Lower panels show colocalization mask (white) between GST-PFO and Tom20 or Lamp1, respectively, highlighted in the squared areas. Scale bar: 10 µm. (B) Cholesterol (PFO+) colocalization with mitochondria (Tom20+) or lysosome (Lamp1+) into hippocampal astrocytes (GFAP+) from AD, DS, and control donors. 10 images per sample were analysed with Image J to assess the index of astrocytic cholesterol colocalization with Tom20 or Lamp1. Values are relativized with control to show differences as n-fold. (*) p<0.05; (**) p<0.01. AGING 8 www.aging-us.com but not p-tau immunoreactivity significantly increased in CA1-3 hippocampal regions only in patients with DS, with a trend for increased Aβ42 levels in CA1 from patients with AD. These findings in DS are consistent with the intrinsic Aβ overproduction in these subjects [8]. Moreover, neuropathological analysis of amyloid pathology in DS described the onset of mid-severity changes in hippocampal CA1 region at 35 years of age, in which Aβ42 deposition occurred in the absence of tau pathology [18]. Conversely, tauopathies and the presence of NFTs that commonly coexist with LOAD can occur without amyloid pathology [19, 20]. DISCUSSION In addition, it has been suggested that the earliest appearance of tau pathology in AD occurs in the locus caeruleus instead of hippocampus [21], which could account for the lack of p-tau immnunoreactivity in hippocampal samples from our cohort of patients with AD. While the present work is the first to our knowledge to address the expression of putative intracellular cholesterol carriers (e.g. STARD1 and NPC1) in AD and DS and their correlation with pathological markers, the role of changes in total cholesterol levels in AD is controversial [2, 14], consistent with the unsettled impact of statins in the prevention or treatment of the disease, which will require further randomized controlled trials [22, 23]. (Figure 2), the NPC1 immunolabeling as a disease marker of AD does not discriminate AD-pathology in patients with DS from the controls (Figure 3), suggesting that the AD continuum in the hippocampus of subjects with DS differs from NPC disease. Cholesterol is known to promote the amyloidogenic processing of APP, which occurs predominantly in lipid- rafts where most components of the amyloidogenic machinery, such as APP, Aβ, BACE1, presenilins (PSEN1/2), and γ-secretase are present [26, 27]. Moreover, cholesterol is thought to interfere with the α- secretase-dependent non-amyloidogenic APP processing [28], and PSEN1/2 and γ-secretase have been localized at the mitochondrial ER-associated membrane (MAM) [29, 30]. Interestingly, although mitochondrial membranes are low in cholesterol, the pool of cholesterol of the mitochondrial inner membrane (MIM) is crucial for the synthesis of neurosteroids to maintain physiological GABAergic responses that modulate memory function, which is particularly affected in subjects with DS [31, 32]. The STARD1-dependent trafficking of cholesterol to MIM is the rate-limiting step for steroidogenesis and changes in mitochondrial cholesterol levels can impact this process and affect mitochondrial antioxidant defense [2, 5–7, 33]. However, the role of STARD1 in human AD is poorly understood and has not been examined in DS. We show for the first time that the hippocampal overexpression of STARD1 correlates with amyloid deposition suggesting a relationship between the accumulation of mitochondrial cholesterol and the development of AD-pathology (Figure 2). Unexpectedly, our findings in hippocampal samples from patients with DS and AD suggest that STARD1 immunolabeling can act as a pathological mark of AD even better than Aβ42 deposition in post-morten samples (Figure 3), implying that the hippocampal alterations in the expression of STARD1 could occur in a temporal pattern parallel to the pathogenic amyloidogenic burden. DISCUSSION Our findings suggest that while altered hippocampal NPC1 expression could be a common feature of DS and AD AGING 9 www.aging-us.com Although not statistical significant, our findings do suggest a trend for lower expression of STARD3/MLN64 in the cortex of AD samples (Figure 1B), whose impact in regulating the mitochondrial pool of cholesterol remains to be understood. In this regard, it is interesting to note that increased expression of MLN64 has been reported in the lysosomal storage disorder Niemann-Pick type C disease, which correlated with increased mitochondrial cholesterol accumulation [36]. However, it has also been reported that targeted mutations of the MLN64 START domain have been shown to cause minor alterations in metabolism and intracellular distribution of cholesterol [37]. Further investigation will be required to decipher the impact of MLN64 in mitochondrial cholesterol regulation and AD pathogenesis. implies accumulation of mitochondrial cholesterol in activated astrocytes within CA1 independently of NPC1. Whether this outcome reflects that post-mortem samples from patients with AD represent a late stage of the disease masking the early intra-organelle cholesterol mobilization remains to be further investigated. Finally, whether the increase in hippocampal Aβ42 deposits reflects an impaired Aβ clearance by increased lysosomal cholesterol remains to be further confirmed in human neurodegeneration. Although the astrocyte- dependent lipidation of ApoE could contribute to the ability of glia to clear Aβ burden, this event does not seem to occur in ApoE4-carrying subjects [2], and defects in Aβ clearance have been detected in cerebrospinal fluid of >98% of LOAD cases [43], which may reflect defects in the endolysosomal/autophagy system in the early neuropathological stages of AD [44]. In line with this possibility, we have recently reported that elevated intracellular cholesterol levels in a hypercholesterolemic mouse model increased Aβ- induced autophagosome formation, but impaired the fusion with lysosomal vesicles causing deficient autophagy-dependent Aβ degradation [45]. Considering that DS might serve as a model for early AD [12], the observations of increased lysosomal cholesterol loading support the notion that abnormal cholesterol distribution in lysosomes can impact mitochondrial function through sustained mitochondrial cholesterol accumulation and Aβ clearance, emerging as an early event in AD pathogenesis. Reactive astrogliosis has emerged as a relevant pathological response in the early stages of AD [38], which correlates with cognitive decline [16]. DISCUSSION Whether these alterations in STARD1 occur before Aβ42 deposition in human AD requires further investigation. However, previous evidence in experimental models pointed that enhanced mitochondrial cholesterol levels in AD mouse models have been shown to sensitize neurons to Aβ- induced inflammation and toxicity by depleting mGSH by an ER stress-dependent mechanism [6, 7, 33]. Moreover, as Aβ-induced ER stress is considered an indirect effector of the Aβ-neurotoxicity in early stages of AD [34], our data suggest that STARD1 overexpression in the hippocampus may be a potential early molecular event associated with AD, as strengthened by the increase seen in DS, an accelerated genetic form of AD. In this context, it is widely recognized that neuro- inflammation in AD is an early pathological-associated response, which is exacerbated with ageing and contributes to disease progression [18, 35]. Although the groups studied were not age-matched given the limited number of samples and the life-expectancy of individuals with DS [8], we performed the comparisons with AD and controls considering AD pathogenesis as a function of age in DS, a population that exhibit a high risk to develop AD-type dementia [12, 24]. Moreover, as described previously [18], individuals with DS developed signs of AD-pathology by 50-55 years of age, which coincides with the age range of the subjects with DS analyzed in our study (Table 1). In this context, interestingly we found increased expression of NPC1 and STARD1 in cortical samples from patients with AD and DS, respectively, (Figure 1). A link between lysosomal cholesterol and Aβ42 deposition in neurodegeneration has been described in Niemann–Pick type C (NPC) disease, a rare autosomal recessive disease associated mostly with NPC1 mutations, characterized by lysosomal accumula- tion of unesterified cholesterol [25]. While the etiology and epidemiology of AD and NPC differ, these neurodegenerative diseases share many disease-related molecular pathways, including cholesterol accumulation, lysosomal abnormalities, tau hyperphosphorylation, APP processing and Aβ deposition [2, 25]. Moreover, while increased mRNA and protein levels of NPC1 have been described within the hippocampus of both patients with AD and mice [3], the hippocampal expression pattern of NPC1 in human DS-brains has not been reported. DISCUSSION Since astrocytes are the most prevalent cell type in the brain and form an intricate system of connections to control a wide range of brain functions, including regulation of blood-brain barrier, the astroglial atrophy could have far- reaching consequences on synaptic transmission that accounts for the spatio-temporal progression of AD- neurodegeneration [17]. We confirm the presence of reactive astrocytes surrounding amyloid plaque in the hippocampus of AD and DS, and observed a hippo- campal region-specific increased expression of STARD1 within astocytes (Figure 4) that correlates with the accumulation of mitochondrial cholesterol in both groups (Figure 5). Similarly, we also found astroglial NPC1 overexpression and astroglial accumulation of lysosomal cholesterol in AD and DS (Figures 4 and 5). These results are in line with findings reporting the activation of rat astrocytes induced by cholesterol exposure in vitro, resulting in enhanced APP/BACE-1 interaction within lipid-rafts, increased APP content, and enhanced ROS production [39]. Moreover, recent observations from a single cell brain atlas of human AD indicated the diversity of astrocytes in AD under the control of the transcription factor EB, a master regulator of lysosomal function, which initiated a regulatory cascade containing multiple AD GWAS genes [40]. Taken in consideration that subjects with DS display abnormal lipid metabolism from the embryonic stages [41] and that SOD1, BACE-2, S100β and APP genes are located at HSA21 [42], it is conceivable that subjects with HSA21 trisomy could have a basal cholesterol-mediated astrocyte activation. These findings along with the observed increased NPC1 expression in DS individuals (Figure 2) suggests that an enhanced hippocampal lysosomal cholesterol trafficking could result in increased mitochondrial cholesterol loading in hippocampal areas, possibly coinciding with signs of early AD-pathogenesis. Moreover, elevated astrogial-STARD1 expression in individuals with AD In conclusion, this exploratory study in post-mortem brains from patients with AD and DS revealed increased mitochondrial and lysosomal cholesterol levels in hippocampus from patients with AD and DS, which correlate with higher expression of STARD1 and NPC1. Moreover, our findings indicate the ability of STARD1 expression to discriminate controls from AD in the general population and in subjects with DS and suggest that STARD1 could be a potential marker associated with early molecular events of AD pathology. Further studies with a higher number of human samples are needed to validate these findings. In addition, future research using mice with tissue-specific deletion of STARD1 are warranted to define its role in AD pathology. Immunofluorescence Paraffin sections (5 µm) of hippocampus were dewaxed/rehydrated and treated for antigen retrieval as was described above for immunohistochemical analysis. Sections were permeabilized with 0.2% Triton X-100 in blocking buffer (5% goat serum + 1% BSA in PBS) during 10 min, followed by washing ×3 with PBS and incubation overnight at 4°C with primaries antibodies (Supplementary Table 4) into a dark-humid chamber, as described in detail in Supplementary Methods. Western blotting Human frozen cortex (350 mg) were homogenized on ice in anti-proteases/anti-phosphatases (Complete/ PhosSTOP, Roche) containing RIPA lysis buffer. Protein quantitation was assessed by BCA (Pierce) and samples (90 µg/lane) were resolved by 4-12% SDS- PAGE (Bio-Rad), electrotransferred to nitrocellulose membranes (Trans-Blot Turbo, Bio-Rad), followed by 5% BSA-blocking and incubation with primary antibodies (Supplementary Table 4) at 4°C overnight. After washing, membranes were incubated 1 hr at RT with the corresponding horseradish peroxidase-coupled secondary antibodies and visualized using the Pierce ECL Western Blotting Substrate (Thermo Scientific). Immunoblots images were captured using LAS4000 (GE Healthcare) and quantitation of the bands was performed by Image J free software (NIH). Immunohistochemistry Paraffin sections (5 µm) of hippocampus were processed according to the avidin–biotin–peroxidase staining method (Vectastain ABC kit; Vector Lab), as described previously [7] and detailed in Supplementary Methods. Statistics Data are shown as mean ± S.E.M and statistical analysis performed with the GraphPad Prism-5 software (San Diego, CA). Due to the number of analysed samples (≤7 for each group), nonparametric tests were employed. Differences between AD, DS and control samples were analysed with Kruskall-Wallis test followed by Mann-Whitney U-test to analyze the differences between two groups. The Spearman's rank-correlation coefficient rs was also determined when pertinent. Two- tailed p values <0.05 were considered statistically significant. ROC curves were generated and the area under ROC curves (AUC) was calculated to evaluate sensitivity and specificity of immunolabeling within hippocampal regions. ROC curves from control group were compared to AD or DS or AD+DS groups. The cut-off points on the ROC curves at which accuracy of disease detection was maximal were selected. Human brain samples Twenty-one cases from the Biobank of Hospital Clinic/IDIBAPS of Barcelona were collected following approval of the Clinical Research Ethics Committee of the Hospital Clinic of Barcelona (HCB/2015/0595). AGING 10 www.aging-us.com Transferase (GST-PFO), as described [46]. In brain tissues, PFO binds and detects cholesterol in membranes when its levels exceed 30% mol, while the fusion with GST allows PFO detection by immunofluorescence. The sequence to design the plasmid was DNA M36704 (NCBI database) corresponding to the gen of PFO in the Clostridium perfringens genome. Additionally, the signal peptide was eliminated from the PFO gen to enable the intracellular stance of the protein. The resulted sequence was synthesized into the plasmid pGEX 4T-1 (GenScript) between the BamHI and SmaI restriction sites. The plasmid was engineered to make a fusion protein with the GST tag. After bacterial production, protein extraction and purification, the GST-PFO probe was dialyzed, concentrated, quantified and stored at −80°C. Samples were scored by CERAD scale (A-C) and Braak stage (0-VI) and categorized as AD, DS, and control groups. For each group, demographic data as well as clinical and anatomopathological diagnosis are detailed in Table 1. Please find the BRISQ checklist in Sup- plementary Methods detailing the biospecimen samples collected from patients with AD and DS. Samples were scored by CERAD scale (A-C) and Braak stage (0-VI) and categorized as AD, DS, and control groups. For each group, demographic data as well as clinical and anatomopathological diagnosis are detailed in Table 1. Please find the BRISQ checklist in Sup- plementary Methods detailing the biospecimen samples collected from patients with AD and DS. mRNA isolation and RT-qPCR Total RNA was extracted from 150 mg of frozen cortex of human brains, using TRIzol reagent (Invitrogen), cleaned by RNeasy columns (Qiagen), and quantified through Nanodrop spectrophotometer (Thermo-Fisher Scientific). Real-time qPCR was performed using the iScript™ One- Step RT-PCR Kit with SYBR® Green (Bio-Rad) following the manufacturer’s instructions. Briefly, 200 ng of total RNA were mixed with 300 µmol/l of specific primers for each gene assessed (Supplementary Table 3) in 1× reaction buffer at final volume of 10.5 µl. RT- qPCRs were performed in triplicate using a CFX380 Real-Time System (Bio-Rad) following the manufac- turer’s instructions. Gene expression values were normalized using actin as housekeeping gene. Image analysis Detection and quantitation of immunoreactivity for Aβ42, p-tau, NPC1, and STARD1 was performed from high- resolution scanned immunohistochemical images of hippocampus using the Image J Software after Color Deconvolution plug-in [47], as detailed in Supplementary Methods. Recombinant GST-PFO probe To optimally assess the localization of cholesterol in hippocampal tissues, we generated a recombinant Perfringolysin O (PFO) fusioned with Glutathione-S- AGING 11 www.aging-us.com https://doi.org/10.1016/j.bbamem.2018.03.015 2. Arenas F, Garcia-Ruiz C, Fernandez-Checa JC. Intracellular cholesterol trafficking and impact in neurodegeneration. Front Mol Neurosci. 2017; 10:382. https://doi.org/10.3389/fnmol.2017.00382 PMID:29204109 3. Kågedal K, Kim WS, Appelqvist H, Chan S, Cheng D, Agholme L, Barnham K, McCann H, Halliday G, Garner B. Increased expression of the lysosomal cholesterol transporter NPC1 in Alzheimer’s disease. Biochim Biophys Acta. 2010; 1801:831–38. https://doi.org/10.1016/j.bbalip.2010.05.005 PMID:20497909 3. Kågedal K, Kim WS, Appelqvist H, Chan S, Cheng D, Agholme L, Barnham K, McCann H, Halliday G, Garner B. Increased expression of the lysosomal cholesterol transporter NPC1 in Alzheimer’s disease. Biochim Biophys Acta. 2010; 1801:831–38. REFERENCES 1. Bharadwaj P, Solomon T, Malajczuk CJ, Mancera RL, Howard M, Arrigan DW, Newsholme P, Martins RN. Role of the cell membrane interface in modulating production and uptake of Alzheimer’s beta amyloid protein. Biochim Biophys Acta Biomembr. 2018. [Epub ahead of print]. 1. Bharadwaj P, Solomon T, Malajczuk CJ, Mancera RL, Howard M, Arrigan DW, Newsholme P, Martins RN. Role of the cell membrane interface in modulating production and uptake of Alzheimer’s beta amyloid protein. Biochim Biophys Acta Biomembr. 2018. [Epub ahead of print]. CONFLICTS OF INTEREST Additional visualization of the association between markers and subject status (i.e. control, AD, or DS) was performed through multivariate data analysis by PCA using JMP 9.0 software (SAS Institute Inc.). PCA show the data variability as the covariance of samples for each marker (descriptors) projected into a subspace made of orthogonal linear axis, so-called principal components. The authors declare there are no conflicts of interest. ACKNOWLEDGMENTS We want to thank Dr. María Carmona from the Hospital de la Santa Creu y San Pau for critically reading the manuscript and valuable suggestions. 5. Webber KM, Stocco DM, Casadesus G, Bowen RL, Atwood CS, Previll LA, Harris PL, Zhu X, Perry G, Smith MA. Steroidogenic acute regulatory protein (StAR): evidence of gonadotropin-induced steroidogenesis in Alzheimer disease. Mol Neurodegener. 2006; 1:14. Abbreviations AD: Alzheimer´s disease; Aβ42: beta amyloid peptide 42; DS: Down syndrome; EOAD: early-onset AD; LOAD: late-onset AD; mGSH: mitochondrial GSH; MAM: mitochondrial ER-associated membranes; MIM: mitochondrial inner membrane; NFTs: neurofibrillary tangles; NPC1: Niemann Pick type C1 protein; PCA: principal component analysis; PFO: recombinant perfringolysin; p-tau: phosphorylated tau; StARD1: steroidogenic acute regulatory protein. AUTHOR CONTRIBUTIONS All authors read and approved the final manuscript. F.A. and S.N. performed gene expression, WB and immunohistochemistry procedures. F.A., G.G. and F.C. synthesized GST-PFO and performed immuno- fluorescence. F.A., C.G-R and J.C. F-Ch analysed and discussed data and wrote the manuscript. https://doi.org/10.1016/j.bbalip.2010.05.005 PMID:20497909 4. Elustondo P, Martin LA, Karten B. Mitochondrial cholesterol import. Biochim Biophys Acta Mol Cell Biol Lipids. 2017; 1862:90–101. 4. Elustondo P, Martin LA, Karten B. Mitochondrial cholesterol import. Biochim Biophys Acta Mol Cell Biol Lipids. 2017; 1862:90–101. https://doi.org/10.1016/j.bbalip.2016.08.012 PMID:27565112 8. Wiseman FK, Al-Janabi T, Hardy J, Karmiloff-Smith A, 8. Wiseman FK, Al-Janabi T, Hardy J, Karmiloff-Smith A, https://doi.org/10.3389/fneur.2019.01168 15. Braak H, Del Trecidi K. Neuroanatomy and pathology of sporadic Alzheimer’s disease. Adv Anat Embryol Cell Biol. 2015; 215:1–162. https://doi.org/10.1186/1750-1326-1-14 PMID:17018137 We acknowledge the support from grants SAF2014- 57674R, SAF-2015-69944R, and SAF2017-85877R from Plan Nacional de I+D, by the CIBEREHD from the Instituto de Salud Carlos III, by AGAUR of the Generalitat de Catalunya SGR-2017-1112, and by the “ER stress-mitochondrial cholesterol axis in obesity- associated insulin resistance and comorbidities”- Ayudas FUNDACION BBVA, Spain. We also acknowledge support from the center grant P50AA011999 Southern California Research Center for ALPD and Cirrhosis funded by NIAAA/NIH and by the European Cooperation in Science and Technology (COST) ACTION CA17112 Prospective European Drug-Induced Liver Injury Network, and Red Nacional 2018-102799-T de Enfermedades Metabólicas y Cáncer. 6. Barbero-Camps E, Fernández A, Baulies A, Martinez L, Fernández-Checa JC, Colell A. Endoplasmic reticulum stress mediates amyloid β neurotoxicity via mitochondrial cholesterol trafficking. Am J Pathol. 2014; 184:2066–81. https://doi.org/10.1016/j.ajpath.2014.03.014 PMID:24815354 6. Barbero-Camps E, Fernández A, Baulies A, Martinez L, Fernández-Checa JC, Colell A. Endoplasmic reticulum stress mediates amyloid β neurotoxicity via mitochondrial cholesterol trafficking. Am J Pathol. 2014; 184:2066–81. 7. Barbero-Camps E, Fernández A, Martínez L, Fernández- Checa JC, Colell A. 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Alzheimer’s disease in Down syndrome: neurobiology and risk. Ment Retard Dev Disabil Res Rev. 2007; 13:237–46. AGING 14 www.aging-us.com Immunohistochemistry analysis After paraffin sections were dewaxed and rehydrated, the antigen retrieval of hippocampus sections was performed using 99% formic acid (5 min at RT), following by heating-incubation (120°C for 20 min) with 10 mM Tris/1mM EDTA/0.05% Tween 20; pH 9.0. Endogenous peroxidase was blocked using 3% H2O2/methanol for 45 min. In a dark-humid chamber, blocking of sections was performed using Dako antibody diluent background reducing components (Dako) for 20 min, and treated with the Avidin/Biotin blocking kit from Vector Lab according to the manufacturer's instructions and incubated overnight (4°C) with antibodies against human Aβ, pathological phospho-tau (Ser202 and Thr205), NPC1, and StARD1 (Supplementary Table 2). Sections were then incubated (1 hr) with the corresponding biotinylated secondary antibodies diluted 1:200, followed by ABC staining for 30 min. The immunoreactivities were visualized with diaminobenzidine (DAB enhanced liquid substrate system, Sigma). Sections were counterstained with hematoxylin (Dako) and mounted with a coverslip. The final stained hippocampal sections were then scanned in a 43X resolution using Panoramic DESK digital slice scanner with Carl Zeiss objectives (3DHISTECH) and images of entire hippo- campus regions where capture using Panoramic Viewer software (3DHISTECH). Images for all samples were taken with a Leica TCS SP5 laser scanning confocal system with a 63X oil immersion objective APO CS numerical aperture 1.4 equipped with a DMI6000 inverted microscope. Image analysis Briefly, after background subtraction and filtering processes (median, radius 2.0), segmentation of immunoreactivities was performed by the combination of H-DAB vector matrix of Color Deconvolution plug- in [14] – which separate channels corresponding to 3 determined colors of hematoxylin-DAB stain – with the local standard threshold of the “Colour-2” (brown) resulted images. Immunoreactivities were then sub- jected to particle analysis for acquiring the percentage of immunolabeled area relative with the total area of the image. Confocal images of immunoreactivities for GFAP, NPC1 and StARD1 from hippocampal paraffin sections were analysed by Image J Software. In 10 different images of each hippocampal region (CA1, CA2 or CA3), percentage of total NPC1 or StARD1 mass containing astrocytes (GFAP+) were analysed using the Colocalization nBits n-images plug-in (Confocal Microscopy Unit, Medicine Faculty, University of Barcelona), which highlights the colocalized points of two 32-bits images (Figure 4A). Two points are considered as colocalized if their respective intensities are strictly higher than the threshold of their channels and if their ratio of intensity is strictly higher than the ratio setting value, which have been defined at 50%. Colocalization index is calculated as the ratio of colocalized points between total threshold-passed intensity and relativized with control group. SUPPLEMENTARY MATERIALS with primaries antibodies (Supplementary Table 4). Secondary antibodies were diluted 1:200 in 1% Goat Serum containing 0.05% Triton X-100 in PBS and incubated for 90 min at RT with the mix of anti-rabbit Alexa fluor-647 (for Tom20 or Lamp1), anti-mouse Alexa fluor-532 (for GST) and anti-rat Alexa fluor-488 (for GFAP). After washing, slices were incubated 5 min in Sudan black 0.1% in 70% ethanol to minimize autofluorescence and mounted with prolong antifade mountant with Dapi (Dako). https://doi.org/10.1002/mrdd.20163 PMID:17910085 43. Mawuenyega KG, Sigurdson W, Ovod V, Munsell L, Kasten T, Morris JC, Yarasheski KE, Bateman RJ. Decreased clearance of CNS beta-amyloid in Alzheimer’s disease. Science. 2010; 330:1774. https://doi.org/10.1126/science.1197623 PMID:21148344 46. Kwiatkowska K, Marszałek-Sadowska E, Traczyk G, Koprowski P, Musielak M, Lugowska A, Kulma M, Grzelczyk A, Sobota A. Visualization of cholesterol deposits in lysosomes of Niemann-Pick type C fibroblasts using recombinant perfringolysin O. Orphanet J Rare Dis. 2014; 9:64. https://doi.org/10.1186/1750-1172-9-64 PMID:24775609 44. Cataldo AM, Peterhoff CM, Troncoso JC, Gomez-Isla T, Hyman BT, Nixon RA. Endocytic pathway abnormalities precede amyloid beta deposition in sporadic Alzheimer’s disease and Down syndrome: differential effects of APOE genotype and presenilin mutations. Am J Pathol. 2000; 157:277–86. https://doi.org/10.1016/S0002-9440(10)64538-5 PMID:10880397 47. Ruifrok AC, Johnston DA. Quantification of histochemical staining by color deconvolution. Anal Quant Cytol Histol. 2001; 23:291–99. PMID:11531144 45. Barbero-Camps E, Roca-Agujetas V, Bartolessis I, de Dios C, Fernández-Checa JC, Marí M, Morales A, Hartmann T, Colell A. Cholesterol impairs autophagy- mediated clearance of amyloid beta while promoting its secretion. Autophagy. 2018; 14:1129–54. AGING 15 www.aging-us.com Immunofluorescence analysis Secondary antibodies (Thermofisher) were diluted 1:200 in 1% Goat Serum containing 0.05% Triton X-100 in PBS and incubated (1 hr at RT) with the mix of anti- rabbit Alexa fluor-532 (for StARD1 or NPC1), anti- mouse Alexa fluor-635 (for Aβ42), and anti-rat Alexa fluor-488 (for GFAP). Finally, sections were incubated (10 min) with 20 mM Hoechst 33342 dye (Thermofisher), washed and incubated (5 min) with 0.1 % sudan black dye (Sigma) in 70% ethanol to block autofluorescence, followed by mounting using fluo- rescent mounting medium (Dako). On the other hand, similar to as been described above to paraffin sections, detection of cholesterol within lyso- somes or mitochondria into astrocytes was performed in cryopreserved hippocampal sections and analysed by confocal imaging using Image J Software. Immuno- fluorescence images were submitted to background subtraction and filtering processes with Median filter set at 2.0 of radius. Then, 0.4 µm spaced consecutive Human hippocampal cryopreserved 14 µm thin sections were fixed in 4% paraformaldehyde for 20 min. In a dark-humid chamber, the sections were permeabilized with 0.2% Triton X-100 in blocking buffer (5% goat serum + 1% BSA in PBS) for 2 hr. Then, slices were incubated (3 hr at 4°C) with the probe GST-PFO (20µg/ml) in 1% Goat Serum containing 0.05% Triton X-100 in PBS, followed by incubation overnight (4°C) AGING 16 www.aging-us.com Intracellular cholesterol accumulation associated with astrogliosis in postmortem brains from patients with AD and DS collected from from Biobank of Hospital Clinic (IDIBAPS) with the approval of the Clinical Research Ethics Committee of the Hospital Clinic of Barcelona (HCB/2015/0595). images were stacked at maximum intensity and segmented by threshold to select the area of astrocytes (GFAP+). All marks outside GFAP+ area were clean in the corresponding images for GST+ and Tom20+/Lamp1+. Resulted images were then analysed using the Colocalization nBits n-images plug-in (Confocal Microscopy Unit, Medicine Faculty, University of Barcelona) as is described above. BRISQ checklist Based on Moore et al, Cancer Cytopathol 2011; 119(2):92–101. https://doi.org/10.1002/cncy.20147. Biospecimen type Brain sections Anatomical site Cortex and Hippocampus Disease status of patients Alzheimer with or without Down Syndrome, Controls without neurological disease Clinical characteristics of patients Patients with Dementia Vital State of patients Postmortem Clinical diagnosis of patients Alzheimer dementia Pathology diagnosis CERAD B-C and Braak V-VI; detailed in Methods and in Table 1 Collection mechanism Postmortem dissection Type of stabilization On ice Type of long-term preservation Formalin fixation, freezing Constitution of preservative 10% neutral-buffered formalin Storage temperature −80 ºC, 20 to 25 ºC Storage duration 5-10 years Shipping temperature −170 ºC to −190 ºC, 20 to 25 ºC Composition assessment and selection Brain sections used for anatomopathological diagnosis of Alzheimer Brain sections AGING 17 www.aging-us.com www.aging-us.com Supplementary Figures ementary Figure 1. Principal Component Analysis (PCA) of Aβ42, p-tau, NPC1, and StARDl markers. For CA1, ampus regions is show (left panel) the covariance between %area immunodetected by IHC of the corresponding marker al plane (Component 1 + Component 2) represented on the first vectorial plan of the PCA. Histogram of Eigenvalue on. (Right panel) Distribution of AD, DS, and control samples onto the two first axes of the PCA. Supplementary Figure 1. Principal Component Analysis (PCA) of Aβ42, p-tau, NPC1, and StARDl markers. For CA1, CA2, and CA3 hippocampus regions is show (left panel) the covariance between %area immunodetected by IHC of the corresponding marker, and the first principal plane (Component 1 + Component 2) represented on the first vectorial plan of the PCA. Histogram of Eigenvalues explain the variation. (Right panel) Distribution of AD, DS, and control samples onto the two first axes of the PCA. AGING 18 www.aging-us.com plementary Figure 2. Principal Component Analysis (PCA) of lysosomal and mitochondrial cholesterol conta ers within hippocampal astrocytes. (Left panel) First vectorial plan of the PCA that describe the covariance between de ent of both glial cholesterol carriers and lysosomal/mitochondrial cholesterol content) and the first principal plane (Compo ponent 2). Histogram of Eigenvalues explain the variation. (Right panel) Distribution of AD, DS, and control samples onto the of the PCA. Supplementary Figure 2. Principal Component Analysis (PCA) of lysosomal and mitochondrial cholesterol contain and carriers within hippocampal astrocytes. BRISQ checklist (Left panel) First vectorial plan of the PCA that describe the covariance between descriptors (content of both glial cholesterol carriers and lysosomal/mitochondrial cholesterol content) and the first principal plane (Component 1 + Component 2). Histogram of Eigenvalues explain the variation. (Right panel) Distribution of AD, DS, and control samples onto the two first axes of the PCA. AGING 19 www.aging-us.com Supplementary Tables pp y Supplementary Table 1. Overview of modulation of key proteins involved in intracellular cholesterol trafficking in the brain (1). Control Cortical levels (n-fold) mean±SEM Hippocampal levels (n-fold) mean±SEM CA1 CA2 CA3 Marker mRNA Protein(a) Proteln(b) GFAP+ colocalization Proteln(b) GFAP+ colocalization Proteln(b) GFAP+ colocalization Aβ42 n.a. n.a. 1.00 ± 0.262 n.a. 1.00 ±0.471 n.a. 1.00 ±0,323 n.a p-tau n.a. n.a. 1.00 ±0.342 n.a. 1.00 ±0.368 n.a. 1.00 + 0.288 n.a. NPC1 1.00 ±0.019 1.00 ± 0.017 1.00 ±0.173 1.00 ±0.196 1.00 ±0.357 1.00 ±0.120 1.00 ± 0.331 1.00 ±0.192 StARDl 1.00 ±0.015 1.00 ± 0.044 1.00 ±0.321 1.00 ±0.271 1.00 ±0.458 1.00 ±0.331 1.00 ±0.396 1.00 ±0.178 StARD3/ MLN64 1.00 ±0.030 1.00 ± 0.237 n.a. n.a. n.a. n.a. n.a. n.a. StARD4 1.00 ±0.023 n.a. n.a. n.a. n.a. n.a. n.a. n.a. INSIG n.a. 1.00 ± 0.053 n.a. n.a. n.a. n.a. n.a. n.a. SREBP2 n.a. 1.00 ± 0.028 n.a. n.a. n.a. n.a. n.a. n.a. Alzheimer´s disease Cortical levels (n-fold) mean±SEM Hippocampal levels (n-fold) mean±SEM CA1 CA2 CA3 Marker mRNA Protein(a) Proteln(b) GFAP+ colocalization Proteln(b) GFAP+ colocalization Proteln(b) GFAP+ colocalization Aβ42 n.a. n.a. 7.04 ± 2.106 n.a. 1.97 ±0.727 n.a. 1.91 ±0.556 n.a. p-tau n.a. n.a, 2.42 ±0.736 n.a. 1.63 ±0.554 n.a. 1.67 ±0.621 n.a. NPC1 1.02 ±0.039 1.12 ±0.025 p1=0.0043 8.07 ± 1.834 p1=0.0006 0.92 ±0.194 3.77 ±0.800 p1=0.0111 1.25 ±0.238 8.06 ± 1.539 p1=0.0006 1.08 ± 0.087 p2=0.0023 StARDl 1.00 ±0.014 1.25 ±0.056 P1=0.0087 2.31 ±0.419 p1=0.0379 2.60 ±0.563 P1=0.0111 2.00 ±0.918 0.67 ± 0.232 5.92 ± 2.171 P1=0.0047; p2=0.0130 1.19 ±0.249 StARD3/ MLN64 0.99 ± 0.062 0.64 ± 0.150 n.a. n.a. n.a. n.a. n.a. n.a. StARD4 1.00 ±0.020 n.a, n.a. n.a. n.a. n.a. n.a. n.a. INSIG n.a. 1.05 ± 0.160 n.a. n.a. n.a. n.a. n.a. n.a. SREBP2 n.a. 1.12 ±0.161 n.a. n.a. n.a. n.a. n.a. n.a. Down syndrome Cortical levels (n-fold) mean±SEM Hippocampal levels (n-fold) mean±SEM CA1 CA2 CA3 Marker mRNA Protein(a) Proteln(b) GFAP+ colocalization Proteln(b) GFAP+ colocalization Proteln(b) GFAP+ colocalization A(342 n.a. n.a. 11.30 ±3.423 Pi=0.0012 n.a. 4.27 ±1.275 Pi=0.0177 n.a. 3.99 ± 1.051 Pi=0.0221 n.a. BRISQ checklist p-tau n.a. n.a. 2.59 ±0.783 n.a. 2.29 ±0.784 n.a. 2.88 ± 1.135 n.a. IMPCl 1.08 ±0.028 1.04 ±0.036 9.86 ±2.413 p1=0.0006 1.62 ±0.420 5.41 ±1.740 P1=0.0111 2.05 ± 0.577 8.79 ±1.822 P1=0.0006 1.08 ± 0.087 p1=0.0023 StARDl 1.08 ±0.013 P1=0,0087 1.35 ±0.044 P1=0.0043; p2=0.0159 0.97 ±0.182 p2=0.0111 2.81 ± 0.755 0.56 ±0.212 0.80 ± 0.246 2.62 ±1.290 p2=0.0130 2.01 ±0.311 P1=0.0111 StARD3/ MLN64 1.13 ±0.053 1.47 ±0.277 n.a. n.a. n.a. n.a. n.a. n.a. Supplementary Table 1. Overview of modulation of key proteins involved in intracellular cholesterol trafficking in the brain (1). AGING 20 www.aging-us.com StARD4 1.03 ± 0.008 n.a. n.a. n.a. n.a. n.a. n.a. n.a. INSIG n.a. 1.14 ±0.043 n.a. n.a. n.a. n.a. n.a. SREBP2 n.a. 1.14 ±0.061 n.a. n.a. n.a. n.a. n.a. n.a. NOTE: P values are calculated by differences against control (pi) or differences between AD and DS (pz). Supplementary Table 2. Overview of modulation of key proteins involved in intracellular cholesterol trafficking in the brain (1). Astrocyte (GFAP+) cholesterol (PFO+) colocalization (n-fold) Organelle marker Control AD DS Tom20 (mitochondria) 1.00 ±0.257 2.55 ± 0.297; p1=0.0079 2.77 ± 0.203; p1=0.0159 Lampl (lysosome) 1.00 ±0.136 3.43 ± 0.502; p1=0.0079 14.41 ± 1.322; p1,2=0.0079 Supplementary Table 3. Oligonucleotides used for gene expression analysis by RT-qPCR. Gene Sequence StARD1 5′-GAGGAGGCCATGCAGAA 5′-GAACACCTTGCCCACATC StARD3 5′-AGTGAGGAGCCCAGGGAG 5′-CCGTGGCTGACATGGAG StARD4 5′-CGTTTTCTTAGCAACTCGCC 5′-CTTCCACGTCCTTGCTTCAC NPC1 5′-CATCCTTTGGCAATGGTTTT 5′-CTGCTGCTACTGTGTCCAGC β-Actin 5′-TTGCCGACAGGATGCAGAA 5′-GCCGATCCACACGGAGTACT Supplementary Table 2. Overview of modulation of key proteins involved in intracellular cholesterol trafficking in the brain (1). Astrocyte (GFAP+) cholesterol (PFO+) colocalization (n-fold) Organelle marker Control AD DS Tom20 (mitochondria) 1.00 ±0.257 2.55 ± 0.297; p1=0.0079 2.77 ± 0.203; p1=0.0159 Lampl (lysosome) 1.00 ±0.136 3.43 ± 0.502; p1=0.0079 14.41 ± 1.322; p1,2=0.0079 ementary Table 2. Overview of modulation of key proteins involved in intracellular choleste Overview of modulation of key proteins involved in intracellular cholesterol trafficking in t Supplementary Table 3. Oligonucleotides used for gene expression analysis by RT-qPCR. Gene Sequence StARD1 5′-GAGGAGGCCATGCAGAA 5′-GAACACCTTGCCCACATC StARD3 5′-AGTGAGGAGCCCAGGGAG 5′-CCGTGGCTGACATGGAG StARD4 5′-CGTTTTCTTAGCAACTCGCC 5′-CTTCCACGTCCTTGCTTCAC NPC1 5′-CATCCTTTGGCAATGGTTTT 5′-CTGCTGCTACTGTGTCCAGC β-Actin 5′-TTGCCGACAGGATGCAGAA 5′-GCCGATCCACACGGAGTACT Supplementary Table 3. Oligonucleotides used for gene expression analysis by RT-qPCR. AGING 21 www.aging-us.com Supplementary Table 4. Primary antibodies used in this study. BRISQ checklist Antibody Source and type Company WB dilution IHC/IF dilution StARD1 Rabbit monoclonal Abcam (ab133657) 1:1000 1:200 StARD3 (MLN64) Rabbit polyclonal Sant Cruz (sc-292868) 1:1000 SREBP2 Rabbit polyclonal Abcam (ab28482) 1:500 INSIG-1 Rabbit polyclonal Abcam (ab70784) 1:1000 NPC-1 Rabbit polyclonal Abcam (ab36983) 1:500 1:200 Aβ human (6F/3D) Mouse monoclonal Dako (M0872) 1:2000 Lamp1 Rabbit polyclonal Sant Cruz (sc-5570) 1:200 Tom20 Rabbit polyclonal Sant Cruz (sc-11415) 1:200 GFAP Rat monoclonal Calbiochem (345860) 1:200 Glutathione-S- Transferase (GST) Mouse monoclonal Sant Cruz (sc-374171) 1:200 PHF-tau (AT8) Mouse monoclonal Thermofisher (MN1020) 1:200 β-Actin-HRP Mouse monoclonal Sigma (A3854) 1:20000 NeuN Mouse monoclonal Millipore (MAB377) 1:200 IBA1 Mouse monoclonal Santa Cruz (sc-32725) 1:200 Supplementary Table 4. Primary antibodies used in this study. AGING 22 www.aging-us.com
https://openalex.org/W3163179083
https://publicacoes.epagri.sc.gov.br/RAC/article/download/932/1034
Portuguese
null
Produtividade de frutos e nutrição mineral de pepineiro para conserva submetido a soluções nutritivas em semi-hidroponia
Agropecuária Catarinense/Agropecuária catarinense
2,021
cc-by
4,899
ARTIGO CIENTÍFICO ARTIGO CIENTÍFICO Index terms: Cucumis sativus; fertigation; phenological phases. níveis múltiplos de uma dose padrão de nutrientes sobre o acúmulo e a dis- tribuição da matéria seca da planta de pepino tipo conserva, híbrido Crispina, cultivado em substrato sob abrigo. Estes autores observaram efeito significativo sobre o acúmulo de matéria seca dos órgãos da parte aérea da planta. Entre- tanto, relatam que o efeito das doses sobre o crescimento da planta e dos fru- tos mostrou tendência linear, sem indi- car saturação, sugerindo a necessidade de realização de novos experimentos com níveis mais elevados de fertilizan- tes para determinar o rendimento po- tencial de frutos do híbrido testado. a campo em até 168,5%, dependendo da época de cultivo (VIEIRA NETO et al., 2018). Apesar deste benefício, é neces- sário agregar outras práticas culturais a fim de potencializar a rentabilidade e reduzir custos de produção de pepi- neiro cultivado sob abrigo. Dentre elas, destaca-se a utilização de solução nutri- tiva específica para a cultura cultivada em substrato fertirrigado, levando-se em consideração as diferentes fases fe- nológicas, taxas de crescimento e absor- ção de nutrientes. Recebido em 23/6/2020. Aceito para publicação em 23/12/2020. ¹ Engenheiro-agrônomo, Dr., Epagri/Estação Experimental de Ituporanga, C.P. 121, 88400-000 Ituporanga, SC, fone: (47) 3533-8844, e-mail: joaoneto@epagri.sc.gov.br. ² Engenheiro-agrônomo, Dr., Epagri/Estação Experimental de Itajaí, C.P. 277, 88301-970 Itajaí, SC, fone: (48) 3233-5244, e-mail: rafael.epagri@gmail.com. ³ Químico, MSc., Epagri/Estação Experimental de Ituporanga, C.P. 121, 88400-000 Ituporanga, SC, fone: (47) 3533-8844, e-mail: cmora@epagri.sc.gov.br. Termos de indexação: Cucumis sativus; fertirrigação; fases fenológicas. Termos de indexação: Cucumis sativus; fertirrigação; fases fenológicas. Fruit yield and mineral nutrition of pickling cucumber subjected to nutrient solutions in semi-hydroponics Abstract – The present work was carried out with the objective of evaluating concentrations of the nutrient solution on the productivity and quality of pickling cucumber fruits under protected cultivation. Two experiments were conducted at Estação Experimental de Ituporanga (Epagri/EEItu), SC, in 2019 and 2020 with the hybrid Kybria F1. The experimental design was a randomized block with six replications, with treatments: 80, 90, 100, 110 and 120% of the fertilizer quantities recommended by research, following the distribution table indicated by the industry for each stage of development. There was a significant effect of the different concentrations of nutrient solutions evaluated on the yield of cucumber. The treatments that provided the highest productive performance, using the management indicated by the industry, were 90% of the standard solution and 100% standard solution. Index terms: Cucumis sativus; fertigation; phenological phases. Produtividade de frutos e nutrição mineral de pepineiro para conserva submetido a soluções nutritivas em semi-hidroponia João Vieira Neto¹, Rafael Gustavo Ferreira Morales² e Cristiano Mora³ Resumo – O presente trabalho foi realizado com objetivo de avaliar concentrações da solução nutritiva sobre a produtividade e qualidade de frutos de pepineiro para conserva, sob ambiente protegido. Dois experimentos foram conduzidos na Estação Experimental de Ituporanga (Epagri/EEItu), em SC, nos anos de 2019 e 2020, com o híbrido Kybria F1. O delineamento experimental foi o de blocos casualizados com seis repetições, sendo os tratamentos: 80, 90, 100, 110 e 120% das quantidades de fertilizantes recomendadas pela pesquisa, seguindo tabela de distribuição indicada pela indústria para cada estágio de desenvolvimento. Houve efeito significativo das concentrações de soluções nutritivas avaliadas sobre a produtividade do pepineiro. Os tratamentos que proporcionaram maior desempenho produtivo, utilizando o manejo indicado pela indústria, foram 90% da solução padrão e solução padrão 100%. Material e métodos Durante o experimento foram medi- dos semanalmente, por meio de peagâ- metro e condutivímetro, o pH e a condu- tividade elétrica das soluções nutritivas de cada tratamento (solução aplicada e drenada) para verificar a adequação desses parâmetros em cada fase da cul- tura. O volume de solução nutritiva foi aplicado para possibilitar uma fração de drenagem da ordem de 20 a 30%.i As mudas foram produzidas em ban- dejas de isopor com 72 células e trans- plantadas para os vasos nos dias 2 de outubro de 2019 e 13 de janeiro 2020, no estádio de duas folhas definitivas. Os vasos foram arranjados sobre plata- forma de madeira com 2,5cm de espes- sura, 25cm de largura a 15cm de altura do chão, para evitar contato direto com o chão do abrigo, no espaçamento de 0,4m x 1,0m. As plantas foram condu- zidas verticalmente, com ajuda de fiti- lhos plásticos. Foi utilizado o substrato comercial (MaxFértil®) para a produção de mudas e para o cultivo das plantas nos vasos, nos dois anos de avaliação, sendo utilizado substrato novo em cada ensaio. Este substrato possui abundân- cia na região de estudo, composto por Dois experimentos foram conduzi- dos na Epagri, Estação Experimental de Ituporanga, SC (27°38’ de LS e 49°60’ de LO e altitude de 475m, clima tipo Cfa, segundo a classificação de Köeppen) no segundo semestre de 2019 e primeiro de 2020. Os estudos foram instalados em es- tufa com estrutura de aço galvanizado com pé direito de 4,00m, teto em arco e abertura zenital. O teto era coberto com plástico agrícola difusor de luz ANTI-UV de 150micras. As cortinas laterais so- mente foram fechadas na ocorrência de ventos fortes. Amostras foliares foram retiradas das plantas no início do florescimento para quantificar valores de nutrientes, conforme preconizado pela Comissão de Química e Fertilidade do Solo (CQFS- RS/SC, 2004). As análises de tecido das folhas foram realizadas conforme Te- desco et al. (1995). O delineamento experimental utili- zado foi o de blocos casualizados, com cinco tratamentos e seis repetições, sendo os tratamentos: 80, 90, 100, 110 e 120% das quantidades de fertilizan- tes recomendadas por Andriolo & Peil (2016) para pepineiros em substrato. Introdução Para aplicação dos tratamentos fo- ram consideradas cinco fases fenoló- gicas, adaptado de Yara (2018), bem como as proporções de fertilizantes re- comendadas para cada fase, conforme descritos na Tabela 1. i As soluções, com as quantidades de fertilizantes para cada tratamento, foram aplicadas diariamente nos vasos usando becker graduado nas quantida- des: fase inicial (0,5L planta-1), fase ve- getativa 1 (1,0L planta-1), fase vegetativa 2 (1,5L planta-1), fase vegetativa 3 (2,0L planta-1), fase floração/produção (2,5L planta-1). Todas as irrigações foram fei- tas apenas com soluções nutritivas, uti- lizando-se água coletada da chuva. Introdução O estado de Santa Catarina é o maior produtor nacional de pepino para conserva, produzindo anualmente 15 mil toneladas, equivalendo a cerca de 25% da produção nacional. Uma boa parte da produção está concentrada na região do Vale do Itajaí (FÓRUM BRASI- LEIRO DE PRODUÇÃO DE PEPINO PARA CONSERVA, 2019). i A produtividade dessa hortaliça pode alcançar até 80t ha-1 em lavouras cultivadas em campo aberto (MARTINS, 2004; REBELO et al., 2011). No entan- to, quando cultivado em ambiente protegido, tipo estufa, estima-se que a produtividade obtida em abrigo tenha potencial para superar a produtividade Andriolo & Peil (2016) apresentam uma recomendação de solução nutriti- va para cultivo de pepineiro em subs- trato, mas não há uma especificação quanto ao tipo de pepino, salada, japo- nês ou conserva. No entanto, Espínola et al. (2001) avaliaram o efeito de três O cultivo de pepineiro em substrato vem crescendo na região do Alto Vale do Itajaí, como alternativa ao cultivo tradicional realizado no solo. Isso ocor- Este periódico está licenciado conforme Agropecuária Catarinense, Florianópolis, v.34, n.1, 48-53, jan./abr. 2021 48 vasos centrais considerados como par- cela útil. uma mistura de casca de pínus compos- tada e vermiculita. re devido à salinização e à incidência de doenças no solo, em consequência do manejo incorreto desse sistema de produção, sem práticas de conservação do solo e pelo uso incorreto dos ferti- lizantes. Normalmente, os substratos apresentam quantidades de nutrientes insuficientes para o desenvolvimento das plantas, sendo necessário o forne- cimento de nutrientes via fertirrigação para atender suas necessidades nutri- cionais. O presente trabalho foi realiza- do com objetivo de avaliar concentra- ções da solução nutritiva sobre a pro- dutividade e a qualidade de frutos de pepineiro para conserva sob ambiente protegido. Segundo análise feita pelo Labo- ratório de Análise de Substratos para Plantas da Faculdade de Agronomia do Departamento de Horticultura e Silvi- cultura da UFRGS, o substrato apresen- ta as seguintes características químicas, conforme extrato aquoso 1:5 (v/v): pH (H2O) = 5,56; CE = 0,55mS cm-1; densida- de seca = 337,5kg m-3; umidade atual = 43,7%; porosidade total = 79,6%; espa- ço de aeração = 26,0%; água facilmente disponível = 16,4%; água tamponante = 2,8%; água remanescente = 34,2%; e capacidades de retenção de água a 10 cm = 53,5%, 50cm = 37,1% e 100cm = 30,2%. Resultados e discussão Houve efeito significativo dos trata- mentos sobre a massa fresca de frutos comerciais por planta (MFFP) apenas no experimento de 2019 (Tabela 2). Os melhores resultados foram obtidos com os tratamentos 90% e 100%, com mé- dias de 2,69 e 2,87kg planta-1, respecti- vamente. Em 2020, foram observados valores inferiores aos obtidos em 2019 para a MFFP, com valores variando en- tre 0,55 a 0,65kg planta-1. Os baixos va- lores para MFFP observados em 2020 foram consequência de um ataque se- vero de pulgões, associados a sintomas de viroses. Este ataque reduziu o ciclo de cultivo e o número de colheitas. Em 2019 foram realizadas 21 colheitas, en- quanto que em 2020 apenas oito. Santa Maria, estado do Rio Grande do Sul. ao observado para o mesmo período de colheita em 2019. Neste mesmo perío- do as médias de temperatura média e umidade relativa do ar apresentaram pouca variação entre os anos avalia- dos, respectivamente, 2019 (20,11°C; 73,70%) e 2020 (21,82°C; 76,62%). O número de frutos comerciais por planta (NFP) foi afetada pelos tratamen- tos nos dois anos de avaliação (Tabela 2). Em 2019, observou-se maior núme- ro de frutos comerciais por planta para 80% (154,4), 90% (161,6) e 100% (171,4) e, em 2020, para 80% (34,0), 90% (32,7) e 100% (33,7). Do mesmo modo que ocorrido com MFFP em 2020, o NFP foi afetado pela incidência de pulgões nas plantas de pepineiro naquele ano. Estudo realizado por Vieira Neto et al. (2019) em condição experimental semelhante, na mesma localidade, al- cançou rendimento de 1,83kg de MFFP para o híbrido Kybria. Este resultado equivale a 34,2% a menos na produção em comparação à média resultante dos dois melhores tratamentos do presente trabalho, 90% e 100% (2,78kg planta-1). Por outro lado, Espínola et al. (2001) obtiveram produtividade próxima a 31t ha-1, equivalente a 1,55kg planta-1, para pepino tipo conserva, híbrido Crispina, cultivado em substrato sob abrigo em Quanto à massa fresca de frutos comerciais (MFF), em 2019, não houve diferença entre os diferentes tratamen- tos, variando entre 16,7 a 17,2g (Tabela 2). Em 2020, houve efeito de tratamen- tos, sendo que os maiores valores para MFF foram de 19,4, 19,4, e 19,8g obti- dos com os tratamentos 100%, 110% A radiação solar pode ter sido o principal fator climático a ter contribu- ído para a maior incidência de pulgões nas plantas em 2020. Material e métodos Means of fresh weight of commercial fruits per plant (MFFP), number of commer- cial fruits per plant (NFP), fresh weight of commercial fruits (MFF), percentage of commer- cial fruits (% FC) and percentage of non-commercial fruits ( % FNC), for pickling cucumber in the different treatments, obtained at the end of the experiments. Ituporanga, SC, Epagri, 2019 and 2020 Foram avaliadas as seguintes variá- veis: o número de frutos comerciais por planta, a porcentagem de frutos comer- ciais e não comerciais (frutos com mais de 9cm de comprimento, defeituosos e danificados por pragas), a massa fres- ca de frutos comerciais (g) e a massa fresca de frutos comerciais por planta (kg planta-1). Os dados dessas variáveis acumulados até a última colheita foram submetidos à análise de variância pelo teste F e as médias comparadas pelo teste de Scott-Knott, a 5% de probabili- dade, utilizando-se o software livre “R”. Os valores médios de macro e micronu- trientes foliares encontrados nas amos- tras foram comparados aos valores de nutrientes considerados adequados para o pepineiro segundo a CQFS-RS/SC (2004) pelo teste t de Student a 5% de probabilidade. Ano/ 2019 2020 2019 2020 2019 2020 Tratamentos MFFP (kg planta-1) NFP MFF (g) 80% 2,59 b 0,61 NS 154,4 a 34,0 a 16,8 NS 17,9 b 90% 2,69 a 0,59 161,6 a 32,7 a 16,7 18,3 b 100% 2,87 a 0,65 171,4 a 33,7 a 16,7 19,4 a 110% 2,40 b 0,55 142,1 b 28,1 b 17,1 19,4 a 120% 2,40 b 0,55 139,4 b 27,9 b 17,2 19,8 a CV% 10,62 14,52 10,39 16,06 8,15 5,67 Ano/ 2019 2020 2019 2020 Tratamentos %FC %FNC 80% 97,7 NS 98,9 NS 2,3 NS 1,02NS 90% 98,0 99,7 2,0 0,26 100% 97,2 98,7 2,8 1,23 110% 98,1 96,8 1,9 3,13 120% 97,7 96,9 2,3 3,03 CV% 0,96 2,50 38,01 118,35 1 Médias não seguidas da mesma letra minúscula na vertical, dentro da mesma variável, diferem entre si pelo teste de Scott-Knott a 5% de probabilidade NS: Não significativo pelo teste F a 5% 50 Agropecuária Catarinense, Florianópolis, v.34, n.1, 48-53, jan./abr. 2021 Material e métodos A solução padrão 100% (em g L-1) foi composta das seguintes concentra- ções de fertilizantes: nitrato de cálcio (0,865), MKP (0,204), sulfato de magné- sio (0,370), nitrato de potássio (0,425), acrescido de ConMicros Standard® (composição em %): B (1,82), Cu EDTA (1,82), Fe EDTA (7,26), Mn EDTA (1,82), Mo (0,36), Ni (0,335), Zn EDTA (0,73), na dose de 0,03g L-1. ii Em 2019 a colheita de pepino teve início no dia 13/11/2019 e estendeu- Tabela 1. Fase fenológica, intervalo de cada fase, porcentagem do total da mistura de fer- tilizantes aplicada em cada fase (PMF) e quantidade de solução da mistura de fertilizantes fornecida por planta a cada dia em cada tratamento por fase fenológica Table 1. Phenological phase, interval of each phase, percentage of total fertilizer mixture applied in each phase (PFM) and amount of fertilizer mixture solution supplied per plant each day in each treatment per phenological phase Tabela 1. Fase fenológica, intervalo de cada fase, porcentagem do total da mistura de fer- tilizantes aplicada em cada fase (PMF) e quantidade de solução da mistura de fertilizantes fornecida por planta a cada dia em cada tratamento por fase fenológica Table 1. Phenological phase, interval of each phase, percentage of total fertilizer mixture ii Mistura de fertilizantes (g L-1) Fase fenológica Intervalo (Dias) PMF (%) 80% 90% 100% 110% 120% Fase inicial 1 a 10 13 0,202 0,228 0,253 0,278 0,304 Vegetativa 1 11 a 20 27 0,405 0,456 0,507 0,557 0,608 Vegetativa 2 21 a 30 76 1,160 1,305 1,450 1,595 1,740 Vegetativa 3 31 a 40 80 1,216 1,369 1,521 1,673 1,825 Floração/ produção > 41 100 1,525 1,715 1,906 2,097 2,287 Foram utilizados vasos de polieti- leno com volume de 12 litros cada. As parcelas experimentais foram compos- tas por quatro plantas do híbrido Kybria F1, uma planta por vaso, sendo os dois se até 06/01/2020, totalizando 21 co- lheitas. Em 2020 foram realizadas oito colheitas no período de 02/03/2020 a 18/03/2020. As colheitas foram realiza- das em média a cada dois dias, quando os frutos apresentavam entre 4 a 9cm de comprimento, padrão exigido pelas agroindústrias (REBELO et al., 2011). Table 2. 1 Médias não seguidas da mesma letra minúscula na vertical, dentro da mesma variável, diferem entre si pelo teste de Scott-Knott a 5% de probabilidade. NS: Não significativo pelo teste F a 5%. Resultados e discussão (2019), com 98,3% dos frutos do cul- tivar Kybria com padrão comercial. li 1 Faixa de referência com base na Comissão de Química e Fertilidade do Solo (CQFS-RS/SC, 2004). Inferior (Inf.), nível adequado (NA) e superior (Sup.) aos valores de referência, significativos pelo teste t de Student a 5%. A boa qualidade dos frutos, refletida na alta porcentagem de frutos comer- ciais, sugere um bom equilíbrio entre os nutrientes nas soluções nutritivas utili- zadas, e que a quantidade de nutrientes associada ao manejo nutricional ade- quado são os fatores mais determinan- tes nas elevações de produtividade do pepineiro em substrato. i P, K, Ca e Mg das folhas de plantas do híbrido de pepineiro Magnum F1, gru- po caipira, cultivadas em substrato de fibra de coco. Esses autores utilizaram soluções nutritivas nas concentrações de 12,5%, 17%, 25%, 50% e 100% da solução nutritiva sugerida por Furlani et al. (1999). Os níveis de pH oscilaram entre 5,70 a 6,45 e entre 5,60 a 6,50, respectiva- mente, para a solução nutritiva aplicada e drenada nos distintos tratamentos e fases (Tabela 5). Os níveis observados de pH, nos experimentos, estão den- tro dos parâmetros considerados ideais para solução nutritiva indicada por An- Na Tabela 3 é possível verificar que os níveis de nutrientes foliares para macronutrientes, de maneira geral, não foram influenciados pelos trata- mentos. Embora apenas P esteja den- tro dos valores de referência definidos pela Comissão de Química e Fertilidade do Solo (CQFS-RS/SC, 2004), os demais nutrientes, mesmo estando abaixo (N, K, S) e acima (Ca, Mg), estão próximos aos valores dos limites de intervalos de normalidade para a cultura. Tabela 4. Valores médios de micronutrientes e semi-amplitude do intervalo de confiança para a média, nas folhas de pepineiro em mg kg-1. Ituporanga, SC, Epagri, 2019 e 2020 Table 4. Means values of micronutrients and semi-amplitude of the confidence interval for the mean, in cucumber leaves in mg/kg. Ituporanga, SC, Epagri, 2019 and 2020 Tratamento B (mg kg-1) Cu (mg kg-1) Fe (mg kg-1) Mn (mg kg-1) Zn (mg kg-1) 80% 66,5 NA (7,4) 12,3 NA (2,80) 408,1 NA (116,04) 252,0 NA (48,73) 143,6 Sup. (15,81) 90% 78,7 NA (8,97) 12,3 NA (2,53) 528,7 Sup. (42,54) 267,4 NA (48,24) 129,4 Sup. (22,84) 100% 75,6 NA (12,31) 11,8 NA (2,58) 737,6 Sup. (216,68) 291,9 NA (59,68) 116,0 NA (27,87) 110% 70,0 NA (12,22) 14,9 NA (3,76) 710,0 Sup. (175,30) 337,4 Sup. Resultados e discussão Durante o período de colheita de 2020, com duração de 16 dias, a soma de radiação média diária foi de 3.724W/m2, valor 10,81% inferior 50 Tabela 3. Valores médios de macronutrientes e semiamplitude do intervalo de confiança para a média, nas folhas de pepineiro em %. Ituporanga, SC, Epagri, 2019 e 2020 Table 3. Mean values of macronutrients and semiamplitude of the confidence interval for the mean, in cucumber leaves in %. Ituporanga, SC, Epagri, 2019 and 2020 Tratamento N% P% K% Ca% Mg% S% 80% 3,2 Inf. (0,68) 0,9 NA (0,16) 2,5 Inf. (0,46) 6,5 Sup. (1,35) 2,4 Sup. (0,33) 0,3 Inf. (0,03) 90% 3,0 Inf. (0,56) 0,9 NA (0,14) 2,6 Inf. (0,43) 6,7 Sup. (0,31) 2,4 Sup. (0,29) 0,2 Inf. (0,06) 100% 2,3 Inf. (1,07) 0,9 NA (0,22) 2,4 Inf. (0,37) 7,1 Sup. (1,28) 2,5 Sup. (0,50) 0,2 Inf. (0,03) 110% 3,7 Inf. (0,48) 1,0 NA (0,17) 2,7 Inf. (0,75) 7,3 Sup. (0,96) 2,4 Sup. (0,22) 0,2 Inf. (0,08) 120% 3,6 Inf. (0,58) 0,9 NA (0,13) 2,4 Inf. (0,49) 7,1 Sup. (0,83) 2,5 Sup. (0,32) 0,2 Inf. (0,06) Referência 1 4,5-6,0 0,3-1,2 3,5-5,0 1,5-3,5 0,3-1,0 0,4-0,7 1 Faixa de referência com base na Comissão de Química e Fertilidade do Solo (CQFS-RS/SC, 2004). Inferior (Inf.), nível adequado (NA) e superior (Sup.) aos valores de referência, significativos pelo teste t de Student a 5%. Tabela 3. Valores médios de macronutrientes e semiamplitude do intervalo de confiança para a média, nas folhas de pepineiro em %. Ituporanga, SC, Epagri, 2019 e 2020 Table 3. Mean values of macronutrients and semiamplitude of the confidence interval for the mean, in cucumber leaves in %. Ituporanga, SC, Epagri, 2019 and 2020 e 120%, respectivamente. Estes resul- tados são compatíveis aos valores nor- malmente encontrados em trabalhos feitos com pepino tipo conserva, devido à existência de um padrão de colheita previamente estabelecido pela agroin- dústria para frutos destinados ao en- vasamento. Ou seja, os resultados en- contrados por Vieira Neto et al. (2018) e Vieira Neto et al. (2019) situam entre 18,53 a 21,52g. As porcentagens de frutos comer- ciais e de frutos não comerciais não foram influenciadas pelos tratamentos nos dois anos de avaliação (Tabela 2). O rendimento médio de frutos comer- cializáveis dos cinco tratamentos foi de 97,7% e 98,2% para 2019 e 2020, res- pectivamente. Resultado bem próximo a este foi encontrado por Vieira Neto et al. 1 Faixa de referência com base na Comissão de Química e Fertilidade do Solo (CQFS-RS/SC, 2004). Inferior (Inf.), nível adequado (NA) e superior (Sup.) aos valores de referência, significativos pelo teste t de Student a 5%. Resultados e discussão (63,69) 133,9 Sup. (30,21) 120% 83,0 NA (12,52) 14,4 NA (3,68) 644,6 Sup. (138,31) 328,7 NA (82,94) 116,2 NA (21,03) Referência 1 50-120 7-20 50-300 50-250 25-100 1 Faixa de referência com base na Comissão de Química e Fertilidade do Solo (CQFS-RS/SC, 2004). Inferior (Inf.), nível adequado (NA) e superior (Sup.) aos valores de referência, significativos pelo teste t de Student a 5%. Tratamento B (mg kg-1) Cu (mg kg-1) Fe (mg kg-1) Mn (mg kg-1) Zn (mg kg-1) Tratamento B (mg kg-1) Cu (mg kg-1) Fe (mg kg-1) Mn (mg kg-1) Zn (mg kg-1) Quanto aos micronutrientes (Tabela 4), os níveis foliares amostrais apresen- taram-se adequados para B e Cu, para todos os tratamentos, e para Fe (80%), para Mn ((80%, 90%, 100% e 120%) e Zn (100% e 120%). Assim como observado para macronutrientes, esse resultado sugere uma falta de relação entre as concentrações de nutrientes dos dife- rentes tratamentos com os níveis dos elementos nas folhas. No entanto, Diniz et al. (2015) verificaram que a aplicação de diferentes proporções de nutrientes na solução nutritiva exerceu efeitos sig- nificativos sobre os teores foliares de N, 1 Faixa de referência com base na Comissão de Química e Fertilidade do Solo (CQFS-RS/SC, 2004). Inferior (Inf.), nível adequado (NA) e superior (Sup.) aos valores de referência, significativos pelo teste t de Student a 5%. 51 Agropecuária Catarinense, Florianópolis, v.34, n.1, 48-53, jan./abr. 2021 51 driolo & Peil, (2016), que é de 5,5 e 6,5. i co fases fenológicas proposta por Yara (2018), pode ter contribuído para a ma- nutenção dos valores de CE um pouco mais próximos aos valores de referência propostos pelo referido autor, para cada fase de desenvolvimento das plantas de pepineiro, a saber: fase 1 (0,33mS cm-1), vegetativa 1 (0,64mS cm-1), vegetativa 2 (1,03mS cm-1), vegetativa 3 (0,88mS cm- 1) e floração/produção (0,88mS cm-1).i O manejo da solução nutritiva indi- cado pela indústria, considerando cinco fases fenológicas, bem como as propor- ções de fertilizantes recomendadas para cada fase, pode servir como referência para produção de pepino para conserva em cultivo semi-hidropônico. driolo & Peil, (2016), que é de 5,5 e 6,5. Quanto à condutividade elétrica (CE) (Tabela 5), para os tratamentos 110% e 120%, com maiores concentrações e fer- tilizantes na solução aplicada, os valores oscilaram, respectivamente, entre 0,94 a 2,37mS cm-1 e 0,98 a 2,67mS cm-1 da fase inicial à fase de produção/floração. Referências ANDRIOLO, J.L.; PEIL, R.M.N. Sistemas espe- ciais de produção. In: Leandro Souza da Sil- va; Luciano Colpo Gatiboni. (Org.). Manual de Adubação e Calagem para os estados do Rio Grande do Sul e Santa Catarina. 11ed. Porto Alegre: Comissão de Química e Ferti- lidade do Solo- RS/SC, 2016, v., p. 287-293. ANDRIOLO, J.L.; PEIL, R.M.N. Sistemas espe- ciais de produção. In: Leandro Souza da Sil- va; Luciano Colpo Gatiboni. (Org.). Manual de Adubação e Calagem para os estados do Rio Grande do Sul e Santa Catarina. 11ed. Porto Alegre: Comissão de Química e Ferti- lidade do Solo- RS/SC, 2016, v., p. 287-293. Agradecimentos Desta forma, as soluções nutritivas representadas pelos tratamentos 90% e 100%, utilizando o manejo adotado no presente trabalho para a elaboração das soluções nutritivas ao longo do ciclo de cultivo, são indicadas no manejo do pe- pineiro fertirrigado por terem propor- cionado maior produtividade. Aos colaboradores técnico agrícola David Junior Rodrigues e assistente de campo Marcelo Andrade, da Epagri, Es- tação Experimental de Ituporanga, SC. Resultados e discussão Os maiores valores de CE, observados principalmente na fase de produção/ floração, acima do parâmetro de refe- rência indicado para solução nutritiva em cultivo de pepineiro, ou seja, 1,8mS cm-1 (ANDRIOLO & PEIL, 2016), podem ter contribuído com o menor número de frutos por planta, refletindo numa menor produção. Pois, conforme obser- vado por Diniz et al. (2015), o pepino absorve e utiliza grande quantidade de nutrientes, mas é muito sensível ao ex- cesso de fertilizantes na solução do solo. Para os tratamentos 90% (1,95mS cm-1) e 100% (2,12mS cm-1) os valores da CE situaram-se mais próximos do valor de referência, com ganhos de produção. Conclusões Porto Alegre, RS: SBCS/Núcleo Regional Sul; Comissão de Química e Fertilidade do Solo – RS/SC, 2004. 400p. TEDESCO, M.J.; GIANELLO, C.; BISSANI, C.A.; BOHNEN, H. Análise de solo, plantas e ou- tros materiais. 2.ed. Porto Alegre: UFRGS, 1995. (Boletim Técnico, 5). DINIZ, A. A.; DIAS, N. da S.; SOUZA, F. I. de S.; SOUZA, A. C. M.; MESQUITA, F. de O.; SOUZA, F. I. de. Efeito da solução nutritiva sob o crescimento e composição mineral em pepino cultivado em substrato de fibra de coco. Semina: Ciências Agrárias (Onli- ne), v. 36, p. 3043-3054, 2015. Disponível em: https://www.researchgate.net/publica- tion/283686114_Efeito_da_solucao_nutriti- va_sob_o_crescimento_e_composicao_mi- neral_em_pepino_cultivado_em_substra- to_de_fibra_de_coco. Acesso em: 25 maio 2020. VIEIRA NETO, J.; GONÇALVES, P.A. de S.; MENEZES JÚNIOR, F.O.G. de. Produtividade de cultivares de pepino para conserva em diferentes épocas de plantio sob ambiente protegido. Revista Thema, v. 15, p. 93-101, 2018. Disponível em: http://periodicos.ifsul. edu.br/index.php/thema/article/view/809. Acesso em: 05 maio 2020. FURLANI, P. R.; BOLONHEZI, D.; SILVEIRA, L. C. P.; FAQUIN, V. Nutrição mineral de horta- liças, preparo e manejo de soluções nutriti- vas. Informe Agropecuário: Cultivo protegi- do de hortaliças em solo e hidroponia, v. 20, n. 200/201, p. 90-98, 1999. VIEIRA NETO, J.; MENEZES JÚNIOR, F.O.G. de; GONÇALVES, P.A. de S. Avaliação da pro- dução de cultivares de pepino para conser- va e de mini tomate com e sem aplicação de fertilizante foliar. Revista Thema, v.16, p.855-864, 2019. Disponível em: http://pe- riodicos.ifsul.edu.br/index.php/thema/ar- ticle/view/1473. Acesso em: 05 maio 2020. VIEIRA NETO, J.; MENEZES JÚNIOR, F.O.G. de; GONÇALVES, P.A. de S. Avaliação da pro- dução de cultivares de pepino para conser- va e de mini tomate com e sem aplicação de fertilizante foliar. Revista Thema, v.16, p.855-864, 2019. Disponível em: http://pe- riodicos.ifsul.edu.br/index.php/thema/ar- ticle/view/1473. Acesso em: 05 maio 2020. MARTINS, C.N. Pepino: produção triplicada. Revista Cultivar Hortaliças e Frutas, Pelotas, 2004. Disponível em: http://www.grupocul- tivar.com.br/arquivos/hf24_producao.pdf. Acesso em: 19 abr. 2020. ESPÍNOLA, H.N.R.; ANDRIOLO, J.L.; BARTZ, H.R. Acúmulo e repartição da matéria seca da planta de pepino tipo conserva sob três doses de nutrientes minerais. Ciência Ru- ral, Santa Maria, RS, v. 31, n.3, p. 387-392, 2001. Disponível em: https://www.scielo.br/ pdf/cr/v31n3/a04v31n3.pdf. Acesso em: 11 maio 2020. ESPÍNOLA, H.N.R.; ANDRIOLO, J.L.; BARTZ, H.R. Acúmulo e repartição da matéria seca da planta de pepino tipo conserva sob três doses de nutrientes minerais. Ciência Ru- ral, Santa Maria, RS, v. 31, n.3, p. 387-392, 2001. Disponível em: https://www.scielo.br/ pdf/cr/v31n3/a04v31n3.pdf. Acesso em: 11 maio 2020. Conclusões O melhor desempenho de produção de pepineiro para conserva, em semi- hidroponia, foi obtido por soluções nu- tritivas com 90% e 100% das quantida- des de fertilizantes recomendadas pela pesquisa. A estratégia de fornecer as soluções nutritivas em diferentes concentrações de fertilizantes, considerando as cin- CQFS-RS/SC. Manual de calagem e aduba- ção para os estados do Rio Grande do Sul Tabela 5. Médias de duas safras 2019/20 do potencial hidrogeniônico (pH) e condutividade elétrica (CE, mS cm-1) da solução nutritiva apli- cada e da solução drenada do substrato. Ituporanga, SC, Epagri, 2019 e 2020 Table 5. Means of two harvests 2019/20 of hydrogen potential (pH) and electrical conductivity (EC, mS cm-1) of the applied nutrient solu- tion and the solution drained from the substrate. Ituporanga, SC, Epagri, 2019 and 2020 52 Tabela 5. Médias de duas safras 2019/20 do potencial hidrogeniônico (pH) e condutividade elétrica (CE, mS cm-1) da solução nutritiva apli- cada e da solução drenada do substrato. Ituporanga, SC, Epagri, 2019 e 2020 Table 5. Means of two harvests 2019/20 of hydrogen potential (pH) and electrical conductivity (EC, mS cm-1) of the applied nutrient solu- tion and the solution drained from the substrate. Ituporanga, SC, Epagri, 2019 and 2020   Solução aplicada   80% 90% 100% 110% 120% Fase fenológica pH CE pH CE pH CE pH CE pH CE Fase 1 (inicial) 6,40 0,64 6,43 0,74 6,37 0,80 6,33 0,94 6,20 0,98 Vegetativa 1 6,45 0,69 6,40 0,76 6,30 0,80 6,30 0,98 6,25 1,01 Vegetativa 2 6,28 0,73 6,43 0,78 6,35 0,83 6,25 1,03 6,20 1,03 Vegetativa 3 5,90 1,21 5,90 1,39 5,73 1,95 5,73 2,32 5,70 2,50 Floração/produção 6,08 1,21 5,95 1,95 5,96 2,12 5,85 2,37 5,81 2,67   Solução drenada Fase fenológica pH CE pH CE pH CE pH CE pH CE Fase 1 (inicial) 6,37 0,43 6,27 0,66 6,03 0,68 5,83 0,89 5,70 0,92 Vegetativa 1 6,50 0,47 5,90 0,68 5,95 0,70 5,75 0,92 5,60 0,95 Vegetativa 2 6,20 0,59 5,90 0,69 6,20 0,70 5,70 0,92 5,60 0,91 Vegetativa 3 6,10 0,66 6,10 0,84 5,77 1,50 5,80 2,07 5,63 2,23 Floração/produção 6,31 0,72 5,91 0,91 5,81 1,80 5,82 2,18 5,60 2,46 Agropecuária Catarinense, Florianópolis, v.34, n.1, 48-53, jan./abr. 2021 52 FÓRUM BRASILEIRO DE PRODUÇÃO DE PE- PINO PARA CONSERVA, 2. 2019, Indaial. Pro- dução sustentável com alta tecnologia. Dis- ponível em: http://forumbrasilpepinocon- serva.com.br/como-proteger-a-producao- de-pepinos-de-pragas-ou-doencas/. Acesso em: 21 maio 2020. e de Santa Catarina. 10.ed. Conclusões REBELO, J.A.; SCHALLENBERGER, E.; CANTÚ, RR. Cultivo do pepineiro para picles no Vale do Rio Itajaí e Litoral Catarinense. Florianó- polis: Epagri, 2011. 55p. (Boletim Técnico, 154). YARA. Yara GranHorti: Programa nutricional para pepino – fetirrigação. [2018]. 40p. 53 Agropecuária Catarinense, Florianópolis, v.34, n.1, 48-53, jan./abr. 2021
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Variation in heat shock protein 40 kDa relates to divergence in thermotolerance among cryptic rotifer species
Scientific reports
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Katrin Kiemel | Marie Gurke | Sofia Paraskevopoulou | Katja Havenstein | Guntram Weithoff | Ralph Tiedemann Variation in heat shock protein 40 kDa relates to divergence in thermotolerance among cryptic rotifer species Suggested citation referring to the original publication: Scientific Reports 12 (2022), Art. 22626 DOI https://doi.org/10.1038/s41598-022-27137-3 ISSN 2045-2322 Journal article | Version of record Secondary publication archived on the Publication Server of the University of Potsdam: Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe 1305 ISSN: 1866-8372 https://nbn-resolving.org/urn:nbn:de:kobv:517-opus4-578635 DOI: https://doi.org/10.25932/publishup-57863 Terms of use: This work is licensed under a Creative Commons License. This does not apply to quoted content from other authors. To view a copy of this license visit https://creativecommons.org/licenses/by/4.0/. Katrin Kiemel | Marie Gurke | Sofia Paraskevopoulou | Katja Havenstein | Guntram Weithoff | Ralph Tiedemann Variation in heat shock protein 40 kDa relates to divergence in thermotolerance among cryptic rotifer species Suggested citation referring to the original publication: Scientific Reports 12 (2022), Art. 22626 DOI https://doi.org/10.1038/s41598-022-27137-3 ISSN 2045-2322 Journal article | Version of record Secondary publication archived on the Publication Server of the University of Potsdam: Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe 1305 ISSN: 1866-8372 https://nbn-resolving.org/urn:nbn:de:kobv:517-opus4-578635 DOI: https://doi.org/10.25932/publishup-57863 Secondary publication archived on the Publication Server of the University of Potsdam Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe 1305 ISSN: 1866-8372 https://nbn-resolving.org/urn:nbn:de:kobv:517-opus4-578635 DOI: https://doi.org/10.25932/publishup-57863 Mathematisch-Naturwissenschaftliche Fakultät Mathematisch-Naturwissenschaftliche Fakultät OPEN K. Kiemel  1, M. Gurke  2,3, S. Paraskevopoulou  4, K. Havenstein 1, G. Weithoff  5 & R. Tiedemann  1* K. Kiemel  1, M. Gurke  2,3, S. Paraskevopoulou  4, K. Havenstein 1, G. Weithoff  5 & R. Tiedemann  1* Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species. According to the biological species ­concept1, a species is defined as a group that is reproductively isolated from other species. Reproductive isolation can be maintained either by pre-zygotic isolation, post-zygotic isolation, or a combination of ­both2. Pre-zygotic isolation occurs before a zygote is formed and involves physiological or systemic barriers that prevent successful mating, such as differences in mating behaviour, habitat preferences or isolation through ecological or geographical ­barriers3. Post-zygotic isolation mechanisms, such as increased zygote mortality or hybrid sterility, occur after zygote ­formation3. Reproductive isolation mechanisms are how- ever often imperfect, so that many closely related species such as cryptic species ­hybridize4–7, which counteracts species divergence or may even erode species ­boundaries8. Cryptic species are species that require genetic markers to inform species ­delimitations9–11. Such genetically identified species not only call for a revised ­taxonomy12–14, but also pose a major challenge to evolutionary and ecological theories. Due to the lack of morphological and physiological differences, high similarity in ecologi- cal traits and adaptations is ­expected15. When these species occur in ­sympatry16–19, the principle of competitive ­exclusion20 is compromised, which further challenges the understanding of co-existence and the niche concept. Terms of use: This work is licensed under a Creative Commons License. This does not apply to quoted content from other authors. To view a copy of this license visit https://creativecommons.org/licenses/by/4.0/. https://creativecommons.org/licenses/by/4.0/. www.nature.com/scientificreports www.nature.com/scientificreports Scientific Reports | (2022) 12:22626 www.nature.com/scientificreports/ ­traits32, adaptation and the underlying regulatory ­mechanisms33–35, as well as on the robustness of species bounda- ries through hybridisation ­experiments6,7. These studies are of great importance to understand not only how these species have diverged, but also which of their adaptations are critical for the co-existence or exclusion of certain species in a specific environment. p pi A previous lifetable ­experiment36 has demonstrated diverging temperature optima between Brachionus caly- ciflorus s.s. (heat-tolerant) and Brachionus fernandoi (heat-sensitive). Comparison of transcriptome data from the heat-tolerant B. calyciflorus s.s. and the heat-sensitive B. fernandoi revealed differential expression of Heat Shock Protein (HSP) genes relative to ­temperature35. HSP gene expression levels correlated with life history traits such that the upregulation of HSP gene expression consistently occurred when the population growth rate was low. The two species were found to exhibit optimal growth at a different temperature (B. calyciflorus s.s. at 26 °C and B. fernandoi at 20/23 °C) and increased their HSP expression outside their optimal temperature range, demonstrating a stress response of the organisms when optimal growth was not ­feasible35. The pronounced fit- ness differences at different thermal conditions indicate underlying mechanisms of phenotypes’ responses to environmental conditions that allow them to occur in sympatry, but in different seasons of the ­year31,35. y p yf y Temperature as an environmental variable is one of the most important drivers of evolution and ­diversification37. Temperature adaptation is particularly interesting in aquatic invertebrates which as ecto- therms are stronger influenced by temperature changes than ­homeotherms38. Increased temperature acceler- ates ontogeny, shortens the time to maturation and the generation ­time35,39–41. The associated faster population growth can foster competitive superiority and accelerate the underlying divergent selection that enforces niche ­partitioning42–44. An organism’s adaptation to a particular environment or resource availability may occur at the protein level through the regulation of gene ­expression45–48. This gene expression regulative mechanism can be observed in situations of rapid environmental changes (i.e., length of growing seasons) in B. plicatilis s.s.49,50, or in stress response via HSP ­upregulation35,51, which is a rapid and often the first response mechanism to environmental perturbation. However, a differential regulatory response among genotypes/species to the same environmental cue (genotype x environment (G x E) variation) has to be encoded somewhere in the genome, typically upstream in gene regulatory elements (e.g., transcription factors, ­promoters52,53). www.nature.com/scientificreports/ In addition, a diver- gent adaptation to different environmental conditions may also yield adaptive differences in protein structure, i.e., altered amino acid sequences. Such changes stem from non-synonymous substitutions in the underlying protein coding genes (as the HSP genes), such that signatures of selection can occur in specific genes or distrib- uted over the whole ­genome54,55. Evolution of gene expression and protein structure do not necessarily occur independently of each ­other56,57, and we often find their respective contribution correlating with the progress of time, i.e., altered gene expression typically evolves more rapidly than altered protein ­structure53. Furthermore, discovering signs of selection in gene sequences between different species allows us to understand the genetic underpinning of the ­differentiation58,59. When put into perspective with the divergence time, the time frame of the adaptation/speciation can be ­unravelled60. In this study, we investigated sequence/protein evolution and divergence in the HSP 40 kDa gene, which was inferred by a candidate gene selection for temperature adaptation, both by its temperature-related differential ­expression35 and by a transcriptome-wide SNP comparison among two species of the B. calyciflorus species complex, i.e., the heat-tolerant species B. calyciflorus s.s. and the heat-sensitive B. fernandoi. To put HSP40kDa gene evolution into perspective, this gene was further analysed in three Brachionus species outside of the species complex. We hypothesise, (I) that the adaptation of B. calyciflorus s.s. and B. fernandoi to different environments is driven by divergent selection on the structure of particular proteins (here, HSP 40 kDa) and (II) that the selection for different temperatures can promote niche partitioning, and hence constitute a pre-zygotic isolation mechanism. OPEN 21 p g g p Rotifers, with their approximately 2000 described species, belong to a very diverse ­phylum21, in which an increasing number of nominal species have been declared cryptic species complexes in the last ­decades22. Among them, the monogonont freshwater Brachionus calyciflorus species complex has recently been subdivided into four species using genetics and morphometrics: Brachionus calyciflorus sensu stricto (s.s.), Brachionus dorcas, Brachionus fernandoi, and Brachionus elevatus5,23. Prior to its delimitation into four species, the Brachionus caly- ciflorus species complex had been studied with regard to molecular ­phylogeny23–25, co-existence26, life history ­characteristics27, ­phylogeography28,29, and reproductive ­isolation28–30. More recent studies, which have taken into account the new species classification, focus on ecological processes, e.g., niche ­differentiation31, life history 1Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Karl‑Liebknecht Straße 24‑25, 14476 Potsdam, Germany. 2Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115  Berlin, Germany. 3Department of Biology, Humboldt-University, Invalidenstraße 42, 10115  Berlin, Germany. 4Department of Biology, Lund University, Microbiology Group, Sölvegatan 35, 223 62 Lund, Sweden. 5Unit of Ecology and Ecosystem Modelling, Institute for Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, 14469 Potsdam, Germany. *email: tiedeman@uni-potsdam.de | https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 www.nature.com/scientificreports/ Results C did Candidate gene selection. To identify candidate genes within the B. calyciflorus species complex we assembled 72,165 and 94,884 super-transcripts in B. calyciflorus s.s and B. fernandoi transcriptomes, respec- tively. The reciprocal best blast hit identified 9655 putative orthologs which were reduced to 7976 after predicting open reading frames, locally aligning, and translating into proteins. In the selection tests, out of 7976 orthologs, 649 were significant (< 0.05) in all four pairwise Likelihood Ratio Test (LRT) comparisons, hence inferred to be putatively under positive selection. Comparing the orthologous genes under positive selection with the gene expression ­data35, 155 genes were differentially expressed relative to temperature (control: 20 °C, mild heat: B. calyciflorus s.s. 26 °C, B. fernandoi 23 °C, high heat: B. calyciflorus s.s. 32 °C, B. fernandoi 26 °C) in at least one of the two species (125 in B. calyciflorus s.s., 22 in B. fernandoi, and 8 in both species). Twenty-seven of these genes were assigned to the GO term GO:0006950 (response to stress), of which one gene was annotated to “response to heat” (GO:00009408). This gene (i.e., HSP 40 kDa) was differentially expressed in B. calyciflorus s.s. in cultures grown after 4 h of heat exposure to different temperature (20 °C vs. 32 °C and 20 °C vs. 26 °C), while it did not show a temperature-specific expression in B. fernandoi (Fig. 1). HSP 40 kDa sequence diversity. The sequence diversity of all five Brachionus species (B. calyciflorus s.s., B. fernandoi, B. rubens, B. angularis, and B. diversicornis) was assessed by comparing HSP 40 kDa and Cytochrome Oxidase Subunit I (COI) genes. We detected an overall higher nucleotide divergence in the mito- chondrial COI compared to the HSP 40 kDa gene fragment (Fig. 2). For the HSP 40 kDa sequences, the lowest nucleotide divergence was detected between B. angularis and B. diversicornis (0.103), followed by B. calyciflorus s.s. and B. fernandoi (0.121). The highest nucleotide divergence was found between B. fernandoi and B. rubens (0.198). For the COI fragment, the highest nucleotide divergence was detected between B. calyciflorus s.s. and B. diversicornis (0.243), while the lowest was between B. calyciflorus s.s. and B. fernandoi (0.154). Results C did The cross-species https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ response to heat response to cold response to topologically incorrect protein response to starvation regulation of response to stress response to hypoxia defense response cellular response to stress 0 5 10 15 20 Number of genes assigned to GO terms 20°C vs. 32°C 20°C vs. 26°C 26°C vs. 32°C 20°C vs. 26°C 20°C vs. 23°C 23°C vs. 26°C 0.0 1.0 2.0 3.0 4.0 B. fernandoi B. calyciflorus s.s. d e s s e r p x e yllait n e r e ffid s e n e g f o r e b m u N n oit pir c s e d m r e t O G Figure 1. Annotation and differential expression of genes inferred to be under positive selection. Bar plot shows the genes which were assigned to the term GO:0006950 (response to stress). Bars represent the number genes assigned to one of the child terms of GO:0006950. More than one GO term can be assigned to the same gene. The heatmap shows the number of genes differentially expressed in each GO term category in B. calyciflorus s.s. and B. fernandoi under different temperatures ­regimes35. response to heat response to cold response to topologically incorrect protein response to starvation regulation of response to stress response to hypoxia defense response cellular response to stress 0 5 10 15 20 Number of genes assigned to GO terms n oit pir c s e d m r e t O G Number of genes assigned to GO terms Figure 1. Annotation and differential expression of genes inferred to be under positive selection. Bar plot shows the genes which were assigned to the term GO:0006950 (response to stress). Bars represent the number genes assigned to one of the child terms of GO:0006950. More than one GO term can be assigned to the same gene. The heatmap shows the number of genes differentially expressed in each GO term category in B. calyciflorus s.s. and B. fernandoi under different temperatures ­regimes35. Figure 2. Nucleotide divergence of nuclear and mitochondrial genes. Nucleotide divergence of the nuclear HSP 40 kDa (orange) and the mitochondrial Cytochrome Oxidase Subunit I (COI) (grey) genes, based on comparisons of B. calyciflorus s.s., B. fernandoi, B. rubens, B. angularis, and B. diversicornis. The colour intensity indicates increasing nucleotide divergence between the compared sequences. Figure 2. Results C did Nucleotide divergence of nuclear and mitochondrial genes. Nucleotide divergence of the nuclear HSP 40 kDa (orange) and the mitochondrial Cytochrome Oxidase Subunit I (COI) (grey) genes, based on comparisons of B. calyciflorus s.s., B. fernandoi, B. rubens, B. angularis, and B. diversicornis. The colour intensity indicates increasing nucleotide divergence between the compared sequences. comparison of non-synonymous (dN) vs. synonymous (dS) substitutions in the HSP 40 kDa gene yielded an overall dN/dS: 0.049, with the the highest dN/dS ratio between B. angularis and B. diversicornis (0.085), while the lowest one was found between B. calyciflorus s.s. and B. diversicornis, followed by B. calyciflorus s.s. and B. fernandoi (0.040 and 0.042, respectively) (Supplementary Fig. s4). Structural variation in HSP 40 kDA between B. calyciflorus s.s. and B. fernandoi. We produced 88 genomic HSP 40kDA gene sequences for our two focus species (B. calyciflorus s.s., n = 50; B. fernandoi, n = 38) by polymerase chain reaction (PCR). The network approach based on all 88 phased sequences identified 32 unique HSP 40 kDa alleles (corresponding to 27 unique protein sequences) from which 13 alleles were exclu- sively found in B. fernandoi specimens and 19 alleles were solely found in B. calyciflorus s.s. specimens (Fig. 3). https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ A1 A2 A3 A4 A5 A6 A7 A8 A9 A10 A11 A12 A13 A14 A15 A16 A17 A18 A19 A20 A21 A22 A23 A24 5 2 A A26 A27 A28 A29 A30 A31 A32 B. fernandoi Germany B. calyciflorus s.s. Results C did Labels A1-A32 stand for the identified alleles, red alleles are derived from B. calyciflorus s.s. and blue alleles from B. fernandoi. B. calyciflorus s.s. alleles found in more than one location are coloured orange. Only one allele, which phylogenetically clustered to the B. calyciflorus s.s. HSP 40 kDa allele type 18 (A18) was found in a B. fernandoi specimen (2484_4). The translated protein alignment (Supplementary Fig. s5) revealed 51 non-synonymous substitutions, among them the 14 found in the transcriptome data. The highest rate dN of non-synonymous substitutions per non-synonymous site among the two species was detected in position 256, followed by position 292 (Fig. 4). Only one allele, which phylogenetically clustered to the B. calyciflorus s.s. HSP 40 kDa allele type 18 (A18) was found in a B. fernandoi specimen (2484_4). The translated protein alignment (Supplementary Fig. s5) revealed 51 non-synonymous substitutions, among them the 14 found in the transcriptome data. The highest rate dN of non-synonymous substitutions per non-synonymous site among the two species was detected in position 256, followed by position 292 (Fig. 4). Congruence among ITS1, HSP 40 kDa, and COI species affinity. The comparison of the nuclear Internal Transcribed Spacer 1 (ITS1), HSP 40 kDa, and the mitochondrial COI sequences yielded congruent species assignments for most analysed specimens. However, we identified four descendants of hybridization events between B. calyciflorus s.s. and B. fernandoi (all originating from the same pond; 2484), all of which carry the identical maternally inherited B. calyciflorus s.s. COI haplotype, but were assigned to B. fernandoi based on ITS1 sequences (Fig. 5, Supplementary Figs. s6, s7). Three of these introgressed specimens carried B. fernan- doi—specific HSP 40 kDa alleles (2484_1, 2484_9, 2484_10), while one individual (2484_4) carried a B. caly- ciflorus s.s.—specific HSP 40 kDa allele, such that only its ITS1 sequence points towards a B. fernandoi affinity. Of the three introgressed specimens carrying B. fernandoi—specific HSP 40 kDa alleles, two were heterozygous (2484_1: A11, A1; 2484_10: A12, A2), while one was homozygous for A1 allele (2484_9). The introgressed speci- men which carried a B. calyciflorus s.s. specific allele was homozygous for A18. Inferences on selection and divergence. The conducted four LRT comparisons (M0 vs. M3, M1a vs. M2a, M7 vs. M8, M8a vs. M8) of the site substitution model in PAML significantly inferred positive selection in the HSP 40 kDa gene among the five different Brachionus species (Table 1). Results C did Germany Italy Austria USA 30% 5 40% 6 50% 7 60% 8 9 70% 10 80% 11 90% 12 100% 13 0 0% 1 20% 2 3 40% 4 60% 5 6 80% 7 100% 8 0 1 2 3 4 0 1 0 1 2 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 0% 1 10% 2 3 20% 4 5 30% 6 7 40% 8 9 10 50% 11 60% 12 13 70% 14 15 80% 16 17 90% 18 19 20 100% 0 0% 10% 1 20% 2 30% 3 40% 4 5 50% 60% 6 70% 7 80% 8 90% 9 10 100% 0 1 0 1 2 0 1 0 1 2 3 4 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0% 0 1 2 3 10% 4 5 6 7 20% 8 9 10 11 30% 12 13 14 15 40% 16 17 18 50% 19 20 21 22 60% 23 24 25 26 70% 27 28 29 30 80% 31 32 33 34 90% 35 36 37 100% 38 0 0% 1 2 10% 3 4 20% 5 6 30% 7 8 9 40% 10 11 50% 12 13 60% 14 15 16 70% 17 18 80% 19 20 90% 21 22 100% 23 0 0% 20% 1 40% 2 60% 3 80% 4 5 100% 0 0% 1 20% 2 3 40% 4 5 60% 6 7 80% 8 100% 9 0 0% 1 10% 2 20% 3 30% 4 40% 5 50% 6 7 60% 8 70% 9 80% 10 90% 11 100% 12 Figure 3. HSP 40 kDa allele identification. Circos plot of allele distribution among species B. calyciflorus s.s. and B. fernandoi and country of sample origin (Germany, Italy, Austria, USA). Labels A1-A32 stand for the identified alleles, red alleles are derived from B. calyciflorus s.s. and blue alleles from B. fernandoi. B. calyciflorus s.s. alleles found in more than one location are coloured orange. A21 A22 A23 A24 5 2 A A26 A27 A28 A29 A30 Figure 3. HSP 40 kDa allele identification. Circos plot of allele distribution among species B. calyciflorus s.s. and B. fernandoi and country of sample origin (Germany, Italy, Austria, USA). Results C did The Bayes Empirical Bayes (BEB) analysis detected six sites under selection (Table 1). Visual inspection of these positively selected sites in the protein alignment (Supplementary Fig. s5) showed a species-specific protein variant pattern at one of these sites (292), while variants were shared at the other sites, but differed in their relative frequencies among the species. The comparison of the positively selected sites with the functional domain description of the HSP ­40kDa61 revealed that four out of the six sites are located in functional domains (J-domain and C-terminal domain; Sup- plementary Fig. s5). The branch site model, which was conducted to identify selection and sites under selection https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ om/scientificreports/ 50 100 150 200 250 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0 2.2 Site dN Figure 4. Number of non-synonymous substitutions per non-synonymous site among B. calyciflorus s.s. and B. fernandoi HSP 40 kDa for each amino acid alignment position of the 32 different HSP 40 kDa alleles. 50 100 150 200 250 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0 2.2 Site dN Figure 4. Number of non-synonymous substitutions per non-synonymous site among B. calyciflorus s.s. and B. fernandoi HSP 40 kDa for each amino acid alignment position of the 32 different HSP 40 kDa alleles. Figure 4. Number of non-synonymous substitutions per non-synonymous site among B. calyciflorus s.s. and B. fernandoi HSP 40 kDa for each amino acid alignment position of the 32 different HSP 40 kDa alleles. 5 Scientific Reports | (2022) 12:22626 | https://doi.org/10.1038/s41598-022-27137-3 Figure 5. Relationship between HSP 40 kDa and COI. Tanglegram based on the nuclear HSP 40 kDa and the mitochondrial COI of species (B. calyciflorus s.s., B. fernandoi, B. rubens, B. angularis, B. diversicornis) (n = 41). Black lines indicate connections of specimens outside of the Brachionus calyciflorus species complex, blue lines indicate connections between specimens of B. fernandoi and red lines connect specimens of B. calyciflorus s.s. Yellow coloured connections indicate specimens originating from an introgression/hybridization event between B. calyciflorus s.s. and B. fernandoi. They all occurred at the same location and all carried a B. fernandoi ITS sequence. Figure 5. Relationship between HSP 40 kDa and COI. Tanglegram based on the nuclear HSP 40 kDa and the mitochondrial COI of species (B. calyciflorus s.s., B. fernandoi, B. rubens, B. angularis, B. diversicornis) (n = 41). Results C did Likelihood ratio tests of seven different site models performed on 296 amino acids (888 bp) of the HSP 40 kDa, including 29 of the 32 unique alleles (A11, A12 and A18 were excluded from the analysis, as they only occurred in specimens affected by hybridization/introgression). Underlying phylogeny is based on the ITS1 (532 bp) of B. calyciflorus s.s., B. fernandoi, B. angularis, B. diversicornis and B. rubens. For each likelihood ratio test (LRT), we provide log likelihood (l) values of the compared tests (2∆l), degrees of freedom (df), p-values, estimated average ratio of non-synonymous vs. synonymous substitutions (ω), and the sites inferred to be under positive selection by Bayes Empirical Bayes (BEB) analysis, labeled with an * for a posterior probability of > 95% and ** for > 99%. Table 1. Likelihood ratio tests of seven different site models performed on 296 amino acids (888 bp) of the HSP 40 kDa, including 29 of the 32 unique alleles (A11, A12 and A18 were excluded from the analysis, as they only occurred in specimens affected by hybridization/introgression). Underlying phylogeny is based on the ITS1 (532 bp) of B. calyciflorus s.s., B. fernandoi, B. angularis, B. diversicornis and B. rubens. For each likelihood ratio test (LRT), we provide log likelihood (l) values of the compared tests (2∆l), degrees of freedom (df), p-values, estimated average ratio of non-synonymous vs. synonymous substitutions (ω), and the sites inferred to be under positive selection by Bayes Empirical Bayes (BEB) analysis, labeled with an * for a posterior probability of > 95% and ** for > 99%. Branch site model Branch 2∆l df p-value l BEBs Selection CD 7.398576 1 0.0065 − 3477.294043 – Neutral − 3480.993331 Selection C 0 1 1.0000 − 3480.993266 – Neutral − 3480.993266 Selection D 3.859588 1 0.0495 − 3477.544980 – Neutral − 3479.474774 Table 2. Likelihood ratio test of branch site model performed on 296 amino acids (888 bp) of the HSP 40 kDa including the 29 of the 32 unique alleles (A11, A12 and A18 hybrid alleles are excluded from the analysis) of B. calyciflorus s.s. and B. fernandoi, B. angularis, B. diversicornis and B. rubens. Phylogeny is based on 532 bp of the ITS1. For each branch selection test, we provide log likelihood (l) value of the compared tests (2∆l), degrees of freedom (df), and the p-value. Results C did Black lines indicate connections of specimens outside of the Brachionus calyciflorus species complex, blue lines indicate connections between specimens of B. fernandoi and red lines connect specimens of B. calyciflorus s.s. Yellow coloured connections indicate specimens originating from an introgression/hybridization event between B. calyciflorus s.s. and B. fernandoi. They all occurred at the same location and all carried a B. fernandoi ITS sequence. https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ Table 1. Likelihood ratio tests of seven different site models performed on 296 amino acids (888 bp) of the HSP 40 kDa, including 29 of the 32 unique alleles (A11, A12 and A18 were excluded from the analysis, as they only occurred in specimens affected by hybridization/introgression). Underlying phylogeny is based on the ITS1 (532 bp) of B. calyciflorus s.s., B. fernandoi, B. angularis, B. diversicornis and B. rubens. For each likelihood ratio test (LRT), we provide log likelihood (l) values of the compared tests (2∆l), degrees of freedom (df), p-values, estimated average ratio of non-synonymous vs. synonymous substitutions (ω), and the sites inferred to be under positive selection by Bayes Empirical Bayes (BEB) analysis, labeled with an * for a posterior probability of > 95% and ** for > 99%. Site model LRT 2∆l df p-value l ω BEBs M0 (one-ratio) M0 vs. M3 262.398852 4 << 0.001 − 3598.034542 0.0718 – M3 (discrete) − 3466.835116 0.1439 M1a (nearly Neutral) M1a vs. M2a 11.558380 2 0.003 − 3480.993265 0.1328 – M2a (positive selection) − 3475.214075 0.1815 M7 (β) M7 vs. M8 21.480488 2 << 0.001 − 3477.904393 0.1108 – M8 (β & ω) − 3467.164149 0.1450 M8a (β & ω = 1) M8a vs. M8 31.89007 1 << 0.001 − 3483.109184 0.0769 10*; 38*; 249**; 256*; 286*; 292** Site model LRT 2∆l df p-value l ω BEBs M0 (one-ratio) M0 vs. M3 262.398852 4 << 0.001 − 3598.034542 0.0718 – M3 (discrete) − 3466.835116 0.1439 M1a (nearly Neutral) M1a vs. M2a 11.558380 2 0.003 − 3480.993265 0.1328 – M2a (positive selection) − 3475.214075 0.1815 M7 (β) M7 vs. M8 21.480488 2 << 0.001 − 3477.904393 0.1108 – M8 (β & ω) − 3467.164149 0.1450 M8a (β & ω = 1) M8a vs. M8 31.89007 1 << 0.001 − 3483.109184 0.0769 10*; 38*; 249**; 256*; 286*; 292** Table 1. Results C did No sites were inferred to be under positive selection by BEB in this test framework. Branch site model Branch 2∆l df p-value l BEBs Selection CD 7.398576 1 0.0065 − 3477.294043 – Neutral − 3480.993331 Selection C 0 1 1.0000 − 3480.993266 – Neutral − 3480.993266 Selection D 3.859588 1 0.0495 − 3477.544980 – Neutral − 3479.474774 Branch site model Branch 2∆l df p-value l BEBs Selection CD 7.398576 1 0.0065 − 3477.294043 – Neutral − 3480.993331 Selection C 0 1 1.0000 − 3480.993266 – Neutral − 3480.993266 Selection D 3.859588 1 0.0495 − 3477.544980 – Neutral − 3479.474774 Table 2. Likelihood ratio test of branch site model performed on 296 amino acids (888 bp) of the HSP 40 kDa including the 29 of the 32 unique alleles (A11, A12 and A18 hybrid alleles are excluded from the analysis) of B. calyciflorus s.s. and B. fernandoi, B. angularis, B. diversicornis and B. rubens. Phylogeny is based on 532 bp of the ITS1. For each branch selection test, we provide log likelihood (l) value of the compared tests (2∆l), degrees of freedom (df), and the p-value. No sites were inferred to be under positive selection by BEB in this test framework. Table 2. Likelihood ratio test of branch site model performed on 296 amino acids (888 bp) of the HSP 40 kDa including the 29 of the 32 unique alleles (A11, A12 and A18 hybrid alleles are excluded from the analysis) of B. calyciflorus s.s. and B. fernandoi, B. angularis, B. diversicornis and B. rubens. Phylogeny is based on 532 bp of the ITS1. For each branch selection test, we provide log likelihood (l) value of the compared tests (2∆l), degrees of freedom (df), and the p-value. No sites were inferred to be under positive selection by BEB in this test framework. in specific species was able to identify selection on the CD (B. calyciflorus s.s. & B. fernandoi) and D branch (B. fernandoi), but did not detect any species-specific sites under selection (BEBs) (Table 2). The selection scenario investigation by comparing only B. calyciflorus s.s. and B. fernandoi using a McDonald-Kreitman Test (MKT), calculated a significant Neutrality Index of 12.06, p-value: ≤ 0.001 (i.e., indicative for balancing selection or slightly deleterious mutations), while Tajima’s D (1.538) was not significant (p-value: ≥ 0.10).hiiil in specific species was able to identify selection on the CD (B. calyciflorus s.s. & B. Results C did fernandoi) and D branch (B. fernandoi), but did not detect any species-specific sites under selection (BEBs) (Table 2). The selection scenario investigation by comparing only B. calyciflorus s.s. and B. fernandoi using a McDonald-Kreitman Test (MKT), calculated a significant Neutrality Index of 12.06, p-value: ≤ 0.001 (i.e., indicative for balancing selection or slightly deleterious mutations), while Tajima’s D (1.538) was not significant (p-value: ≥ 0.10).hiiil g y j gi p The comparison of the fixed species-specific sites revealed 11 fixed sites between B. calyciflorus s.s. and B. fernandoi (Table 3). Out of these 11 fixed sites, 9 amino acid substitutions found in B. fernandoi are considered benign in our Polyphen2 analysis, while two (site 63 and 66) may change protein function (inferred "possibly damaging", Table 3). Additionally, among the six positively selected sites, two amino acid substitutions may influence protein function (inferred "possibly damaging", Table 3). The inference of character polarity (ancestral vs. derived) showed a prevalence of B. calyciflorus s.s. to retain the ancestral variant (10/17). For position 292, the status ancestral or derived could not be identified with certainty (Table 3).l i y ( ) We inferred a divergence time of 25–29 Million years (Myr) between B. calyciflorus s.s. and B. fernandoi, based on mitochondrial cds, while the split between the freshwater and the marine species of Brachionus was estimated to be in a range of 41–47 Myr (Supplementary Fig. s8). Discussion C did t (Bc), B. fernandoi (Bf), B. rubens (Br), B. angularis (Ba) and B. diversicornis (Bd). Ancestral amino acid was inferred using the most parsimonious (i.e., fewest substitutions) scenario, taking the species’ phylogeny into account. In case of multiple amino acids (aa) per species, compared aa are bold in the row Code. Asteriks indicate sites under selection inferred by codeML. Note that Polyphen2 does not consider the possibility of a positive effect of an aa substitution, such that it ranks any predicted change in protein function as "damaging". divergent evolution in the HSP 40 kDa. All but one allele, which originated from descendants of a hybrid, were species-specific. The high number of alleles and expressed structural differences (27 unique protein sequences) within and between the two species might be related to their cyclical ­parthenogenesis65. The dominant asexual mode of reproduction via mitotic eggs from amictic females (i.e., clones) and a less frequent switch to sexual reproduction together with a short generation ­time66 strongly reduces genomic recombination, making purify- ing selection to eliminate slightly deleterious mutations less effective for those organisms, a phenomenon known as Muller’s ­ratchet67–69.hil The comparison between all five analysed species revealed that the species from the B. calyciflorus species complex are more similar (based on nucleotide divergence of the HSP 40 kDa and COI species-wise consensus sequences) to one another than to representatives from outside that species complex (B. rubens, B. angularis and B. diversicornis), with an overall higher nucleotide diversity in the COI. The higher diversity in the mito- chondrial COI compared to nuclear HSP 40 kDa gene was expected as mitochondrial DNA in general exhibits a higher mutation rate than nuclear ­genes70, a phenomenon observed as well in ­rotifers71. While HSP 40 kDa gene divergence among Brachionus species generally resembled their phylogenetic affinity, the dN/dS ratio is the smallest, when comparing the not directly related species B. diversicornis and B. calyciflorus s.s. This may have arisen from similar environmental parameters that lead to similar selection ­pressures72. Indeed, a recent study found the occurrence of B. diversicornis to be correlated with warmer water ­temperatures73, which could indicate a higher thermotolerance—as observed in B. calyciflorus s.s.35,36—also in this species. Selection scenario of the HSP 40 kDa. Within the HSP 40KDa gene, six amino acid sites were inferred to be under positive selection. Discussion C did t Candidate gene selection pipeline. The utilization of available transcriptomes and different expres- sion patterns of B. calyciflorus s.s. and B. fernandoi allowed us to identify a candidate gene which likely plays a role in the differences in temperature adaptation among the two Brachionus species. Indeed, HSPs have been shown to be involved in the response to various environmental stressors such as thermal stress, toxins, oxida- tive ­conditions62–64 and ­aging61. The importance of HSPs in the process of thermotolerance for invertebrates, particularly HSP 40 kDa, HSP 60 kDa and HSP 70 kDa, was previously ­shown51 in the monogonont rotifer B. manjavacas. Genetic variation in the HSP 40 kDa gene among Brachionus species. The analysis of the success- fully amplified HSP 40 kDa gene of the 44 specimens of the B. calyciflorus cryptic species complex (B. calyciflorus s.s. and B. fernandoi) from 14 different locations (Europe, North America) revealed 32 unique alleles, indicating https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ Site (aa) Code Bc–Bf–Br–Ba–Bd Ancestral Score Sensitivity Specificity Prediction 10* H10V/I H–V/I–H–R–-R H 0.002 0.99 0.30 Benign H10V/I H–V/I–H–R–R H 0.004 0.97 0.59 Benign 27 E27G E–G–E–E–E E 0.000 1.00 0.00 Benign 30 F30- F–F–F–F F – – – – 31 S31- S–S–S–S S – – – – 38* E/K38E/K E/K–E/K–E–E–E E 0.231 0.91 0.88 Benign 63 L63M L–M–L–M–L L 0.953 0.97 0.93 Possibly damaging 66 T66S/F T–F–T–F–T T 0.143 0.92 0.86 Benign T66S/F T–F–T–F–T T 0.997 0.41 0.98 Possibly damaging 127 T127A T–A–T–T–T T 0.019 0.95 0.80 Benign 175 F175V F–V–V–F–V V 0.001 0.99 0.15 Benign 177 Y177N Y–N–Y–Y–Y Y 0.000 1.00 0.00 Benign 226 R226K R–K–R–K–R R 0.000 1.00 0.00 Benign 242 H242L H–L–I–H–H H 0.000 1.00 0.00 Benign 249* P/S249P P/S–P–P–Q–Q E 0.116 0.93 0.86 Benign 256* L/F/N256L L/F/N–L–L–L–L L 0.024 0.95 0.81 Benign L/F/N256L L/F/N–L–L–L–L L 0.094 0.93 0.85 Benign 285 D285E D–E–D–E–D E 0.000 1.00 0.00 Benign 286* I/K286I I/K–I–I–I–I I 0.914 0.81 0.94 Possibly damaging 292* T/I292R T/I–R–A–S–V ? 0.001 0.99 0.15 Possibly damaging T/I292R T/I–R–A–S–V ? 0.000 1.00 0.00 Benign Table 3. Prediction of impact of non-synonymous (fixed or under selection cf. Table 1) amino acid substitutions between B. calyciflorus s.s. and B. fernandoi in comparison to B. rubens, B. angularis and B. diversicornis. Predictions were made using Polyphen2. The code provides details on the amino acid substitution and the position. Bc–Bf–Br–Ba–Bd provides the information of the respective amino acid of B. calyciflorus s.s. Table 3.   Prediction of impact of non-synonymous (fixed or under selection cf. Table 1) amino acid b b l fl d f d b l d www.nature.com/scientificreports/ calyciflorus s.s. and the marine clade comprising B. plicatilis, B. manjavacas, B. rotundiformis and B. koreanus to about 41–47 Myr. This latter estimate is considerably larger than an earlier estimate of divergence time between the freshwater species B. calyciflorus (species undefined) and the marine B. plicatilis, using COI and 18S as markers (~ 25 ­Myr85). This dis- crepancy could be due to the increased number of Brachionus species used in our analysis and the different genes and substitution rates used in the present study, relative to Tang et al. (2014)85. Tang et al. used a substitution rate of 1.76% ­Myr−1 for COI and 0.02% ­Myr−1 for ­18S85, while we used the standard mitochondrial substitution rate for invertebrates (1.15% ­Myr−1)86. However, all these rates are derived from distant taxa and—to the best of our knowledge—no rotifer-specific substitution rates are available so far. Hence, these analyses should be repeated when substitution rate estimates for our target species (B. calyciflorus s.s. and B. fernandoi) become available. In any case, we note that estimated divergence times within the freshwater B. calyciflorus species complex are in the same order of magnitude as in the marine B. plicatilis species complex (represented by B. plicatilis and B. manjavacas in our analysis; cf. Supplementary Fig. s8). Hybridization event. Our study revealed a natural hybridization event between B. fernandoi and B. caly- ciflorus s.s. individuals originating at one sampling location (a single pond): Among the specimens collected there, four exhibited B. fernandoi ITS1 alleles, but shared the same B. calyciflorus s.s COI haplotype.). This comprises—to the best of our knowledge—the first reported in-situ hybridization among these two species. The ability of the species within the B. calyciflorus species complex to hybridize has already been suggested by the widespread occurrence of mitonuclear ­discordance23. However, only recent studies under laboratory conditions observed hybridization between the most closely related species B. calyciflorus s.s. and B. elevatus6,7, but with a significantly lower intraspecific fertilization (i.e., pre-zygotic isolation) and higher dormant propagule mortality (i.e., post-zygotic isolation)6. Another study detected signs of hybridization between B. elevatus and B. dorcas87. The comparison of alleles/haplotypes (HSP, ITS1, COI) in our four hybrid specimens with other samples from the same location revealed the hybrids to be ­F2 or a subsequent generation and that genes from B. calyciflorus s.s. introgressed into the local B. fernandoi gene pool. www.nature.com/scientificreports/ downstream stress response, which is underlined by the predicted impact of amino acid substitutions on protein function at two of the six sites. However, among the inferred sites under positive selection, only one (292, cf. Sup- plementary Fig. s4) exhibited species-specific amino acids. One explanation could be that the large geographic range of our study correlated with different local selection pressures, such that most substitutions were not fixed among the entire distribution range of a species. Another explanation could be a low genomic recombination rate (Muller’s ratchet), whereby clonal organisms easily accumulate slightly deleterious mutations that can gen- erate noise in the selection analysis, hindering the identification of species-specific sites under ­selection82. The latter is in line with the findings of the McDonald-Kreitman Test (MKT) where a high Neutrality Index of 12.05 was found between the unique alleles of B. calyciflorus s.s. and B. fernandoi. This indicates an overabundance of replacement-site polymorphisms, which can arise from slightly deleterious polymorphic variants not eliminated by purifying ­selection83, a phenomenon known from clonal ­organisms84. y p y g p g Because of the potentially compromised power of selection analyses in clonal ­organisms82, we inspected all further amino acid substitutions as well. Indeed, among them eleven fixed positions between our species were identified, two of which (positions 63 and 66; cf. Table 3) with a potential impact on protein function. These sites are not located in known functional domains of the HSP 40 kDa, yet they may have an impact on the structure of the protein. The results of the branch site model test indicated positive (directional) selection in B. fernandoi, but not in B. calyciflorus s.s. This is corroborated by character polarity, i.e., B. fernandoi predominantly exhibit- ing derived substitutions, while B. calyciflorus s.s. mostly retaining the ancestral amino acids. This allows us to draw the conclusion that B. fernandoi diverged from B. calyciflorus s.s. A divergent selection scenario for both species is compatible with the positive Tajima’s D statistics (albeit not significant).hl p p p j ( gi ) The substantial nucleotide divergence among the two formerly cryptic species B. fernandoi and B. calyciflorus s.s. suggest these lineages to be evolutionary more ancient than one might expect for morphologically hardly distinguishable sister species. We had inferred their divergence time as ~ 25–29 Myr. The same analysis dated the split between the Brachionus freshwater clade comprising B. angularis, B. fernandoi and B. Discussion C did t A closer inspection of those sites revealed that four of them are in functional domains of the gene. One site is located in the J-domain, a region known to be important in the chaperone activ- ity of HSP 40 kDa and the HSP 70 kDa by interacting with the ATP domain of the HSP ­70kDa74, which acceler- ates ATP ­hydrolysis75,76 and thus, regulates the ATPase ­activity77. Three other sites are located in the C-terminal domain of the HSP 40 kDa. Although the exact function of these sites is still undetermined, it is known that the C-terminal domain of yeast Saccharomyces cerevisiae contains a peptide binding ­site78,79 and is therefore enabled to interact with other proteins. Changes in amino acid composition at these sites can affect folding patterns and thus binding with other proteins (e.g., HSP 70 kDa) through suboptimal structures or ­polarities80,81. These sub- optimal structures can affect the strength of HSP 70 kDa ATPase regulation and potentially alter an organism’s https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ Materials and methods Candidate gene selection. Candidate gene selection. To identify candidate genes with a sequence divergence pattern related to dif- ferential temperature adaptation, previously published transcriptome ­data35 (GenBank accessions number SRA: SRR10426055-76) was analysed using the following customized bioinformatic pipeline (Supplementary Fig. s1): De novo transcriptome assemblies were used to generate a super transcript for each species using Trinity v. 2.11.0 gene splicer ­modeler89. This super transcript step was integrated to minimize redundancy in the data by inferring original genes and alternative splice ­forms90. A reciprocal best blast hit process was performed, using the blastn program of BLAST 2.9.0+91 to detect orthologous genes shared by B. calyciflorus s.s. and B. fernandoi. To determine the best blast hit, results were filtered using a combination of E-value, which is a size corrected measure of statistical significance, and the bit score, which is a measure of matches and mismatches between two ­sequences91. When E-values of the first two or more hits were the same, the best hit was chosen using the bit score. For each search, a list was created that contained one best hit per query. Orthologous gene pairs were extracted, and open reading frames were predicted using TransDecoder v 5.5.092. To calculate ratios of the rates of non-synonymous and synonymous substitutions (dN/dS) from protein-coding regions, sequences were then translated into amino acid sequences using ­Biopython93 and locally aligned within the Biopython integrated package pairwise2 using a Smith-Waterman algorithm. Locally aligned coding sequences and the corresponding unaligned DNA sequences were used to create codon alignments using ­pal2nal94. Selection tests were conducted using all available seven (M0, M1a, M2, M3, M7, M8 and M8a) codeML models (Supplementary Table s1), as implemented in PAML v. 4.995. These models where then compared in four (M0 vs. M3, M1a vs. M2, M7 vs. M8, M8 vs. M8a) predefined likelihood-ratio tests (LRT) to decide whether the different null models (i.e., models that do not allow for any codons ω > 1, corresponding to absence of positive selection) can be ­rejected95.i y g j Orthologous genes that were significant (< 0.05) in all four LRT comparisons were annotated using Gene Ontology (GO) ­terms96. These terms are hierarchically ordered descriptions of genes or proteins molecular func- tions, biological processes, and cellular components. The GO term annotation was done on the online Server Argot2.5 and its batch processing ­function97. Materials and methods Candidate gene selection. To use this function, the longest available amino acid sequence of each protein was used in a blast search against the Uniprot Swiss-Prot ­database98 and a hmmer ­search99,100 against the Pfam-A ­database100. In addition, we compared the genes exhibiting positive selection in the selection tests with those found to be differentially expressed relative to species and temperature (control: 20 °C; mild heat: B. calyciflorus s.s. 26 °C, B. fernandoi 23 °C; high heat: B. calyciflorus s.s. 32 °C, B. fernandoi 26 °C)35. Among those genes functionally related to temperature tolerance (GO:00009408; “response to heat”; GO:00009409; “response to cold”), only one orthologous gene, the HSP 40 kDa, exhibited signs of positive selection and was differentially expressed in more than one temperature category, hence chosen for in-depth analysis. DNA extraction. To extract DNA, single rotifer specimens were collected from laboratory cultures, washed in 96% EtOH and stored in a 1.5 mL reaction tube in10µL HPLC-H20. In total, 56 rotifer individuals (B. caly- ciflorus s.s., n = 25; B. fernandoi, n = 19; B. rubens, n = 4; B. diversicornis, n = 3; B. angularis, n = 5), comprising 56 clonal cultures (WC medium at 20 °C under 16:8 light:dark photoperiod) which were established from one individual isolated from the field, were collected from different locations in Germany. For B. calyciflorus s.s., additional samples from USA, Italy and Austria were available (Supplementary Fig. s2, Supplementary Table s2). To prevent that the DNA from single individuals is lost during the extraction process, 3 µL carrier RNA [1 µg/µL] (QIAGEN, Germany) was added to the sample during the lysis. DNA was extracted using the NucleoSpin®Tissue extraction kit (Macherey–Nagel, Germany) following the manufacturer’s protocol for animal tissue (page 12–14). Primer design HSP 40 kDa. To amplify the HSP 40 kDa from all five different Brachionus species, primers were designed using the candidate gene sequences (B. calyciflorus s.s. and B. fernandoi) as well as the published HSP 40 kDa sequence of B. calyciflorus (unknown species assignment regarding current taxonomy; Genbank: KC176712.161). Sequences were aligned in Geneious v. 8.1.9101 using ­ClustalW102 and the implemented primer3 ­algorithm103 was used to design primer pairs. Amplification and sequencing of the ITS1, COI and HSP 40 kDa. To determine the species and clonal diversity, both the nuclear internal transcribed spacer (ITS1) and the mitochondrial Cytochrome Oxidase Subunit I (COI) were amplified, using universal invertebrate ­primers104,105. www.nature.com/scientificreports/ This is because all the introgressed specimens we detected in this study were homozygous for B. fernandoi alleles at the ITS1 locus. Furthermore, three detected hybrids carried B. fernandoi specific HSP 40 kDa alleles, while in one case a B. calyciflorus s.s. specific HSP 40 kDa allele occurred. This different genetic makeup among the hybrids suggests that they either have emerged from independent hybridization events or that the hybridization was sufficiently ancient to allow for repeated sexual recombination after the hybridization event. In any case, our findings demonstrate that B. calyciflorus s.s. and B. fernandoi can naturally hybridize at sites where they occur in sympatry. It was found in the marine B. plicatilis species complex that niche differentiation of very similar species (e.g., body size, biotic niches, competition abili- ties) is facilitated by their response to changing physical environments in combination with life and diapause his- tory ­traits16. In the B. calyciflorus species complex, a previous study reported strongest pronounced differences in life history traits of B. fernandoi compared to B. calyciflorus s.s., B. elevatus and B. dorcas, such as prolonged egg and juvenile development times and an overall lower egg production rate and mictic ­ratio32. The adaptation to different temperature ­optima34, associated with differences in HSP 40 Da ­expression35 and protein structure (this study), may lead to seasonal isolation of the two species. This illustrates the above example that the niche of very similar species can be determined by their response to abiotic environmental conditions. The differential niches (here preferred temperature) occupied by the respective species reflect divergent adaptation. This acts as a pre-zygotic isolation mechanism by facilitating differences in timing of reproduction and population growth based on distinct environmental cues (i.e., temperature, photoperiod) and thus maintaining the species bounda- ries. Such pre-zygotic isolation by season has also been observed among Daphnia species (reviewed ­in88). This https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ mechanism may however be imperfect under certain environmental conditions, leading to occasional hybridiza- tion, as observed in our study. mechanism may however be imperfect under certain environmental conditions, leading to occasional hybridiza- tion, as observed in our study. Conclusion We used transcriptome and expression data to infer a suitable candidate, the HSP 40 kDa gene, which may play a role in temperature adaptation in the Brachionus calyciflorus species complex. Species-specific alleles and fixed amino acid substitutions sites as well as positively selected sites located in functional domains of the protein were identified. The high number of detected alleles, the results of the branch site selection test, and the fixed sites indicate a divergent adaptation process with B. calyciflorus s.s. retaining ancestral features, from which B. fernandoi derived by positive directional selection. Furthermore, the study revealed descendants of an in-situ hybridization event between B. calyciflorus s.s. and B. fernandoi. This finding indicates that hybridization between those species is possible. We hypothesize that the temporally isolated niches they populate serve as pre-zygotic isolation mechanisms. This isolation may be imperfect under certain environmental conditions, yet hybridiza- tions seem rare and seasonal niche separation generally prevents species boundaries from becoming blurred. Materials and methods Candidate gene selection. calyciflorus s.s., n = 50; B. fernandoi, n = 38) were translated using the published translation reading frame of the HSP 40 kDa gene of B. calyciflorus (Genbank: KC176712.1). As we did not yield the complete sequence for all specimens, the alignment was truncated to 888 bp present in all sequences. Number of non-synonymous substitutions per non-synonymous site between the two species were compared using SLAC analysis implemented in ­Datamonkey110,111. HSP 40 kDa allele identification. To identify different allele types within the B. calyciflorus species com- plex, allele networks were generated from the resulting 88 phased sequences (B. calyciflorus s.s. n = 50 and B. fernandoi n = 38) using the program popART version 1.7112. Subsequently, a Circos ­plot113 was generated using the web interface based on allele types identified by popART, species, and specimens’ origin. Sequence divergence in the HSP 40 kDa gene relative to established barcoding markers. Spe- cies recognition within the B. calyciflorus complex relies on species-specific ITS1 sequences and clonal lineages are further characterized by their mitochondrial COI haplotype. For 41 specimens (B. fernandoi n = 18, B. calyci- florus s.s. n = 20, and consensus sequences of B. rubens, B. angularis, and B. diversicornis), sequences were avail- able for both these marker genes and the HSP 40 kDa gene. For these specimens, congruence in genetic affinity across genetic markers was assessed using a tanglegram approach. The respective phylogenies were calculated using RaxML v.8114, performing 1000 bootstrap iterations. Dendrograms and the tanglegrams were generated in R v.4.0.5 with the package dendextend v.1.15.1115. Selection tests and divergence time. To test whether the expressed genetic variation among the the five different Brachionus species is under selection, a selection test was performed based on the 29 HSP 40 kDa species-specific alleles using the Program PAML v.4.995. A specific focus was on the divergence of the two spe- cies B. calyciflorus s.s. and B. fernandoi. This analysis needs a phylogeny as input which was based on the 532 bp long ITS1 fragment and calculated using RaxML v.8, performing 1000 bootstrap iterations. The phylogeny was viewed in FigTree version 1.4.4.116 and adapted using Inkscape version 1.0.1.117 (Supplementary Fig. s3). Materials and methods Candidate gene selection. This ITS1 phylogeny as well as the HSP 40 kDa unique alleles were used to infer sites under selection according to the codeML site model implemented in PAML, testing all seven (M0, M1a, M2, M3, M7, M8 and M8a) different sub- stitution models. The different models vary regarding substitution rates of synonymous and non-synonymous sites (ω values; see Supplementary Table s1) with a subsequent site under selection inference via Bayes Empiri- cal Bayes (BEBs) (for parameter setting see Supplementary Table s9). The models were compared in four (M0 vs. M3, M1a vs. M2, M7 vs. M8, M8a vs. M8) predefined Likelihood Ratio Tests (LRTs) to decide whether the respective null models can be rejected. Significance of the M0 vs. M3 comparison indicates variation in ω, a pre- requisite for further tests on positive selection. The null model M1a allows only negatively selected and neutral sites (2 ω values), to which M2a adds a third ω for positively selected sites. M7 and M8 resemble M1a and M2a, but allow for rate variation among negatively selected sites (10 ω values < 1 taken from a β distribution), without consideration of neutral sites (ω = 1). The last comparison of M8a vs. M8 tests for positive selection against a null model (M8a) resembling M7, but with an additional fixed ω = 1 (allowing for sites under selective neutrality); this comparison has been found to increase robustness by yielding fewer false positive ­results118. An additional branch site test was performed to identify patterns of selection on three different branches: (I) the shared branch of B. calyciflorus s.s. and B. fernandoi, (II) B. calyciflorus s.s. only and (III) B. fernandoi only (Supplementary Fig. s3). Subsequently, to further compare the two formerly cryptic species of B. calyciflorus s.s. and B. fernandoi, a codon-based McDonald–Kreitman test (MKT) and Tajima’s D statistics (allele frequency based) were calcu- lated based on the unique inferred alleles using DNAsp v. 6.iili q g p Species-specific fixed amino acid substitutions within the B. calyciflorus species complex were identified (Sup- plementary Fig. s5) and the ancestral amino acid was inferred under parsimony, using sequence information from B. rubens, B. angularis and B. diversicornis and the ITS1 phylogeny (Supplementary Fig. s3). The functional effects of the specific amino acid (aa) substitutions were predicted with ­Polyphen2119 using B. calyciflorus s.s. as a reference. Materials and methods Candidate gene selection. PCR conditions, primer sequences, and used PCR chemicals mixes can be found in the Supplementary Tables s3, s4 and s5. The HSP 40 kDa gene of https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 | www.nature.com/scientificreports/ all five Brachionus species was amplified using newly designed primer pairs (Supplementary Tables s3, s6 and s7). Successfully amplified HSP 40 kDa, COI and ITS1 products were purified using an enzymatic (ExoAP) proce- dure and sequenced on a Sanger sequencing platform (Applied Biosystems™ 3500 Genetic Analyzer). Sequences from all specimens used in this study (Supplementary Table  s2) were visually inspected using Geneious v. 8.1.9 and heterozygous positions (for ITS1 and HSP 40 kDa) were encoded with the standard IUPAC code for ­ambiguity106. To reconstruct both alleles of the diploid nuclear DNA, the PHASE algorithm version 2.1107,108 was used, as implemented in DNAsp v. ­6109. HSP 40 kDa sequence diversity. To compare sequence divergence in the HSP 40 kDa gene among the five different species, consensus sequences per species were generated. In order to avoid any bias which may arise from uneven geographic sampling across species, we only used specimens originating from the same region “Uckermark” for this analysis: B. calyciflorus s.s. (n = 11), B. fernandoi (n = 8), B. rubens (n = 4), B. diversicornis (n = 3) and B. angularis (n = 5). Sequence ambiguities in the consensus sequence were coded as N’s (see Supple- mentary Table s8). Pairwise nucleotide diversities of the 1,025 bp long HSP 40 kDa gene sequence and the 435 bp long COI sequences between the five species were calculated. For an 888 bp fragment of the HSP 40 kDa gene (see below), non-synonymous resp. synonymous substitutions were identified using DNAsp v. 6. Expressed variation in the HSP 40  kDa gene between B. calyciflorus s.s. and B. fernan- doi. Sequences originating from multiple individuals (B. calyciflorus s.s., n = 50; B. fernandoi, n = 38) were translated using the published translation reading frame of the HSP 40 kDa gene of B. calyciflorus (Genbank: KC176712.1). As we did not yield the complete sequence for all specimens, the alignment was truncated to 888 bp present in all sequences. Number of non-synonymous substitutions per non-synonymous site between the two species were compared using SLAC analysis implemented in ­Datamonkey110,111. Expressed variation in the HSP 40  kDa gene between B. calyciflorus s.s. and B. fernan- doi. Sequences originating from multiple individuals (B. www.nature.com/scientificreports/ such that it ranks any substitution without a predicted change in protein function as "benign" (i.e., no effect), while any predicted change is ranked as "damaging" (i.e., predicted to impact protein function).ll To estimate the within B. calyciflorus species complex divergence time between B. calyciflorus s.s. and B. fer- nandoi the program BEAST v.1.10.4120 was used. Whole mtGenome coding sequences (cds) of different rotifer species were downloaded from NCBI: B. calyciflorus s.s.121, B. fernandoi121, B. angularis122, B. manjavacas123, B. plicatilis124, B. koreanus125, B. rotundiformis126, B. rubens127 and P. similis128 (for Genebank accession numbers cf. Supplementary figure s8). In absence of a published substitution rate for rotifers, the standard divergence rate for invertebrates/insects (2.3% ­Myr−1) with a constant substitution rate of 0.0115 per million years per ­lineages86 was used to calibrate the phylogeny. Cds were aligned in Geneious v. 8.1.9 using ClustalW and the IQ-Tree ­webserver129 was used to determine the best fitting substitution model. The BEAST run was conducted with 10 million MCMC iterations, with GTR + G4 + I chosen as the substitution model. Convergence was checked with Tracer v.1.7.2130, using the first million MCMC iterations as the burn-in value and tree was visualized using FigTree version 1.4.4. and adapted in Inkscape version 1.0.1. References 1. Mayr, E. Systematics and the Origin of Species, from the Viewpoint of a Zoologist (Harvard University Press, 1942). 2. Ostevik, K. L., Andrew, R. L., Otto, S. P. & Rieseberg, L. H. Multiple reproductive barriers separate recently diverged sunflowe ecotypes. 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Hwang, D.-S. et al. Complete mitochondrial genome of the monogonont rotifer, Brachionus koreanus (Rotifera, Brachionidae) Mitochondrial DNA B. 25, 29–30 (2014). 26. Kim, H.-S. et al. Complete mitochondrial genome of the monogonont rotifer Brachionus rotundiformis (Rotifera, Brachionidae) Mitochondrial DNA B. 2, 39–40 (2017). 27. Choi, B.-S. et al. Complete mitochondrial genome of the freshwater monogonont rotifer Brachionus rubens (Rotifera, Brachio- nidae). Mitochondrial DNA B. 5, 5–6 (2019). 28. Choi, B.-S. et al. Complete mitochondrial genome of the marine monogonont rotifer Proales similis (Rotifera, Proalidae) Mitochondrial DNA B. 5, 1151–1152 (2020).i 29. Trifinopoulos, J., Nguyen, L.-T., von Haeseler, A. & Minh, B. Q. W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 44, W232–W235 (2016). y ( ) 30. Drummond, A. J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007). Author contributions K.K., R.T. and G.W. designed the research. K.K. and S.P. collected the samples. K.K. performed laboratory pro- cessing of samples with support from K.H. K.K., M.G. and S.P. analysed the data with input from R.T. and G.W. K.K. produced the graphics and wrote the manuscript with the support of R.T. S.P., M.G. and G.W. All authors approved the final version of the manuscript. © The Author(s) 2022 Funding g Open Access funding enabled and organized by Projekt DEAL. This work was supported by Deutsche Forschun- gsgemeinschaft (DFG) in the framework of the BioMove Research Training Group (DFG-GRK 2118). Additional information Supplementary Information The online version contains supplementary material available at https://​doi.​org/​ 10.​1038/​s41598-​022-​27137-3. Additional information Supplementary Information The online version contains supplementary material available at https://​doi.​org/​ 10.​1038/​s41598-​022-​27137-3. Correspondence and requests for materials should be addressed to R.T. Reprints and permissions information is available at www.nature.com/reprints. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and nstitutional affiliations. Open Access  This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. https://doi.org/10.1038/s41598-022-27137-3 Scientific Reports | (2022) 12:22626 |
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Phenotyping and Quantitative Trait Locus Analysis for the Limited Transpiration Trait in an Upper-Mid South Soybean Recombinant Inbred Line Population (“Jackson” × “KS4895”): High Throughput Aquaporin Inhibitor Screening
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Phenotyping and Quantitative Trait Locus Analysis for the Limited Transpiration Trait in an Upper-Mid South Soybean Recombinant Inbred Line Population (“Jackson” × “KS4895”): High Throughput Aquaporin Inhibitor Screening Sayantan Sarkar1, Avat Shekoofa1*, Angela McClure1 and Jason D. Gillman2 1 Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States, 2 Plant Genetics Research Unit, USDA-ARS University of Missouri Columbia MO United States 1 Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States, 2 Plant Genetics Research Unit, USDA-ARS, University of Missouri, Columbia, MO, United States ORIGINAL RESEARCH published: 20 January 2022 doi: 10.3389/fpls.2021.779834 Keywords: AgNO3, aquaporin inhibitor, genotyping, high throughput phenotyping, water conservation trait Edited by: Edited by: Dejan Dodig, Maize Research Institute Zemun Polje, Serbia Edited by: Dejan Dodig, Maize Research Institute Zemun Polje, Serbia Reviewed by: Giriraj Kumawat, ICAR-Indian Institute of Soybean Research, India Geng Bai, University of Nebraska–Lincoln, United States Reviewed by: Giriraj Kumawat, ICAR-Indian Institute of Soybean Research, India Geng Bai, University of Nebraska–Lincoln, United States *Correspondence: Avat Shekoofa ashekoof@utk.edu Specialty section: This article was submitted to Plant Abiotic Stress, a section of the journal Frontiers in Plant Science Received: 19 September 2021 Accepted: 09 December 2021 Published: 20 January 2022 Soybean is most often grown under rainfed conditions and negatively impacted by drought stress in the upper mid-south of the United States. Therefore, identification of drought-tolerance traits and their corresponding genetic components are required to minimize drought impacts on productivity. Limited transpiration (TRlim) under high vapor pressure deficit (VPD) is one trait that can help conserve soybean water-use during late- season drought. The main research objective was to evaluate a recombinant inbred line (RIL) population, from crossing two mid-south soybean lines (“Jackson” × “KS4895”), using a high-throughput technique with an aquaporin inhibitor, AgNO3, for the TRlim trait. A secondary objective was to undertake a genetic marker/quantitative trait locus (QTL) genetic analysis using the AgNO3 phenotyping results. A set of 122 soybean genotypes (120-RILs and parents) were grown in controlled environments (32/25-d/n ◦C). The transpiration rate (TR) responses of derooted soybean shoots before and after application of AgNO3 were measured under 37◦C and >3.0 kPa VPD. Then, the decrease in transpiration rate (DTR) for each genotype was determined. Based on DTR rate, a diverse group (slow, moderate, and high wilting) of 26 RILs were selected and tested for the whole plant TRs under varying levels of VPD (0.0–4.0 kPa) at 32 and 37◦C. The phenotyping results showed that 88% of slow, 50% of moderate, and 11% of high wilting genotypes expressed the TRlim trait at 32◦C and 43, 10, and 0% at 37◦C, respectively. Genetic mapping with the phenotypic data we collected revealed three QTL across two chromosomes, two associated with TRlim traits and one associated with leaf temperature. Analysis of Gene Ontologies of genes within QTL regions identified several intriguing candidate genes, including one gene that when overexpressed had previously been shown to confer enhanced tolerance to abiotic stress. Collectively these results will inform and guide ongoing efforts to understand how to deploy genetic tolerance for drought stress. INTRODUCTION evaporative demand is higher. Under field conditions, drought- tolerant peanut genotypes (with partial stomata closure trait) displayed a downward LT slope with an increase in VPD during midday (1100 to 1400 EST) (Balota and Sarkar, 2020). Bai and Purcell (2018) observed an interaction between LT and slow and fast-wilting soyabean genotypes, where slow-wilting genotypes had a lower LT during water-deficit stress. Plant photosynthesis and transpirational rates are highly coupled (Sinclair, 2017). Most of the water lost by plants under stress is due to transpiration, which is linked to stomatal opening to allow CO2 diffusion (Devi and Reddy, 2018a; Shekoofa and Sinclair, 2020). Hence, water loss due to transpiration is linked to plant biomass growth and yield (Tanner and Sinclair, 1983; Blum, 2009). Low water availability reduces assimilate partitioning to reproductive sinks, and on a cellular level impairs cell growth and division (Blum, 2011; Sarkar, 2020; Bennett et al., 2021; Sarkar et al., 2021a). Water related stresses, such as direct drought stress and associated factors including high temperature and evaporative demand, reduce both transpiration and photosynthesis, resulting in reduced crop yield (Sinclair, 2017; Balota et al., 2021). It is essential that any putative water saving trait should result in monetarily relevant yield benefit and should have genetic variability within the target crop species (Sadok and Sinclair, 2011). In fact, soybean genotype PI 416937 has been identified as expressing the TRlim trait (i.e., slow-wilting) phenotype in the field under high VPD (>2.5 kPa), and this has been traced to low leaf hydraulic conductance (Sinclair et al., 2008). Sadok and Sinclair (2012) suggested that the low leaf hydraulic conductance in PI 416937 might be related to a unique population of aquaporins (AQPs) in its leaves. Further studies have shown that soybean genotypes expressing TRlim trait are insensitive to aquaporin inhibitors, such as silver and zinc ions (Sadok and Sinclair, 2010, 2012; Devi et al., 2016). However, it is suggested that under extreme drought or high atmospheric vapor pressure deficit (VPD) conditions, restriction of stomatal conductance might increase photosynthetic return per unit of transpiration (Sinclair et al., 2005, 2010; Devi et al., 2009; Gholipoor et al., 2010; Carpentieri-Pipolo et al., 2012; Gaffney et al., 2015; Shekoofa et al., 2020). These traits result in restricted TR under high vapor pressure conditions, such that water is conserved in the soil and is available during subsequent drought periods. INTRODUCTION Thus, plants resort to drought avoidance mechanism such as limited transpiration (TRlim) and minimizing stomatal conductance (Kooyers, 2015; Basu et al., 2016; Devi et al., 2016). These studies also suggested that reduced TR and stomatal conductance are controlled by gene expression. Such mechanisms have been successfully studied in crop species, including: maize (Zea Mays L.) (Fletcher et al., 2007; Shekoofa et al., 2016), peanut (Arachis hypogaea L.) (Devi et al., 2009; Shekoofa et al., 2013, 2017), cotton (Gossypium hirsutum L.) (Devi and Reddy, 2018b; Shekoofa et al., 2020), sorghum (Sorghum bicolor L.) (Gholipoor et al., 2010; Choudhary et al., 2013), and soybean [Glycine max (L.) Merr.] (Bunce, 1981; Devi et al., 2014; Sarkar et al., 2021b). Of particular interest, soybean showed a decrease in stomatal conductance between VPD of 1.0 and 2.5 kPa, differing within genotypes (Bunce, 1981). In plants, AQPs occur in multiple isoforms in both plasmalemma and tonoplast membranes resulting in regulation of water flow in and out of cells. Physiological and molecular studies have identified AQPs as playing key roles in regulating hydraulic conductance in leaves and roots (Beaudette et al., 2007; Shekoofa and Sinclair, 2018; Sung et al., 2021). Therefore, the high-throughput phenotyping of structured soybean populations, along with molecular genotyping is needed for marker development. This type of research is essential for making the soybean genome sequence useful for breeding purposes, in particular for screening drought-tolerant soybean lines based on their sensitivity to aquaporin inhibitors. In this work, we used a two-tiered screening method to identify soybean genotypes with the TRlim trait. Our method is similar to the three-tiered approach by Sinclair et al. (2000). Direct measures of the transpiration response rate to increasing VPD are low-throughput, tedious, and require specialized equipment. Furthermore, the number of genotypes that can be directly phenotyped for the TRlim trait is very limited. Thus, an indirect measurement of TR that may be less accurate but can allow characterization of a large number of genotypes would be helpful in breeding for the TRlim trait (Choudhary and Sinclair, 2014). Choudhary and Sinclair (2014) suggested that one possibility is that the response in TR to feeding of chemical inhibitors to leaves or roots of plants might allow discrimination among genotypes under varying VPD levels. Appropriate parents have to be chosen for crossing when it comes to screening for drought tolerance traits. Abbreviations: TRlim, limited transpiration; VPD, vapor pressure deficit; RIL, recombinant inbred line; QTL, quantitative trait locus; TR, transpiration rate; DTR, decrease in transpiration rate; LT, leaf temperature; AQPs, aquaporins; TRH2O, transpiration in water; TRAgNO3, transpiration rate following exposure to silver nitrate; PCA, principle component analysis; H2, broad sense heritability; DAP, days after planting; BP, breakpoint. Citation: Sarkar S, Shekoofa A, McClure A and Gillman JD (2022) Phenotyping and Quantitative Trait Locus Analysis for the Limited Transpiration Trait in an Upper-Mid South Soybean Recombinant Inbred Line Population (“Jackson” × “KS4895”): High Throughput Aquaporin Inhibitor Screening. January 2022 | Volume 12 | Article 779834 1 Frontiers in Plant Science | www.frontiersin.org Limited Transpiration in Soybean RILs Sarkar et al. INTRODUCTION Previous studies have reported that soybean genotypes “KS4895” and “Jackson” differ in drought tolerance traits such as delayed wilting, ureide, and nitrogen concentration (Sinclair et al., 2007; Charlson et al., 2009; Hwang et al., 2013, 2015a,b; King et al., 2014). Therefore, the objectives of this study were to (a) evaluate 120 recombinant inbred lines (RILs; F3 and F5 derived from “KS4895” × ”Jackson”) through a high-throughput phenotyping technique while measuring the RILs transpiration sensitivity rate to aquaporin inhibitor (AgNO3) under high VPD condition (initial/indirect screening Decreases in transpiration rate and stomatal conductance are affected by leaf temperature (LT) (Gates, 1964; Blum, 2011). Gates (1964) argued convincingly that increase in LT can be lethal for plants and that transpiration is required to cool the leaves. The study also argues that even a slow rate of transpiration can dissipate enough heat from leaves to have a huge impact on photosynthesis and growth of plants. This implies that plants with slower rate of transpiration (with subsequently warmer leaves than plants with higher rates of transpiration) could be better drought-tolerant by conserving moisture during low water stress, which would be available later in the season when January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 2 Limited Transpiration in Soybean RILs Sarkar et al. the derooted shoots were moved to a greenhouse in which both temperature and VPD were high (Table 1). for TRlim) (b) directly measure the TR of 26 selected RILs from objective “a” and categorize them for the TRlim trait under high VPD and temperature (direct screening for TRlim), and finally (c) undertake genetics/quantitative trait loci (QTLs) analysis for the RIL population in objective “a” and associate the potential QTLs with the drought tolerance trait, i.e., TRlim. Water-cooled lamps provided the photosynthetic photon flux density, which was 600 µmol m−2 s−1 at plant level (Mullen and Koller, 1988; Devi et al., 2016). The derooted shoots were allowed to acclimatize for 60 min and then the flasks plus derooted shoots were weighed (TR H2O initial). After another 60 min, the flasks plus derooted shoots were reweighed (TR H2O final), and the difference between the two weights divided by the time interval was used to calculate the TR in water (TRH2O). INTRODUCTION Following the second weighing of the derooted shoots in water, the individual shoots were quickly transferred to dark-brown, 30-mL glass bottles for exposure to the solution of 200 µM, AgNO3 aquaporin inhibitor (Sadok and Sinclair, 2010). The AgNO3 solution was freshly prepared on the day before each set of experiment. The AgNO3 solution concentration of 200 µM was selected because this concentration was the lowest concentration resulting in maximum transpiration decrease (Sadok and Sinclair, 2010). The derooted shoots were allowed to take up the AgNO3 solution for 60 min by which time TR of the shoots had again reached a constant value (Sadok and Sinclair, 2010). Leaf Temperature h In each set, LT was measured for all tested derooted shoots using a FLIR C3 Thermal Camera with WiFi (Teledyne FLIR LLC, Wilsonville, OR, United States) between 1300 and 1500 CST. In each set of experiment, the corresponding thermal images were taken 1 m above the plant at a resolution of 0.9 cm per pixel for three replications of derooted shoots. The temperature at the central point of a fully expanded trifoliate leaf was obtained for each of the three plants from a thermal image using the camera software. The thermal data were collected after the last stage of exposure to AgNO3 when the final weighing was done. These data sets were used for calculating the average LT for each genotype. q p g Five soybean seeds were planted in 3-L pots filled with soil (commercially available Miracle-Gro potting mix) and inoculated with Bradyrhizobium japonicum (Verdesian Life Sciences, Cary, NC, United States). They were thinned to three plants per pot after 1 week in three-pot replicates per genotype. Plants were maintained in a well-watered condition, in 250 mL pots (i.e., pot capacity) during the initial growth pretreatment period. After approximately 4 weeks, the plants were ready for AgNO3 test. For the measurement of TR response to AQPs inhibitor, AgNO3, the technique explained by Sadok and Sinclair (2010), Shekoofa et al. (2013), and Devi et al. (2016) was followed. Phenotyping and Phenotypic Traits Experiment I Indirect Measurement of Transpiration Under High Vapor Pressure Deficit: High Throughput Screening Using Aquaporins Inhibitor, AgNO3 Frontiers in Plant Science | www.frontiersin.org Plant Materials and Study Site The experiments were conducted at the University of Tennessee West Tennessee Research and Education Center (WTREC), in Jackson, TN between 2018 and 2020. A group of 122 soybean genotypes including 120 RILs and their parents “Jackson” and “KS4895” that were tested during the study (Table 1) were provided by Dr. Larry Purcell (Hwang et al., 2015a). Genotype “KS4895” (PI 595081) is a maturity group (MG) IV developed in Kansas (Schapaugh and Dille, 1998), and “Jackson” (PI 548657) is an MG VII genotype developed by the USDA-ARS in North Carolina (Johnson, 1958). Due to greenhouse space limitations, and to increase the accuracy during data collection since a large number of bottles were involved in each weighing process, only a subset of genotypes was tested with the silver nitrate test. Thus, the RILs were grown in six sets under controlled environments in a greenhouse at 33–35◦C and 35–50% humidity during day, and 20–22◦C and 45–60% humidity during the night. Each set was grown for 4 weeks and included both parents. After the 60 min period, all bottles were weighed to get an initial weight for the transpiration measurement following exposure to AgNO3 (TR AgNO3 initial). After 180 min, each bottle was again weighed (TR AgNO3 final). Measurements of TR for each shoot were generally completed in about 240 min after AgNO3 treatment. The TR following exposure to silver (TRAgNO3) was calculated based on the difference between these two weights divided by the time interval. The difference between TRH2O and TRAgNO3 were used to quantify decrease in TR using various arithmetic combinations (Table 2). Statistical Analysis The evening before the application of AgNO3, three replicate plants per soybean genotype were removed from the soil and derooted by cutting the base of the plant stem underwater using a sharp blade (Table 1). Then derooted soybean shoots were immediately placed in 150-mL Erlenmeyer flasks filled with deionized water. The shoots were kept in a dark laboratory room overnight for about 14 to 15 h with temperature maintained at 24◦C. The following morning, the derooted shoots were transferred to another 150-mL Erlenmeyer flask containing fresh deionized water and sealed with Parafilm-“M” (Pechiney Plastic Packaging, Chicago, IL, United States) to avoid direct water evaporation from the flask. Then, in each set of experiment, A mixed linear model was applied to TR response data using the Fit Model function of JMP 14 (SAS Institute) using an input of 120 RIL lines (and two parental lines), for which we had both genotypic and phenotypic information. For mixed linear models, three factors were included: (1) genotype; (2) experiment; and (3) replication within each experiment. Only genotype was considered fixed, whereas other factors were considered random, and replication was nested within experiment. Principle component analysis (PCA) was run to create a PCA biplot of phenotypic measurements. Pearson’s correlation matrix was used to measure correlation among phenotypes. Polynomial January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 3 “Jackson” and “KS4895” evaluated in this study. Statistical Analysis ) RIL Date Temp (◦C) VPD (kPa) RIL Date Temp (◦C) VPD (kPa Set 3 #90 07/31/2018 35.5–38 2.5–4 Set 6 #7 04/10/2019 37–38 2.5–4.2 #91 07/31/2018 35.5–38 2.5–4 #8 04/10/2019 37–38 2.5–4.2 #92 07/31/2018 35.5–38 2.5–4 #12 04/10/2019 37–38 2.5–4.2 #94 07/31/2018 35.5–38 2.5–4 #22 04/10/2019 37–38 2.5–4.2 #95 07/31/2018 35.5–38 2.5–4 #24 04/10/2019 37–38 2.5–4.2 #96 07/31/2018 35.5–38 2.5–4 #42 04/10/2019 37–38 2.5–4.2 #97 07/31/2018 35.5–38 2.5–4 #46 04/10/2019 37–38 2.5–4.2 #100 07/31/2018 35.5–38 2.5–4 #47 04/10/2019 37–38 2.5–4.2 #102 07/31/2018 35.5–38 2.5–4 #53 04/10/2019 37–38 2.5–4.2 #104 07/31/2018 35.5–38 2.5–4 #61 04/10/2019 37–38 2.5–4.2 #107 07/31/2018 35.5–38 2.5–4 #68 04/10/2019 37–38 2.5–4.2 #108 07/31/2018 35.5–38 2.5–4 #72 04/10/2019 37–38 2.5–4.2 #109 07/31/2018 35.5–38 2.5–4 #77 04/10/2019 37–38 2.5–4.2 Set 4 #113 08/07/2018 37–38 3–4.2 #78 04/10/2019 37–38 2.5–4.2 #115 08/07/2018 37–38 3–4.2 #80 04/10/2019 37–38 2.5–4.2 #117 08/07/2018 37–38 3–4.2 #86 04/10/2019 37–38 2.5–4.2 #120 08/07/2018 37–38 3–4.2 #88 04/10/2019 37–38 2.5–4.2 #121 08/07/2018 37–38 3–4.2 #93 04/10/2019 37–38 2.5–4.2 #125 08/07/2018 37–38 3–4.2 #98 04/10/2019 37–38 2.5–4.2 #127 08/07/2018 37–38 3–4.2 #106 04/10/2019 37–38 2.5–4.2 #129 08/07/2018 37–38 3–4.2 #124 04/10/2019 37–38 2.5–4.2 #131 08/07/2018 37–38 3–4.2 #128 04/10/2019 37–38 2.5–4.2 #133 08/07/2018 37–38 3–4.2 #130 04/10/2019 37–38 2.5–4.2 #134 08/07/2018 37–38 3–4.2 #135 04/10/2019 37–38 2.5–4.2 #136 08/07/2018 37–38 3–4.2 #138 04/10/2019 37–38 2.5–4.2 #137 08/07/2018 37–38 3–4.2 #143 04/10/2019 37–38 2.5–4.2 #139 08/07/2018 37–38 3–4.2 #144 04/10/2019 37–38 2.5–4.2 #140 08/07/2018 37–38 3–4.2 #147 04/10/2019 37–38 2.5–4.2 #141 08/07/2018 37–38 3–4.2 #151 04/10/2019 37–38 2.5–4.2 #142 08/07/2018 37–38 3–4.2 #152 04/10/2019 37–38 2.5–4.2 #149 08/07/2018 37–38 3–4.2 #153 08/07/2018 37–38 3–4.2 #154 08/07/2018 37–38 3–4.2 Set 5 #155 08/14/2018 37–38 3–4.3 #156 08/14/2018 37–38 3–4.3 (Continued Sarkar et al. Statistical Analysis Limited Transpiration in Soybean RILs RIL Date Temp (◦C) VPD (kPa) RIL Date Temp (◦C) VPD (kPa) RIL Date Temp (◦C) VPD (kPa) #34 07/05/2018 36–37 2.5–3.5 #157 08/14/2018 37–38 3–4.3 #35 07/05/2018 36–37 2.5–3.5 #160 08/14/2018 37–38 3–4.3 #36 07/05/2018 36–37 2.5–3.5 #161 08/14/2018 37–38 3–4.3 #71 07/05/2018 35.5–38 2.5–4 #162 08/14/2018 37–38 3–4.3 #73 07/05/2018 35.5–38 2.5–4 #164 08/14/2018 37–38 3–4.3 #74 07/05/2018 35.5–38 2.5–4 #165 08/14/2018 37–38 3–4.3 #79 07/05/2018 35.5–38 2.5–4 #166 08/14/2018 37–38 3–4.3 #81 07/05/2018 35.5–38 2.5–4 #168 08/14/2018 37–38 3–4.3 #87 07/05/2018 35.5–38 2.5–4 #169 08/14/2018 37–38 3–4.3 #89 07/05/2018 35.5–38 2.5–4 #170 08/14/2018 37–38 3–4.3 The plants were grown at 33–35◦C and 35–50% humidity during day, and 20–22◦C and 45–60% humidity during night. The date in this table presents the data collection date per each set for “experiment 1.” The temperature (temp) and vapor pressure deficit (VPD) are the conditions that the plants were subjected to on the day of data collection. Along with the RILs both parents were tested in each set of data collection. regression was used to explain the variation of relative decrease in TR due to LT. Broad Sense Heritability Broad sense heritability (H2) of all traits was calculated as the ratio of genotypic variance (σ2 G) by phenotypic variance (σ2 P) (Phansak et al., 2016). Variance was calculated as the ratio of total sum of squares (TSS) to population size (n). The heritability data have been included in Supplementary File 1. H2= σ2 G σ2 G+ σ2 Gσ2 E E + σ2 E ER where σ2 P = σ2 G+ σ2 Gσ2 E E + σ2 E ER; o2 E, environmental variance; E, number of environments; R, number of replications. H2= σ2 G σ2 G+ σ2 Gσ2 E E + σ2 E ER where σ2 P = σ2 G+ σ2 Gσ2 E E + 2 where o2 E, environmental variance; E, number of environments; R, number of replications. o2 E, environmental variance; E, number of environments; R, number of replications. Direct Measurement of Transpiration Under High Vapor Pressure Deficit fi Twenty-six soybean genotypes (24 RILs and both parents), based on RDTRK and RNDTRK (from the indirect measurement of transpiration, “Experiment I”), were selected to be tested for the direct TR measurement under varying levels of VPD (0.5 to 4.0 kPa). Soybean genotypes that had RDTRK and RNDTRK values from 0.00 to 0.50 were considered slow wilting, 0.51 to 1.00 were considered moderate wilting, and above 1.00 were considered as fast wilting. The plants were grown in pots constructed from polyvinyl chloride pipe (100-mm diameter and 200-mm long). The bottom of each pot was fitted with a flat end cap, in which a small hole was drilled to allow drainage of excess water. A toilet flange was attached to the top of the pot to allow easy attachment of a VPD chamber during measurements (Fletcher et al., 2007; Shekoofa et al., 2013). The pots were filled with commercially available Miracle-Gro potting mix. Five seeds per pot were sown and inoculated with B. japonicum (Verdesian Life Sciences, Cary, NC, United States). After 1 week, the plants were thinned to one plant per pot. Plants were fertilized with 200 mL of 0.075% V/V liquid fertilizer (0- 10-10, N-P2O5-K2O, GH Inc., Sebastopol, CA, United States) at planting and again at 14 and 24 days after planting (DAP). Plants were grown for 28 days under well-watered conditions, with greenhouse temperatures regulated at 33◦C day/26◦C night. After approximately 4 weeks, four replicate plants of each genotype were selected and moved into a walk-in growth chamber and enclosed in individual humidity-regulated chambers (21 L). As there were 12 individual chambers, this meant that the genotypes had to be measured in batches that included three genotypes in each batch. Measurements of transpiration response to VPD were carried out at 32 and 37◦C. Each individual VPD chamber (21 L) was fitted with a 12-V, 80-mm-diameter cooling fan (Masscool) to continuously stir the air inside the chamber. Stirring of the air helped to maintain plant temperature near ambient air temperature within the VPD chamber. A humidity/temperature data logger (Lascar Electronics) was mounted through the sidewall of each container to monitor the environmental January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 5 Limited Transpiration in Soybean RILs Sarkar et al. Direct Measurement of Transpiration Under High Vapor Pressure Deficit TABLE 2 | Various transpiration rate parameters and its derivatives used for evaluation of soybean genotypes, “experiment 1.” Transpiration rate parameter Full form Formula TRH2O Transpiration rate in water (TR H2O initial)−(TR H2O final) Time interval TRAgNO3 Transpiration rate following the aquaporin inhibitor (AgNO3) exposure (TRAgNO3 initial)−(TRAgNO3 final) Time interval DTR Decrease in transpiration rate TRH2O−TRAgNO3 TRH2O × 100 RTR Ratio of transpiration rate TRH2O TRAgNO3 NDTR Normalized decrease in transpiration rate TRH2O−TRAgNO3 TRH2O+ TRAgNO3 RDTRJ Relative decrease in transpiration rate by “Jackson” DTR DTR of Jackson RDTRK Relative decrease in transpiration rate by “KS4895” DTR DTR of“KS4895′′ RRTRJ Relative ratio of transpiration rate by “Jackson” RTR RTR of“Jackson′′ RRTRK Relative ratio of transpiration rate by “KS4895” RTR RTR of“KS4895′′ RNDTRJ Relative normalized decrease in transpiration rate by “Jackson” NDTR NDTR of“Jackson′′ RNDTRK Relative normalized decrease in transpiration rate by “KS4895” NDTR NDTR of“KS4895′′ BeadChip (Song et al., 2020), an Illumina Infinium R⃝HD array. Genotypes were called using the iScan and Genome Studio software (Illumina, San Diego, CA, United States) by Dr. Qijian Song and Chuck Quigley of the USDA-ARS. Genotypic results were imported into TASSEL 5 (Bradbury et al., 2007), where nonsegregating markers were removed, missing genotypes were imputed using LinkImpute (Money et al., 2015), functionality incorporated into TASSEL 5 (settings = 30 High LD sites, 10 nearest, 10,000,000 maximum distance), and imputed genotypes converted to ABH format (AA = “Jackson” allele homozygote, AB = heterozygote, BB = “KS4895” allele homozygote) using the ABH Genotype add-in. Data were then error-corrected using the R package ABHGenotypeR (Reuscher and Furuta, 2016) with settings maxHapLength = 5 used throughout. This resulted in 2,184 total genetic markers in the final genetic map. Genotypic data were then merged with phenotypic information and imported in the QTL package in R (Broman and Sen, 2009). Distance between genetic markers was estimated using the est.map function with settings typical of an F3 population (error.prob = 0.01, overall genotypes ratios were AA = 33.0%, AB = 33.8%, and BB = 33.3%). Markers which introduced large gaps or increased genetic map length were identified using the droponemarker1 command and manually removed if they reduced the size of the overall genetic mapping significantly. conditions of the chamber. The plants were subjected to three VPD levels: low (0–1.5 kPa), medium (1.5–2.5 kPa), and high (2.5–4 kPa), on two consecutive days for each temperature (i.e., 32 and 37◦C). Quantitative Trait Locus Analysis Genetic mapping was performed within the R/QTL program (Broman and Sen, 2009) using two different QTL detection methods: standard interval mapping (SIM) and composite interval mapping (CIM) using the computer package R/QTL (Broman and Sen, 2009). Lod thresholds were determined from 1,000 permutation testing for each trait. Allelic effects were estimated after using “sim.geno” function (16 draws and an error probability of 0.01). QTL were used to build an additive model, which was fitted, refined, and then refitted using 1https://github.com/kbroman/qtl/blob/master/R/droponemarker.R Direct Measurement of Transpiration Under High Vapor Pressure Deficit The humidity in the VPD chambers was obtained by adjusting the airflow rate through each chamber; in the case of the highest VPD treatment (2.5–4 kPa), the air was also initially flowed through a column of silica gel to dry the input air (Fletcher et al., 2007). The observations of all plants for each genotype were combined for a two-segment linear regression analysis (Prism 8.0, GraphPad, Software Inc., San Diego, CA, United States) of TR versus varying VPD at both levels 32 and 37◦C temperatures. If VPD < BP, TR = Slope 1 (VPD) + Intercept 1. The slopes of the two linear regressions (Slopes 1 and 2) were statistically compared to determine whether they differed significantly (p < 0.05). If the slopes differed, the double-linear regression was retained. When the slopes were not significantly different, a simple linear regression was applied to all the data (Devi et al., 2010; Shekoofa et al., 2020). Summary information on the genetic map is located Supplementary File 2 and the complete R/QTL file containing both genotypic and least square means (LSM) phenotypic data is located in Supplementary File 3. Statistical Analysis The outputs of a successful regression fit to the two-segment model were the coefficients defining two intersecting linear regressions and the VPD value at the breakpoint (BP) between the two linear segments: RESULTS FIGURE 1 | Box and whisker plots showing the differences in transpiration rates of 122 soybean genotypes (A) in water, and (B) following the exposure to an aquaporin inhibitor (AgNO3). the functions “makeqtl,” “refineqtl,” and “fitqtl.” Results were extremely concordant between SIM and CIM; for brevity and clarity only CIM results are presented in this study. 5%) and NDTR (0–0.02) whereas genotypes #52, #64, #17, #157, #91, #23, #34, #136, #73, #45, and #57 had low DTR (5–10%) and NDTR (0.03–0.05) (Supplementary Figure 1). However, the LT had better correlation with RDTRK (r = 0.52, p < 0.0001) and RNDTRK (r = 0.49, p < 0.0001) as compared with DTR (r = 0.39, p < 0.0001) and NDTR (r = 0.38, p < 0.0001) (Table 4 and Figure 2). Furthermore, the analysis of data by a polynomial regression showed that the variation in RDTRK and RNDTRK could be explained by LT (R2 = 0.54 and 0.56) (Figure 3). Therefore, RDTRK and RNDTRK were used to select a diversity of genotypes for further screening. Candidate Gene Analysis of Quantitative Trait Locus Regions Genes present in QTL regions were examined to identify potential candidate genes for the TRlim traits using the G. max genome assembly version Glyma.Wm82.a2.1 (Schmutz et al., 2010). Annotations were downloaded.2 We examined three detected QTL windows (Supplementary Table 1) to investigate Gene Ontologies (GOs) terms for biological process, cellular component, and molecular function. Genes were termed as candidates if they had biological process 2www.soybase.org, accessed November 11, 2021. Genetic Map Construction DNA was isolated from lyophilized leaf tissue for 118 out of 120 RIL lines, as well as the parental lines “KS4895” and “Jackson” using a Promega AS1600 kit (Promega, Madison, WI, United States) using a Maxwell RSC instrument (Promega). Two genotypes did not germinate and the leaf tissue could not be collected. Genotypes for genetic map creation and QTL detection were obtained using the SoySNP6k iSelect January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 6 Limited Transpiration in Soybean RILs Sarkar et al. TABLE 3 | Summary of the phenotypic values distribution for greenhouse “experiment 1.” Category Least Sq mean LT Least Sq mean TRAgNO3 Least Sq mean TRH2O Mean 32.51 0.88 1.32 SD 1.25 0.38 0.60 SEM 0.11 0.03 0.05 Upper 95% mean 32.73 0.95 1.43 Lower 95% mean 32.28 0.81 1.21 N 122 122 122 Variance 1.56 0.14 0.36 Skewness 0.27 0.66 0.52 Kurtosis 0.57 −0.30 −0.14 CV 3.84 42.92 45.34 Jackson (RIL parent) 33.33 ± 0.86 0.94 ± 0.06 1.4 ± 0.1 KS4895 (RIL parent) 32.04 ± 0.86 0.8 ± 0.06 1.23 ± 0.1 TABLE 3 | Summary of the phenotypic values distribution for greenhouse “experiment 1.” FIGURE 1 | Box and whisker plots showing the differences in transpiration rates of 122 soybean genotypes (A) in water, and (B) following the exposure to an aquaporin inhibitor (AgNO3). GO terms associated with: abscisic acid, water transport, root development, leaf senescence, jasmonic acid, heat acclimation, stomata, and/or salicylic acid (Schulze, 1986; Jackson et al., 2000; Schmutz et al., 2010; Khan et al., 2012; Jarzyniak and Jasinski, 2014; Sah et al., 2016). RESULTS Phenotyping and Phenotypic Traits Indirect Measurement of Transpiration Under High Vapor Pressure Deficit: High Throughput Screening Using Aquaporins Inhibitor, AgNO3 Three primary traits (TRH2O, TRAgNO3, and LT) and nine secondary traits (DTR, RTR, NDTR, RDTRJ, RDTRK, RRTRJ, RRTRK, RNDTRJ, and RNDTRK) were phenotyped in the experiment for all tested genotypes (Table 2). Phenotypic values for the three primary traits followed a normal distribution for LT and an approximately normal distribution for TRH2O and TRAgNO3 (Table 3). Mean, upper 95% mean, and lower 95% mean of TRH2O were higher than TRAgNO3 (1.32, 0.1.43, 1.21 for TRH2O compared with 0.88, 0.95, 0.81 for TRAgNO3) (Table 3 and Figure 1). Across RILs genotypes, #162, #89, #97, #74, #16, #31, #161, #30, #168, #71, #26, and #137 had very low DTR (0– 5%) d NDTR (0 0 02) h #52 #64 #17 #157 Phenotyping and Phenotypic Traits Indirect Measurement of Transpiration Under High Vapor Pressure Deficit: High Throughput Screening Using Aquaporins Inhibitor, AgNO3 Three primary traits (TRH2O, TRAgNO3, and LT) and nine secondary traits (DTR, RTR, NDTR, RDTRJ, RDTRK, RRTRJ, RRTRK, RNDTRJ, and RNDTRK) were phenotyped in the experiment for all tested genotypes (Table 2). Phenotypic values for the three primary traits followed a normal distribution for LT and an approximately normal distribution for TRH2O and TRAgNO3 (Table 3). Mean, upper 95% mean, and lower 95% mean of TRH2O were higher than TRAgNO3 (1.32, 0.1.43, 1.21 for TRH2O compared with 0.88, 0.95, 0.81 for TRAgNO3) (Table 3 and Figure 1). Across RILs genotypes, #162, #89, #97, #74, #16, #31, #161, #30, #168, #71, #26, and #137 had very low DTR (0– 5%) and NDTR (0–0.02) whereas genotypes #52, #64, #17, #157, #91, #23, #34, #136, #73, #45, and #57 had low DTR (5–10%) and NDTR (0.03–0.05) (Supplementary Figure 1). However, the LT had better correlation with RDTRK (r = 0.52, p < 0.0001) and RNDTRK (r = 0.49, p < 0.0001) as compared with DTR (r = 0.39, p < 0.0001) and NDTR (r = 0.38, p < 0.0001) (Table 4 and Figure 2). Furthermore, the analysis of data by a polynomial regression showed that the variation in RDTRK and RNDTRK could be explained by LT (R2 = 0.54 and 0.56) (Figure 3). Therefore, RDTRK and RNDTRK were used to select a diversity of genotypes for further screening. Direct Measurement of Transpiration Under High Vapor Pressure Deficit Based on RDTRK and RNDTRK values, 26 soybean genotypes were divided into three levels. Values from 0.00 to 0.50 were January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 7 Sarkar et al. Limited Transpiration in Soybean RILs FIGURE 2 | Principle component biplot of various phenotypic traits of all 122 soybean genotypes evaluated in this work. Traits farther from the center have higher variance, and higher the angle between traits lower the correlation. FIGURE 2 | Principle component biplot of various phenotypic traits of all 122 soybean genotypes evaluated in this work. Traits farther from the center have higher variance, and higher the angle between traits lower the correlation. FIGURE 2 | Principle component biplot of various phenotypic traits of all 122 soybean genotypes evaluated in this work. Traits farther from the center have higher variance, and higher the angle between traits lower the correlation. FIGURE 2 | Principle component biplot of various phenotypic traits of all 122 soybean genotypes evaluated in this work. Traits farther from the center have higher variance and higher the angle between traits lower the correlation TABLE 4 | Pearson’s correlation matrix of all direct and traits measured in this study. Leaf temp (◦C) TR H2O TR AgNO3 DTR RTR NDTR RDTRJ RDTRK RRTRJ RRTRK RNDTRJ RNDTRK Leaf temp (◦C) 1.00 *** *** *** *** *** *** *** ** *** ** *** TR H2O 0.47 1.00 *** *** *** *** *** *** *** *** *** *** TR AgNO3 0.32 0.79 1.00 ns *** ** *** *** ** *** *** *** DTR 0.39 0.50 −0.06 1.00 *** ** *** *** *** *** *** *** RTR 0.34 0.44 −0.16 0.91 1.00 ** *** *** *** *** *** *** NDTR 0.38 0.49 −0.10 0.98 0.96 1.00 *** *** *** *** *** *** RDTRJ 0.14 0.57 0.20 0.79 0.59 0.71 1.00 *** *** *** *** *** RDTRK 0.52 0.53 0.38 0.32 0.18 0.28 0.36 1.00 *** *** *** *** RRTRJ 0.10 0.58 0.10 0.76 0.79 0.79 0.81 0.28 1.00 *** *** *** RRTRK 0.24 0.52 0.41 0.23 0.13 0.19 0.47 0.85 0.43 1.00 *** *** RNDTRJ 0.10 0.59 0.19 0.76 0.62 0.72 0.98 0.35 0.88 0.50 1.00 *** RNDTRK 0.49 0.52 0.37 0.30 0.18 0.26 0.33 1.00 0.28 0.85 0.33 1.00 Bottom left is the coefficient of correlation, top right half is significance level. Frontiers in Plant Science | www.frontiersin.org Direct Measurement of Transpiration Under High Vapor Pressure Deficit Significance levels: ***P < 0.0001; **P < 0.01; ns, non-significant at P > 0.05. TABLE 4 | Pearson’s correlation matrix of all direct and traits measured in this study. considered as “slow wilting,” 0.51 to 1.00 as “moderate wilting,” and above 1.00 “fast wilting.” Genotypes exhibited a decrease in TR slope over increasing VPD, indicating the expression of the TRlim trait, and those with constant linear slope exhibited no decrease in TR under high VPD, indicating the lack of the TRlim trait. For example, between two parents “KS4895” expressed the TRlim trait and “Jackson” did not (Figure 4). For those genotypes that expressed the TRlim trait, the point on x-axis where the slope January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org Frontiers in Plant Science | www.frontiersin.org 8 Limited Transpiration in Soybean RILs Sarkar et al. FIGURE 3 | Regression curves of relative difference in transpiration rate response by “KS4895” (RDTRK) and relative normalized difference in transpiration rate by “KS4895” (RNDTRK) over the leaf temperature for 122 soybean genotypes. FIGURE 3 | Regression curves of relative difference in transpiration rate response by “KS4895” (RDTRK) and relative normalized difference in transpiration rate by “KS4895” (RNDTRK) over the leaf temperature for 122 soybean genotypes. FIGURE 4 | Transpiration rate response of two soybean genotypes (“Jackson” and “KS4895”) over different levels of vapor pressure deficit at 32◦C. FIGURE 4 | Transpiration rate response of two soybean genotypes (“Jackson” and “KS4895”) over different levels of vapor pressure deficit at 32◦C. Quantitative trait locus analysis was performed for four drought-related traits using LSM calculated from phenotypic measurements taken during our greenhouse experiments (Table 6). Three QTLs were identified in total (Tables 6, 7), two QTLs for the TR traits (qTR_Gm10_1 and qTR_Gm12_1), and one associated with LT (qLT_Gm12_1) (Figure 5). q g Furthermore, the effect of each QTL was estimated (Table 6). Alleles from “KS4895” for the qTR_Gm10_1 QTL were associated with reduced transpiration relative to “Jackson” (−0.63 mg H2O m2−1 s−1). In contrast, alleles from “Jackson” for the qTR_Gm12_1 QTL were associated with reduced transpiration relative to “KS4895” (−0.27 mg H2O m2−1s−1). The lowest TR (and presumably most water saving) lines had a combination of QTL from two different parents: qTR_Gm10_1 for “KS4895” allele and qTR_Gm12_1 for the “Jackson” allele (Table 7). Identification of Candidate Genes From Quantitative Trait Locus Regions changed was considered as the VPD breakpoint. Within slow wilting genotypes, 6 out of 7 were found to express the TRlim trait (i.e., VPD breakpoint) at high VPD under 32◦C (Table 5). Among genotypes in moderate wilting category, 5 out of 10, and in high wilting only 1 out of 9 expressed the TRlim trait at 32◦C. Whereas, at 37◦C, the expression of TRlim trait was found to be limited only to 3 out of 7 in slow wilting, 1 out of 10 in moderate wilting, and none among fast wilting genotypes. g For genes within three detected QTL windows in this work (Table 6) using the “Williams 82” genome assembly 2 (Glyma.W82.a2.1), we examined gene ontologies (biological process, cellular component, and molecular function). Genes were termed as candidate genes (Table 7 and Supplementary Table 1) for the TRlim traits if they had biological process GO terms associated with any of the following terms: abscisic acid, water transport, root development, leaf senescence, jasmonic acid, heat acclimation, stomata, and/or salicylic acid. It should be noted that very few genes in soybean have direct experimental or empirical evidence for gene function, and in large part gene annotations are inferred from homologs identified by BLAST searches using genomic assemblies from other species (typically Arabidopsis). Direct Measurement of Transpiration Under High Vapor Pressure Deficit Lines which inherited alleles from “KS4895” for qLT_Gm12_1, which was distinct from the TR QTL, had lower leaf temperatures (0.84◦C lower on average). FIGURE 4 | Transpiration rate response of two soybean genotypes (“Jackson” and “KS4895”) over different levels of vapor pressure deficit at 32◦C. Genotyping and Quantitative Trait Locus Discovery A genetic map was created from genotypic data obtained using the SoySNP6K Illumina array (Akond et al., 2013). The final genetic map was composed of 2,181 genetic markers (average 109/chromosome) encompassing a total of 2,856.4 cm (each chromosome was 142.8 cm on average) (Supplementary File 2). January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 9 Limited Transpiration in Soybean RILs Sarkar et al. TABLE 5 | Vapor pressure deficit (VPD) breakpoints of 26 soybean genotypes at 32 and 37◦C. Genotypes RDTRK RNDTRK VPD breakpoint at 32◦C 37◦C Slow wilting Low-rate RDTRK and RNDTRK #16 0.14 0.13 1.7 2.10 #91 0.24 0.22 2.7 Linear #23 0.29 0.27 1.4 3.34 #73 0.30 0.27 2.9 1.96 #22 0.35 0.26 1.3 Linear #79 0.43 0.40 2.8 Linear #151 0.49 0.38 Linear Linear Moderate wilting Mid-rate RDTRK and RNDTRK #87 0.71 0.67 3.0 2.39 #102 0.72 0.68 Linear Linear #24 0.75 0.66 2.2 Linear #168 0.78 0.78 Linear Linear #55 0.79 0.76 Linear Linear #93 0.79 0.71 2.1 Linear #14 0.86 0.84 Linear Linear #56 0.92 0.91 Linear Linear #147 0.93 0.90 2.9 Linear “KS4895” 1.00 1.00 2.0 Linear Fast wilting High-rate RDTRK and RNDTRK #35 1.07 1.08 2.8 Linear #152 1.08 1.12 Linear Linear #51 1.42 1.52 Linear Linear #108 1.51 1.64 Linear Linear #3 1.81 2.02 Linear Linear “Jackson” 3.05 3.61 Linear Linear #134 3.28 3.49 Linear Linear #142 6.24 7.25 Linear Linear #139 9.77 12.73 Linear Linear These genotypes have been selected based on “experiment 1” results. The wilting categories (slow, moderate, and fast) were determined based on the RDTRK and RNDTRK values. Values from 0.0 to 0.50 were considered slow wilting, 0.51 to 1.0 were considered moderate wilting, and above 1.0 were considered as fast wilting. Both parents were included with the RILs. TABLE 5 | Vapor pressure deficit (VPD) breakpoints of 26 soybean genotypes at 32 and 37◦C. Fast wilting These genotypes have been selected based on “experiment 1” results. The wilting categories (slow, moderate, and fast) were determined based on the RDTRK and RNDTRK values. Values from 0.0 to 0.50 were considered slow wilting, 0.51 to 1.0 were considered moderate wilting, and above 1.0 were considered as fast wilting. Both parents were included with the RILs. Within the qTR_Gm12_1 QTL region (Gm12:35946078- 36388059; Table 7 and Supplementary Table 1), we identified eight candidate genes based on GO annotation (Supplementary Table 1). Genotyping and Quantitative Trait Locus Discovery Unfortunately, none of the candidate genes has any direct evidence for gene function, with all annotations inferred based on BLAST identification of presumably homologous genes from other species. Four of the candidate genes in this region are putative transcription factors (Glyma.12G199100, Glyma.12G199200, Glyma.12G199600, and Glyma.12G203100) whose annotations are associated with abiotic stress responses. Another interesting candidate gene is a homolog of a stomatal patterning gene (Glyma.12G202700). The qTR_Gm12_1 QTL displayed significant allelic differences for TR using H2O (Table 6), but no significant differences between parental alleles in the presence of the aquaporin inhibitor (TRAgNO3). Although, no obvious aquaporin gene is present within the region identified in the “Williams 82” reference genome, it remains possible that a nonobvious Within the qTR_Gm10_1 region (Gm10:116991– 1903082; Table 7), we identified eight candidate genes (Table 7 and Supplementary Table 1). These included three ubiquitin signaling associated genes (Glyma.10G018800, Glyma.10G019000, Glyma.10G019500, and Glyma.10G021500), a glycoside hydrolase/polygalacturonase gene (Glyma.10G016100), an abiotic stress-associated transcription factor (Glyma.10G016500) and two genes of unknown function annotated as involved in root hair cell differentiation (Glyma.10G016600 and Glyma.10G016700). One very intriguing candidate gene is Glyma.10G016600 (UniRef100_E0A235), which is annotated as a “drought resistance protein” and was initially identified via transcriptomic studies in response to drought stress, and the researchers confirmed this gene’s role in abiotic stress tolerance via transgenic overexpression, which conferred increased tolerance for several abiotic stresses (Song et al., 2013). January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 10 Sarkar et al. Genotyping and Quantitative Trait Locus Discovery Limited Transpiration in Soybean RILs Trait QTL name Coincident QTL QTL peak QTL interval df Type III SS LOD %var P-value (Chi2) P-value (F) Allelic effect1 TR-H2O qTR_Gm10_1 qSV_Gm102 Gm10@6.6 cM 2–14 cM 2 10.20 9.26 27.59 0 1.36E-09 −0.63 mg H2O m2−1 s−1 qTR_Gm12_1 qSV_Gm122 Gm12@138.0 cM 136–142 cM 2 5.29 5.21 14.29 0 1.03E-05 0.27 mg H2O m2−1 s−1 TR-AgNO3 q TR_10_1 qSV_Gm102 Gm10@6.6 cM 4–19 cM 2 2.57 7.57 25.58 2.69E-08 4.20E-08 −0.35 mg H2O m2−1 s−1 TR H2O – AgNO3 qTR_Gm10_1 qSV_Gm102 Gm10@6.6 cM 0–18 cM 2 2.48 4.45 13.75 0 5.43E-05 −0.28 mg H2O m2−1 s−1 qTR_Gm12_1 qSV_Gm122 Gm12@138.0 cM 136–142 cM 2 3.37 5.87 18.64 0 2.40E-06 0.25 mg H2O m2−1 s−1 LT (◦C) qLT_Gm12_1 - Gm12@91.0 cM 81–98 cM 2 30.09 4.80 17.10 1.57E-05 2.08E-05 −0.84◦C 1E ti t d ll li ff t f h J k KS4895 ce | www.frontiersin.org aquaporin-encoding gene (but not identified as such either due to problems with the assembly or diverged between “Williams 82” and the parental lines) is present within the qTR_Gm12_1 QTL region, which was affected by the silver inhibitor and forms the underlying genetic basis for qTR_Gm12_1 QTL. Within the qLT_Gm12_1 QTL region associated with differential LT (Gm12:6971475.11867391, Table 7 and Supplementary Table 1), we identified a total of 312 genes, of which 29 were termed candidate genes based on GO term and KOG annotations. Only one gene was noted to have any functional characterization; Glyma.12G104800 was identified through RNA-Seq/RT-PCR analysis as associated with response to salt stress (Sun et al., 2019). Other potential candidate genes for the QTL include an aquaporin (Glyma.12G097800); eight genes are involved in abscisic acid biosynthesis/signaling (Glyma.12G087200, Glyma.12G089200, Glyma.12G094800, Glyma.12G096100, Glyma.12G098900, Glyma.12G103100, Glyma.12G106400, and Glyma.12G108900), and a there were large number of transcription factors with annotations, which suggest involvement in abiotic stress responses (Glyma.12G087000, Glyma.12G094500, Glyma.12G094800, Glyma.12G096100, Glyma.12G098800, Glyma.12G100100, Glyma.12G100600, Glyma.12G103100, Glyma.12G104500, Glyma.12G104600, Glyma.12G104800, Glyma.12G105400, Glyma.12G105600, Glyma.12G106400, and Glyma.12G110400). Frontiers in Plant Science | www.frontiersin.org Phenotyping and Phenotypic Traits Treating the soybean plants with AgNO3, aquaporin inhibitor reduced the TR responses (Table 3 and Figure 1). Silver inhibition has been linked to the sulfhydryl group of cysteine residue of AQPs resulting in blockage of the pore for water passage (Niemietz and Tyerman, 2002). A couple of studies using aquaporin inhibitor, silver nitrate on derooted, and intact soybean plants indicated that most soybean genotypes were quite sensitive to the treatment with silver nitrate (Sadok and Sinclair, 2010; Devi et al., 2015). However, they reported a varying range of DTRs across genotypes. In the current research, the DTR amount varied across genotypes, ranging from 0.46 to 74.6% (Supplementary Figure 1). Twelve RILs had very low DTR (#162, #89, #97, #74, #16, #31, #161, #30, #168, #71, #26, and #137) ranging from 0–5%, whereas the other eleven genotypes had DTR ranging from 5–10% (#52, #64, #17, #157, #91, #23, #34, #136, #73, #45, and #57) (Supplementary Figure 1). These genotypes were almost insensitive to AgNO3 exposure and can be categorized as slow wilting (Sadok and Sinclair, 2010). The results also indicated that AgNO3 could be an effective way for high-throughput screening of drought tolerant soybean genotypes. Previous studies have suggested that silver nitrate (AgNO3) may be an effective initial screen for the expression of the TRlim trait in a multitier screening system (Sadok and Sinclair, 2010; Choudhary and Sinclair, 2014; Shekoofa and Sinclair, 2018). In this work, the second tier (first being January 2022 | Volume 12 | Article 779834 11 Limited Transpiration in Soybean RILs Sarkar et al. TABLE 7 | Candidate gene summary for three QTL regions. Trait QTL QTL interval Physical QTL interval (Gmax.W82.a2.1) Total # genes in region Candidate genes in region1 TR H2O; TRAgNO3; (TR H2O – TRAgNO3) qTR_Gm10_1 4–19 cM Gm10:116991–1903082 81 8 TR H2O; (TR H2O – TRAgNO3) qTR_Gm12_1 136–142 cM Gm12:35946078–36388059 55 8 LT (◦C) qLT_Gm12_1 81–98 cM Gm12:6971475–11867391 312 29 1Candidate genes were determined based on presence of GO terms associated with abscisic acid, water transport, root development, leaf senescence, jasmonic acid, stomata, and/or salicylic acid. FIGURE 5 | Composite interval mapping results. (A) Transpiration rate response (mg H2O m−2 s−1) QTL mapping results. Black indicates TRH2O, blue indicates TRAgNO3, and red indicates TRH2O – TRAgNO3. (B) Leaf temperature (LT) QTL mapping results, black indicates TRH2O results, and blue indicates LT results. Vertical axis is logarithm of odds (LOD) score. Phenotyping and Phenotypic Traits Horizontal axis is markers along chromosomes 10 and 12, ascending in genetic position from left to right. TABLE 7 | Candidate gene summary for three QTL regions. Trait QTL QTL interval Physical QTL interval (Gmax.W82.a2.1) Total # genes in region Candidate genes in region1 TR H2O; TRAgNO3; (TR H2O – TRAgNO3) qTR_Gm10_1 4–19 cM Gm10:116991–1903082 81 8 TR H2O; (TR H2O – TRAgNO3) qTR_Gm12_1 136–142 cM Gm12:35946078–36388059 55 8 LT (◦C) qLT_Gm12_1 81–98 cM Gm12:6971475–11867391 312 29 1Candidate genes were determined based on presence of GO terms associated with abscisic acid, water transport, root development, leaf senescence, jasmonic acid, stomata, and/or salicylic acid. FIGURE 5 | Composite interval mapping results. (A) Transpiration rate response (mg H2O m−2 s−1) QTL mapping results. Black indicates TRH2O, blue indicates TRAgNO3, and red indicates TRH2O – TRAgNO3. (B) Leaf temperature (LT) QTL mapping results, black indicates TRH2O results, and blue indicates LT results. Vertical axis is logarithm of odds (LOD) score. Horizontal axis is markers along chromosomes 10 and 12, ascending in genetic position from left to right. Of all primary and secondary traits, those subjected to PCA, RDTRK, and RNDTRK had the best correlation with LT (Figure 2). The regression curve of RDTRK and RNDTRK with the LT shows that the slope is negligible for temperature rates below 32◦C, but it drastically changes with increasing the temperature above 32◦C (Figure 3). At optimum LT (24– 32◦C), the TR response was almost constant. These findings were confirmed through the direct measurement of TR responses under high VPD conditions at 32 and 37◦C (i.e., the second-tier screening). Almost 88% of slow wilting genotypes (i.e., the least sensitive genotypes to AgNO3 exposure), 50% of moderate wilting genotypes, and 11% of high wilting genotypes (i.e., highly sensitive genotypes to AgNO3 exposure) expressed the TRlim trait at 32◦C. This was consistent with our hypothesis and previous studies done on other legume crops (Devi et al., 2010; Shekoofa et al., 2017). The genotypes with low sensitivity to aquaporin inhibitor, AgNO3, had the TRlim trait with VPD breakpoint (BP) at about 1.3–2.9 kPa (Table 5). The TRlim at lower VPD rates (i.e., 1.3–2.9 kPa) allows those genotypes to conserve moisture so that there would be more water available in the soil during late-season drought to sustain soybeans physiological activities and complete seed fill. Limitations of Our Study and Future Directions about 43, 10, and 0% for slow, moderate, and high wilting genotypes from Experiment I, respectively. This could be because the rest of genotypes which expressed the TRlim (i.e., VPD BP) at 32◦C started to increase TR under 37◦C to disperse excess temperature and heat. Shekoofa et al. (2016) reported that if very high temperatures are frequent, even to the point of being high enough to threaten plants with heat stress, it may be advantageous to consider corn hybrids that lose the TRlim trait at 38◦C rather than at 32◦C or other temperatures below 38◦C. However, soybean genotypes #16, #23, #73, and #87 allowed full expression of the TRlim trait under both temperatures (i.e., 32 and 37◦C) and displayed the maximum water conservation, no matter what the temperature regime was and performed better than both parents. Further evaluation of these genotypes should be done in field by simulating drought conditions. about 43, 10, and 0% for slow, moderate, and high wilting genotypes from Experiment I, respectively. This could be because the rest of genotypes which expressed the TRlim (i.e., VPD BP) at 32◦C started to increase TR under 37◦C to disperse excess temperature and heat. Shekoofa et al. (2016) reported that if very high temperatures are frequent, even to the point of being high enough to threaten plants with heat stress, it may be advantageous to consider corn hybrids that lose the TRlim trait at 38◦C rather than at 32◦C or other temperatures below 38◦C. However, soybean genotypes #16, #23, #73, and #87 allowed full expression of the TRlim trait under both temperatures (i.e., 32 and 37◦C) and displayed the maximum water conservation, no matter what the temperature regime was and performed better than both parents. Further evaluation of these genotypes should be done in field by simulating drought conditions. Although one of the RIL parental lines (“Jackson”) has resequencing data publicly available,3 the other parental line (“KS4895”) to our knowledge has not been resequenced. Moreover, no resources for fine-level genetic mapping (e.g., near-isogenic lines) have previously been developed for detected QTL regions identified for the TRlim traits. As such, fine- mapping, identification of gene polymorphisms, correlation of polymorphisms with water use efficiency, and TRlim traits, and the ultimate cloning of causative polymorphisms from within QTL regions remains to future work. Limitations of Our Study and Future Directions Nevertheless, our results strongly suggest that advanced mapping populations can reveal QTLs for drought-tolerance traits under complicated genetic control to enhance the TRlim trait (i.e., ability to tolerate late-season drought) in a RIL soybean population from crossing “KS4895” × “Jackson.” Validation of identified QTLs will be useful in molecular breeding of these favorable and informative QTL alleles for a superior cultivar with the ability to produce stable yield under water limiting conditions. It will be an interesting approach to associate these alleles with other agronomic traits, which are tightly linked to desirable drought tolerance traits to increase soybean yield and production under dryland conditions. Genotyping and Quantitative Trait Locus Discovery Quantitative trait loci analysis for the RILs population was done to associate the potential QTLs with the drought tolerance traits. Two QTLs (qTR_Gm10_1 and qTR_Gm12_1; Table 6) overlapped with two previously identified QTLs (qSV_Gm10 and qSV_Gm12) associated with drought responses from PI 416937 (Carpentieri-Pipolo et al., 2012). QTL conditioning the sensitivity of plants to silver nitrate were located in the same chromosomal regions reported by Carpentieri-Pipolo et al. (2012). Although, from investigations of pedigrees, it does not appear that the population (“Jackson” × “KS4895”) studied in the current research has any direct pedigree connection to the previously studied PI416937, but these QTL may be evidence that variation in the same underlying genes is causative. DATA AVAILABILITY STATEMENT The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material. Furthermore, it has been hypothesized that insensitivity to AgNO3 could be related to QTLs and the trait could be heritable (Devi et al., 2016). Our study also found that all primary and secondary traits had high broad sense heritability (H2 from 0.68 to 0.90) (Table 8). Therefore, these drought-tolerant traits can be used for phenotypic selection of soybean genotypes in future breeding efforts. 3https://soybase.org/projects/SoyBase.B2014.02.php, accessed November 17, 2021. AUTHOR CONTRIBUTIONS AS and SS: conceptualization and writing – original draft preparation. AS, SS, and JG: methodology and data curation. AS: investigation, resources, visualization, supervision, and funding acquisition. AS, SS, JG, and AM: writing – review and editing. All authors have read and agreed to the published version of the manuscript. The “KS4895” allele of the qTR_Gm10_1 QTL was associated with lower TR (Table 6). This was true for the H2O treatment (−0.63 mg H2O m2−1 s−1) and the AgNO3 treatment (−0.35 mg H2O m2−1 s−1) as well as the differential trait (TR H2O – AgNO3; −0.28 mg H2O m2−1 s−1). In contrast, the “KS4895” allele of the qTR_Gm12_1 QTL had higher TR under the H2O treatment (+0.27 mg H2O m2−1 s−1), and the differential trait (+0.25 mg H2O m2−1 s−1), but not with the AgNO3 treatment alone (Table 6). Phenotyping and Phenotypic Traits The plants with TRlim trait have also shown to delay wilting under rainfed conditions (Devi et al., 2010; Shekoofa et al., 2020). TABLE 8 | Broad sense heritability (H2) values of all direct and indirect traits measured in this study. Trait H2 TR H2O 0.86 TR AgNO3 0.90 DTR 0.78 NDTR 0.88 RTR 0.70 RDTRJ 0.77 RNDTRJ 0.74 RRTRJ 0.69 RDTRK 0.74 RNDTRK 0.87 RRTRK 0.68 LT (◦C) 0.90 H2 values range from 0 to 1; values closer to 1 have better heritability. alues range from 0 to 1; values closer to 1 have better heritability. AgNO3 treatment) would involve selection of fewer genotypes for intensive and direct phenotyping for the TR response under increasing VPD conditions. Therefore, it allowed for considering not only the DTR trait, but also several other secondary traits to represent the reduction in TR response. A simple but less accurate screen that allows a large number of genotypes to be examined is a first-tier screen, followed by tiers of more sophisticated screens of decreasing numbers of genotypes (Sinclair, 2011). AgNO3 treatment) would involve selection of fewer genotypes for intensive and direct phenotyping for the TR response under increasing VPD conditions. Therefore, it allowed for considering not only the DTR trait, but also several other secondary traits to represent the reduction in TR response. A simple but less accurate screen that allows a large number of genotypes to be examined is a first-tier screen, followed by tiers of more sophisticated screens of decreasing numbers of genotypes (Sinclair, 2011). Although the TR response results observed at 37◦C (i.e., Experiment II) show that observations of the TRlim trait at 32◦C do not necessarily predict expression of the trait at higher temperatures, the expression of TRlim trait reduced to January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org Frontiers in Plant Science | www.frontiersin.org 12 Limited Transpiration in Soybean RILs Sarkar et al. REFERENCES doi: 10.2135/cropsci2009.04.0220 Bennett, R. S., Chamberlin, K., Morningweg, D., Wang, N., Sarkar, S., Balota, M., et al. (2021). “Response to drought stress in a subset of the U.S. peanut mini- core evaluated in three states,” in Proceedings of the American Peanut Research and Education Society Annual Meeting, Salt Lake City, UT. Fletcher, A. L., Sinclair, T. R., and Allen, L. H. (2007). Transpiration responses to vapor pressure deficit in well watered ‘slow-wilting’ and commercial soybean. Environ. Exp. Bot. 61, 145–151. doi: 10.1016/j.envexpbot.2007. 05.004 Blum, A. (2009). Effective use of water (EUW) and not water-use efficiency (WUE) is the target of crop yield improvement under drought stress. Field Crops Res. 112, 119–123. doi: 10.1016/j.fcr.2009.03.009 Gaffney, J., Schussler, J., Löffler, C., Cai, W., Paszkiewicz, S., Messina, C., et al. (2015). Industry-scale evaluation of maize hybrids selected for increased yield in drought-stress conditions of the US corn belt. 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F1000Research doi: 10.12688/f1000research.7678.1 Devi, M. J., Sinclair, T. R., and Taliercio, E. (2016). Silver and zinc inhibitors influence transpiration rate and aquaporin transcript abundance in intact soybean plants. Environ. Exp. Bot. 122, 168–175. doi: 10.1016/j.envexpbot.2015. 10.006 Beaudette, P. C., Chlup, M., Yee, J., and Emery, R. J. (2007). Relationships of root conductivity and aquaporin gene expression in Pisum sativum: diurnal patterns and the response to HgCl2 and ABA. J. Exp. Bot. 58, 1291–1300. doi: 10.1093/jxb/erl289 Devi, M. J., Sinclair, T. R., and Vadez, V. (2010). Genotypic variation in peanut for transpiration response to vapor pressure deficit. Crop Sci. 50, 191–196. ACKNOWLEDGMENTS We would like to thank the United Soybean Board (USB) and the University of Tennessee, Plant Sciences Department for sponsoring this research. We would like to thank Qijian Song and Chuck Quigley of the USDA-ARS for running SoySNP6K arrays on their instrument, and recognize the superb technical contribution of USDA-ARS technician Jeremy Mullis who was We identified a relatively small number of candidate genes from within detected QTL regions (8, 8, and 29 for qTR_Gm10_1, qTR_Gm12_1, and qLT_Gm12_1, respectively) based on GO terms associated with abscisic acid, water transport, root development, leaf senescence, jasmonic acid, stomata, and/or salicylic acid. These candidate genes will be useful for future efforts to determine the causative genetic basis for the three QTLs we identified. January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 13 Limited Transpiration in Soybean RILs Sarkar et al. Supplementary Figure 1 | Variation of decrease in transpiration rate (DTR) and normalized decrease in transpiration rate (NDTR) among 122 soybean genotypes. responsible for DNA isolation and quality control. Also, we thank Larry Purcell and Andy King at the University of Arkansas for providing the seeds for this research. We would furthermore like to thank Kendall Sheldon and Sara Safikhan for their assistance during data collection. Supplementary Figure 1 | Variation of decrease in transpiration rate (DTR) and normalized decrease in transpiration rate (NDTR) among 122 soybean genotypes. Supplementary Figure 2 | Diagram of a two-tiered screening method to identify soybean genotypes with the TRlim trait. Supplementary Table 1 | Candidate genes from GO term analysis from within QTL regions identified in this study. Supplementary File 1 | Heritability analysis and values of all direct and indirect traits. SUPPLEMENTARY MATERIAL Supplementary File 2 | Details on genetic map and marker distribution. The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fpls.2021. 779834/full#supplementary-material Supplementary File 3 | R/QTL package file containing genotypic and phenotypic data used for genetic mapping. REFERENCES Transpiration response of ’slow-wilting’ and commercial soybean (Glycine max (L.) Merr.) genotypes to three aquaporin inhibitors. J. Exp. Bot. 61, 821–829. doi: 10.1093/jxb/erp350 Song, Q., Yan, L., Quigley, C., Fickus, E., Wei, H., Chen, L., et al. (2020). Soybean BARCSoySNP6K: an assay for soybean genetics and breeding research. Plant J. 104, 800–811. doi: 10.1111/tpj.14960 Sadok, W., and Sinclair, T. R. (2011). Crops yield increase under water-limited conditions: review of recent physiological advances for soybean genetic improvement. Adv. Agron. 113, v–vii. Song, W. W., Duan, F. M., Li, W. B., Lin, Q., Zhou, H. 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Conflict of Interest: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Conflict of Interest: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Schapaugh, W., and Dille, R. (1998). Registration of ‘KS4895’soybean. Crop Sci. 38, 892–892. doi: 10.2135/cropsci1998.0011183x003800030065x Schmutz, J., Cannon, S. B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., et al. (2010). Genome sequence of the palaeopolyploid soybean. Nature 463, 178–183. Publisher’s Note: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher. Schulze, E. D. (1986). Carbon dioxide and water vapour exchange in response to drought in the atmosphere and in the soil. Annu. Rev. Plant Physiol. 37, 247–274. Shekoofa, A., and Sinclair, T. R. (2018). Aquaporin activity to improve crop drought tolerance. Cells 7:123. doi: 10.3390/cells7090123 Shekoofa, A., and Sinclair, T. R. (2020). Abscisic acid and sulfate offer a possible explanation for differences in physiological drought response of two maize near-isolines. Plants (Basel) 9:1713. doi: 10.3390/plants9121713 Copyright © 2022 Sarkar, Shekoofa, McClure and Gillman. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Shekoofa, A., Devi, J. M., Sinclair, T. R., Holbrook, C. C., and Isleib, T. G. (2013). Divergence in drought-resistance traits among parents of recombinant peanut inbred lines. Crop Sci. 53, 2569–2576. doi: 10.2135/cropsci2013.03. 0153 January 2022 | Volume 12 | Article 779834 Frontiers in Plant Science | www.frontiersin.org 15
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ЛАТИНОАМЕРИКАНСЬКИЙ ВЕКТОР ЗОВНІШНЬОЇ ПОЛІТИКИ ІЗРАЇЛЮ: ТЕХНОЛОГІЧНИЙ ВИМІР
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ЛАТИНОАМЕРИКАНСЬКИЙ ВЕКТОР ЗОВНІШНЬОЇ ПОЛІТИКИ ІЗРАЇЛЮ: ТЕХНОЛОГІЧНИЙ ВИМІР Received 30 September 2020; revised 23 October 2020; аccepted 16 November 2020 DOI: 10.15421/352039 Анотація Аналізуються відносини між Ізраїлем та країнами Латинської Америки за останні десятиліття (2000-2019 роки), і стверджується, що зміцнившийся імідж Ізраїлю як технологічного лідера, грає ключову роль у цьому. Автори приділили особливу увагу з’ясуванню технологій зовнішньої політики Ізраїлю на латиноамериканському напрямку, визначенню особливостей їх реалізації та результатів застосування. Країни Латинської Америки стали розглядати Ізраїль як джерело технологій. Тенденція спостерігається практично повсюдно і незалежно від політичної ситуації на Близькому Сході та триваючого ізраїльсько-палестинського конфлікту. В останні роки, паралельно з політичними кризами та зміною режиму у Латинській Америці, у країнах континенту відбулися значні поліпшення у напрямку Ізраїлю. Перші дипломатичні візити прем’єр-міністра Ізраїлю Бен’яміна Нетан’яху до латиноамериканських країн сприяли підписанню низки двосторонніх угод у різних сферах. Ключові слова: зовнішня політика, Ізраїль, Латинська Америка, вектор, дипломатія, ліві, праві, технологічний підхід. МІЖНАРОДНІ ВІДНОСИНИ Влада Русланівна Нєгіна Аспірантка кафедри міжнародних відносин, Дніпровський національний університет імені Олеся Гончара, пр. Гагаріна 72, Дніпро, 49000, Україна Е-mail: vnegina17@gmail.com, Олександр Юрійович Висоцький Доктор політичних наук, професор, професор кафедри міжнародних відносин Дніпровського національного університету імені Олеся Гончара, пр. Гагаріна 72, Дніпро, 49000, Україна Email: vysalek@gmail.com, УДК 13 +122 ЛАТИНОАМЕРИКАНСЬКИЙ ВЕ ІЗРАЇЛЮ: ТЕХНОЛ Received 30 September 2020; revised 23 O Vlada Niehina Ph.D. student of of the International Relations Department, Oles Honchar Dnipro National University, 72 Gagarin Ave., Dnipro, 49010, Ukraine ORCID ID: https://orcid.org/0000-0002-2293-423X Oleksandr Vysotskyi D.Sc. (Political Science), PhD (History), Professor, Professor of the International Relations Department, Oles Honchar Dnipro National University, 72 Gagarin Ave., Dnipro, 49010, Ukraine ORCID ID: https://orcid.org/0000-0003-0712-8499 Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 Постановка проблеми. вільйон на Всесвітній виставці-2020 [Lazaroff 2019]. Усі ці події свідчать про позитивні змі­ ни сприйняття Ізраїлю щодо до палестинсько­ го питання, і це, безперечно, стосується також країн Латинської Америки. В останні роки дипломатична діяльність Ізраїлю в Латинській Америці активізувалася. У 2017 році прем’єр-міністр Ізраїлю Бен’ямін Нетан’яху відвідав Аргентину, Колумбію, Парагвай та Мексику. У 2018 році він відві­ дав Колумбію, Гондурас, Чилі, Гватемалу та Аргентину. Ближче до кінця цього року він відлетів до Бразилії (ставши першим діючим прем’єр-міністром Ізраїлю, який відвідав цю країну), щоб відвідати церемонію інавгурації президента Жаїра Болсонаро. Президент Бра­ зилії здійснив взаємний візит до Єрусалиму у 2019 році, повторивши свою підтримку ви­ знання Єрусалима столицею Ізраїлю [Landau 2019; Oster 2019]. Дипломатичні зусилля, зда­ ється, приносять свої результати. На додаток до міцних та тривалих економічних відносин між Латинською Америкою та Ізраїлем, по­ літичні зв’язки були посилені. Пропалестин­ ський запал ряду країн, зокрема деяких країн Латинської Америки, зменшився за останнє десятиліття внаслідок наполегливої зовніш­ ньої політики Ізраїлю на глобальному та регі­ ональному рівнях. На відміну від напружених відносин між США та Ізраїлем за адміністра­ ції колишнього президента Барака Обами, зв’язки з Вашингтоном досягли нової куль­ мінації з переїздом в Єрусалим посольства США за часів президентства США Дональда Трампа. Однак у деяких районах цей крок був сприйнятий як загострення ізраїльсько-па­ лестинського конфлікту, оскільки не було за­ пропоновано жодного діючого механізму для просування мирного процесу. Незважаючи на те, що існує значна кіль­ кість літератури про детермінанти ізраїльської зовнішньої політики, є дуже мало досліджень, присвячених зростаючому впливу Ізраїлю у Латинській Америці. Однією з причин цього є своєрідна позиція Ізраїлю у своєму регіоні, тобто більша частина грантів стосовно Ізраї­ лю присвячена арабо-ізраїльському конфлік­ ту, з особливим акцентом на ізраїльсько-па­ лестинський мирний процес. Відповідно, роботи із зовнішньої політики Ізраїлю в ос­ новному досліджують динаміку регіональної політики на Близькому Сході та у Північній Африці. Окрім регіональних справ, іноземні політики в Ізраїлі зробили важливі кроки у напрямку розвитку відносин з країнами Ла­ тинської Америки, Африки та Східної Азії. Тісні зв’язки Ізраїлю з Латинською Америкою простежуються з часів створення єврейської держави. Однак є кілька пояснень пожвав­ лення цього явища. Необхідно вивчити як системні, так і внутрішні фактори. Окрім по­ гляду на Ізраїль, слід звернути увагу на остан­ ні трансформації, що відбулися у Латинській Америці. Ми прагнемо зробити це з позицій технологічного підходу. Це означає, що зов­ нішня політика Ізраїлю розглядається нами як система технологій, спрямованих на реа­ лізацію національних інтересів Ізраїльської держави в латиноамериканському регіоні. Latin American Vector of Israel’s Foreign Policy: Technological Dimension Abstract This article analyzes relations between Latin American countries and Israel over the past decades (2000- 2019) and argues that Israel’s strengthened image as a technological leader. The authors paid special attention to clarifying the technologies of Israel’s foreign policy in the Latin American direction, determining the specifics of their implementation and the results of their application. Latin American countries to start viewing Israel as a new and intriguing source for technology. This trend is almost across the board and irrespective of the political situation in the Middle East and the ongoing Israeli-Palestinian conflict. In recent years, parallel to the political crises and regime changes in Latin America, there has been a significant improvement in countries on the continent towards Israel. The first diplomatic visits of Israeli Prime Minister Benjamin Netanyahu to Latin American countries contributed to the signing of a number of bilateral agreements in various fields. The potential of economic growth in emerging markets such as Latin America makes it an attractive destination for Israeli investors. The region is projected to expand in the next few years despite continued economic uncertainty. The Israeli government is currently endorsing long-term investment channels in Latin America to take advantage of these developments. © В.Р.Нєгіна, О.Ю.Висоцький, 2020. All rights reserved. 94 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 Keywords: foreign policy, Israel, Latin America, vector, diplomacy, left-wing, right-wing, technological approach Keywords: foreign policy, Israel, Latin America, vector, diplomacy, left-wing, right-wing, technological approach. Постановка проблеми. Ми розглядаємо дипломатичні обміни, політи­ ку та торгівлю, а також культуру та оборону. Важливо також дослідити сектори, через які розвиваються відносини, щоб запропонува­ ти всеосяжну основу для розуміння останніх подій у зовнішній політиці Ізраїлю. Нарешті, досліджуємо останні події у відносинах між Ізраїлем та країнами регіону. А і і і і б і Регіональний розвиток також сприяв фор­ муванню середовища в певних частинах сві­ ту, яке є більш прихильним до Ізраїлю. Країни Перської затоки утримуються від пропаганди палестинських справ занадто голосно, щоб не викликати протидії єврейській державі. Багато хто вважав візит Бен’яміна Нетан’яху до Ома­ ну у 2018 році переломним моментом, який відкрив давні, неспокійні зв’язки та нову еру у відносинах. Аналогічним чином, намагаю­ чись нормалізувати відносини з Ізраїлем, Ду­ бай погодився дозволити Ізраїлю відкрити па­ Аналіз останніх досліджень і публіка­ цій. Грунтуючись на аналізі останніх публіка­ цій по темі статті, варто відзначити, що остан­ 95 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 Об’єднаних Націй для нещодавно створеної держави. Однак підтримка Латинською Аме­ рикою створення та визнання Ізраїлю була здебільшого результатом тісних відносин цих країн із США. нім часом з’явилася певна кількість цікавих робіт з зовнішньої політики Ізраїлю у лати­ ноамериканському регіоні. Ми хотіли б ви­ ділити низку цікавих досліджень, серед яких праці Д.Ваксмана [20], М.Діманта [3], А.М. Кацовіча [8], Я.Бар-Сіман-Тов [9], С.Р.Девіда [2], А.Рана [14], Дж.А. Кахана [14], Г.Вермен­ бола [21]. Ці роботи заклали міцну основу для осмислення досліджуваної теми і дали нам значний імпульс для розуміння зовнішньої політики Ізраїлю в технологічному вимірі. Бразилія – найбільша країна Латинської Америки, особливо голосно схвалила «План розділу 1947 року на Генеральній Асамблеї ООН». Хоча Бразилія була не єдиною краї­ ною Латинської Америки, яка проголосувала за, бразильський дипломат Озвалду Аран’я зі­ грав ключову роль у процесі як тодішній гене­ ральний секретар Генеральної Асамблеї ООН. Через його перенесення сесії, прихильники плану мали додатковий час, щоб переконати інші країни проголосувати на підтримку Їзраї­ лю. Гватемала також була особливо важливою учасницею дискусій як член Спеціального ко­ мітету для Палестини (ЮНСКОП), де її пред­ ставляв тодішній посол Хорхе Гарсія Грана­ дос. Ізраїль згодом відзначив обидві країни та їх відповідних представників. Взаємні дипло­ матичні місії були створені в Ізраїлі та різних країнах Латинської Америки, починаючи з 1949 року. Протягом наступних років двосто­ ронні відносини швидко зміцнювались. Мета роботи - з’ясувати технології зов­ нішньої політики Ізраїлю на латиноамерикан­ ському напрямку, визначити особливості їх реалізації та результати застосування. Постановка проблеми. Методологічною основою дослідження став технологічний підхід, який дозволив нам структурувати знання про зовнішню політику Ізраїлю таким чином, щоб виділити її ефек­ тивні практики, які можуть бути інтерпрето­ вані як технології. Виклад основного матеріалу. Коротка історія ізраїльсько-латиноаме­ риканських відносин Коротка історія ізраїльсько-латиноаме­ риканських відносин гатьох країн регіону на прагматичну позицію, яка диверсифікує їх економічних та диплома­ тичних партнерів у всьому світі. Політичний клімат у Латинській Амери­ ці під час «холодної війни» сприяв підтримці Сполученими Штатами військових режимів, які залежали від використання сили для сво­ го виживання. Таким чином, ще одним фак­ тором, який поставив відносини Ізраїлю з країнами Латинської Америки у негативному світлі, було озброєння таких правих урядів. Військові зв’язки між Ізраїлем та Латинською Америкою можна простежити ще до 1970-х років; зброя, що імпортується з Ізраїлю, ча­ сто використовувалася для «придушення вну­ трішнього інакомислення». Як вже зазначалося вище, арабо-ізраїль­ ські війни 1967 та 1973 років породили нега­ тивне ставлення до Ізраїлю у більшості країн, що розвиваються. Протягом перших десяти­ літь незалежності, відносини Ізраїлю з Радян­ ським Союзом відзначалися підозрою і навіть ворожістю, так що до 1970-х років Єрусалим став пріоритетом налагодження міцних зв’яз­ ків із США. Ізраїль також прагнув встановити союзи з «периферійними» державами, таки­ ми, як Туреччина, Ефіопія та з Іраном (до Іс­ ламської революції 1979 року). Зовнішня по­ літика Єрусалиму щодо латиноамериканських держав також може вважатися продовженням стратегії в обхід спроб ворогів Ізраїлю ізо­ лювати його на міжнародній арені. З іншого боку, більш ліберальна перспектива підкрес­ лює демократичні повноваження Ізраїлю, що робить його винятком у регіоні. Наприклад, унікальні відносини між США та Ізраїлем часто пояснюються тим, що обидві країни віддані демократії, а також тим, що багато хто вважає своїм спільним іудейсько-христи­ янським надбанням недержавних суб’єктів у формуванні зовнішньої політики. Прикладом є те, що ізраїльська дипломатія спирається на свої комерційні підприємства у всьому сві­ ті та військово-промисловий комплекс, що об’єднує уряд та приватні підприємства, віді­ грає центральну роль у зміцненні відносин за його межами. Крім того, пояснення «другого образу», репрезентовані представником теорії неореалізму Кеннетом Уолтцом [Waltz 2001], дають корисну основу для аналізу зовнішньої політики Ізраїлю. Як підкреслюють плюраліс­ тичні теорії, процес прийняття рішень є про­ дуктом множинних взаємодій між акторами зовнішньої політики. Дійсно, безліч акторів (починаючи від профспілок та закінчуючи по­ літичними партіями), а також громадська дум­ ка, мають значний вплив на процес прийняття Динаміка зовнішньої політики Ізраїлю щодо Латинської Америки Коротка історія ізраїльсько-латиноаме­ риканських відносин Єврейські громади у Латинській Амери­ ці недостатньо великі, щоб чинити великий вплив на політичні справи своїх країн. У той же час існує триваюча життєздатність двосто­ ронньої міграції, а також зусилля ізраїль­ ського уряду та єврейських фондів в Ізраїлі та Латинській Америці задля підтримки тісних зв’язків між цими громадами та єврейською державою, створили ситуацію, у якій латино­ американська єврейська культура демонструє сильну культурну свідомість. Ця близькість ставиться під сумнів у суспільствах, в яких вони живуть, де іноді вважають, що євреї ма­ ють подвійну лояльність. Оскільки євреї на­ стільки тісно ототожнюються з Ізраїлем або так тісно ототожнюються з ним самі, а також враховуючи яскравість ізраїльсько-палестин­ ського конфлікту, латиноамериканські євреї часто стикаються з критикою, спричиненою діями Єрусалиму [Ran&Cahan 2012]. Існували два основні фактори, які ви­ значали хід відносин у ті роки. Перший – це сильний вплив Вашингтона на зовнішню по­ літику латиноамериканських країн, а другий – незначна роль, яку цей регіон відіграє у гло­ бальних справах [Kacowicz 2017: 203]. Однак особливі стосунки між США та Ізраїлем час від часу перешкоджали зусиллям Ізраїлю роз­ вивати відносини з Латинською Америкою – особливо протягом 1960-х та 70-х років, коли антиамериканські настрої були поширені, а політичні реалії з домінуванням лівих урядів Перу, Куби, Чилі та пероністської Аргентини. Зокрема, Шестиденна війна 1967 року запля­ мувала імідж Ізраїлю, зробивши його схожим на довірену особу Вашингтона та на верхів­ ку західного імперіалізму на Близькому Схо­ ді. Розриви у відносинах США та Латинської Америки призвели до відповідного розриву у відносинах цих країн з Ізраїлем. Нафто­ ва криза 1973 року та одночасне небажання Вашингтона надавати допомогу у розвитку, прискорили перехід у зовнішній політиці ба­ Багато країн Латинської Америки пози­ тивно сприйняли створення Ізраїлю у 1948 році: Ізраїль забезпечив підтримку «блоку вісімнадцяти» латиноамериканських країн, які проголосували за членство в Організації 96 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 Університету Джона Гопкінса Стівен Р.Девід, Ізраїль стикається з набором «екзистенційних загроз», починаючи від внутрішніх демогра­ фічних викликів та закінчуючи зовнішніми бойовими діями [David 2008]. Численні ара­ бо-ізраїльські війни змусили єврейську дер­ жаву зберігати пильність перед постійними загрозами з боку сусідів. гатьох країн регіону на прагматичну позицію, яка диверсифікує їх економічних та диплома­ тичних партнерів у всьому світі. Університету Джона Гопкінса Стівен Р.Девід, Ізраїль стикається з набором «екзистенційних загроз», починаючи від внутрішніх демогра­ фічних викликів та закінчуючи зовнішніми бойовими діями [David 2008]. Численні ара­ бо-ізраїльські війни змусили єврейську дер­ жаву зберігати пильність перед постійними загрозами з боку сусідів. Динаміка зовнішньої політики Ізраїлю щодо Латинської Америки У галузі досліджень зовнішньої політи­ ки Ізраїлю існують суперечливі інтерпретації факторів, що сприяють певному результату зовнішньої політики. Наприклад, американ­ ський професор Шиблі Телхамі стверджує, що зовнішня політика Ізраїлю була розробле­ на не лише з урахуванням абстрактної кон­ цепції «національного інтересу», нав’язаної структурними можливостями та обмеження­ ми міжнародних систем як такої, але також на ідеологічних платформах чинних політичних партій та внутрішньому контексті. Професор Каліфорнійського університету Дов Уоксмен розширює думку, підкреслюючи, що зовніш­ ню політику Ізраїлю неможливо повністю пояснити без урахування його національної ідентичності. Він підкреслює, що неореалізм з його явними матеріалістичними рамками про­ понує лише редукціоністську точку зору на це питання. Отже, щоб надати цілісну перспек­ тиву, ми повинні звернутися як до зовніш­ нього, так і внутрішнього виміру латиноаме­ риканської політики Ізраїлю. Незважаючи на те, що для пояснення зовнішньої політики Із­ раїлю виникло багато теорій, домінуюча пер­ спектива, що базується на реальній політиці, була і залишається повсюдною у літературі. З самого свого заснування Ізраїль, як держа­ ва, оточена ворожими арабськими країнами, стурбована своєю онтологічною безпекою. Як наголосив професор з міжнародних відносин 97 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 ною промисловістю. Було очевидним у період після холодної війни, і особливо в роки «Ро­ жевої хвилі» у Латинській Америці (маючи на увазі широкі зміни у лівому напрямку націо­ нальних урядах). Угода між Ізраїлем та тор­ говельно-економічним союзом МЕРКОСУР (Аргентина, Бразилія, Парагвай, Уругвай) про Вільну торгівлю 2007 року була підписана, незважаючи на напруженість у двосторонніх відносинах. рішень в Ізраїлі. Точно так же ці актори, осо­ бливо оборонна промисловість, приймають участь у формуванні зовнішньої політики Із­ раїлю. У зв’язку з цим продаж зброї Ізраїлем у Східній Азії, Південній Азії та Латинській Америці призвели до розвитку двосторонніх зв’язків. Відповідно, одним із найважливіших елементів ізраїльсько-латиноамериканських відносин є зростання обсягу торгівлі зброєю. ною промисловістю. Було очевидним у період після холодної війни, і особливо в роки «Ро­ жевої хвилі» у Латинській Америці (маючи на увазі широкі зміни у лівому напрямку націо­ нальних урядах). Угода між Ізраїлем та тор­ говельно-економічним союзом МЕРКОСУР (Аргентина, Бразилія, Парагвай, Уругвай) про Вільну торгівлю 2007 року була підписана, незважаючи на напруженість у двосторонніх відносинах. рішень в Ізраїлі. Точно так же ці актори, осо­ бливо оборонна промисловість, приймають участь у формуванні зовнішньої політики Із­ раїлю. У зв’язку з цим продаж зброї Ізраїлем у Східній Азії, Південній Азії та Латинській Америці призвели до розвитку двосторонніх зв’язків. Відповідно, одним із найважливіших елементів ізраїльсько-латиноамериканських відносин є зростання обсягу торгівлі зброєю. Динаміка зовнішньої політики Ізраїлю щодо Латинської Америки Немає сумнівів, що взаємодія Ізраїлю з євреями у всьому світі є важливим аспектом зовнішньої політики, і, звичайно, у Латин­ ській Америці, а також стратегічний контекст, в якому відбувається прийняття зовнішньопо­ літичних рішень з урахуванням історії та про­ блем євреїв. Як і в інших випадках, єврейська діаспора у Латинській Америці є одним із фак­ торів, що впливають на зовнішню політику Із­ раїлю у регіоні. Існування давніх єврейських громад, члени яких мігрували з різних частин старого світу у різний час, зміцнює культурні та економічні зв’язки з Ізраїлем та консолідує м’яку силу Ізраїлю. Однак, незважаючи на ви­ сокий рівень ототожнення латиноамерикан­ ських євреїв з їхньою релігійною та етнічною спадщиною (про що свідчить велика кількість єврейських громадських організацій), немож­ ливо говорити про латиноамериканську єв­ рейську громаду як про однорідну, оскільки її члени дотримуються різноманітних релігій­ них, політичних та соціальних світоглядів. Однак політичний клімат у Латинській Америці за останні кілька років, де спосте­ рігається широка підтримка правих лідерів та помітно посилений вплив євангельських християн, здається, дав Ізраїлю можливість зміцнити свої дипломатичні зв’язки у регіоні, які погіршилися з 1990-х років. У ці роки на­ пруженість з Аргентиною зросла після того, як ця країна ефективно розслідувала вибухи у посольстві Ізраїлю у Буенос-Айресі у 1992 році та у єврейському центрі «Аргентинської єврейської асоціації взаємної допомоги» у 1994 році, які забрали життя понад 100 людей і ще сотні постраждали. Протягом того ж де­ сятиліття сходження венесуельського сильно­ го представника Уго Чавеса, який налагодив тісні стосунки з Іраном, змусило Каракас розі­ рвати колись дружні стосунки з Єрусалимом. Однак ці події не стримували Ізраїль від но­ вих зусиль покращення відносин з латиноаме­ риканськими лідерами. Справді, з 2009 року Ізраїль намагається поліпшити свої відносини з країнами регіону за допомогою політики, ініційованої тодішнім міністром закордонних справ Авігдором Ліберманом. Зміни політичних умов Він порушив такі питання, як зростаюча участь терористичної організації «Хезболла» у торгівлі наркотиками у Латинській Америці та серйозні наслідки, які можуть бути резуль­ татом поглиблення зв’язків Ірану з Венесуе­ лою та Болівією. І також повторив прохання Ізраїлю до Аргентини щодо розслідування ви­ бухів у Буенос-Айресі. Напруженість, спри­ чинена цими проханнями та подальшою реак­ цією уряду президента Крістіни Фернандес де Кіршнер, не зменшилася відразу після візиту Авігдора Лібермана. Однак ізраїльсько-ар­ гентинські відносини набули нового оберту у наступні роки та після виборів 2015 року правоцентристського кандидата у президенти Маурісіо Макрі (колишній мер Буенос-Айре­ са). У січні 2020 року новообраний лівий пре­ зидент Альберто Фернандес відвідав Ізраїль з метою участі у церемонії в меморіальному комплексі Голокосту «Яд-Вашем», в якій взя­ ли участь багато світових лідерів, присвяченій вшануванню пам’яті жертв Голокосту та 75-ї річниці звільнення концентраційного табору Аушвіц-Біркенау. Та зустрівся з прем’єр-мі­ ністром Бен’яміном Нетан’яху, обговоривши можливість поліпшення двосторонніх відно­ син. тичній арені. р У галузі економіки, окрім сировини, Ізра­ їль в основному імпортує з Латинської Аме­ рики такі продукти харчування, як м’ясо, кава, цукор, зерно, кукурудза та какао, а також експортує перероблену сільськогосподарську та хімічну продукцію, електроніку, машини, та програмне забезпечення. Окрім фінансово­ го та будівельного секторів, ізраїльські фірми також беруть активну участь у фазах перед­ виробничої сільськогосподарської діяльності. Нещодавно уряд Ізраїлю поділився планами щодо розробки конкретних схем фінансуван­ ня у рамках Міжамериканського банку роз­ витку з метою надання позик та допомоги латиноамериканським компаніям. Основну увагу планується зосередити на таких сферах, як кібербезпека, водопостачання та сільське господарство, що відображають конкуренто­ спроможність ізраїльських технологій [Azran 2019]. Двосторонні інвестиційні договори між Ізраїлем та країнами Латинської Аме­ рики датуються 1990-ми роками. Такі угоди були підписані з Аргентиною, Сальвадором, Уругваєм та Гватемалою [IMF 2019]. Сьогодні Ізраїль має угоди про Вільну торгівлю з Мек­ сикою (з 2000 року) та блоком МЕРКОСУР (з 2007 року). Гватемала стала помітним торго­ вим партнером Ізраїлю у Центральній Амери­ ці. Під час візиту Бен’яміна Нетан’яху до цієї країни у 2019 році, були підписані різні угоди з метою покращення відносин. З 90-х років минулого століття іранська загроза викликала головне занепокоєння. Од­ нак події у 2000-х роках продемонстрували, що ідеологічні розбіжності серед лівих лати­ ноамериканських лідерів призвели до ряду позицій щодо зміцнення зв’язків з Ісламською Республікою. Більше того, бажання Південної Америки нарощувати економічні зв’язки з арабськими країнами зробили «палестинське питання» набагато складнішим у відносинах Ізраїлю та Латинської Америки. Зміни політичних умов Ізраїльсько-латиноамериканські відноси­ ни, які дружно розпочались у 1940-х роках, з того часу зазнали злетів та падінь – наслідків ідеологічних розбіжностей та антиамерикан­ ських чи проамериканських настроїв у регіо­ ні. Загалом, економічні та військові відносини велися в умовах, сприятливих для всіх сторін. Починаючи з 1960-х років, мовчазне порозу­ міння поділяло відносини на два канали: ди­ пломатичний та економічний. Здається, Ізра­ їль фактично прийняв підтримку Латинської Америки для палестинської справи (за винят­ ком деяких невеликих держав Центральної Америки), але не дозволив цій позиції пере­ шкоджати взаємним зусиллям щодо поліп­ шення економічних зв’язків, в основному за­ снованих на торгівлі із ізраїльською оборон­ Етап ізраїльсько-латиноамериканських відносин після 2009 року набув сильного ан­ тиіранського виміру, не лише завдяки свідчен­ ням стовно вибухів у Буенос-Айресі у 1990-х роках, ініційованих Тегераном та здійснені терористичною організацією «Хезболла», але і присутністю Ірану у регіоні. Для цього від­ бувалися характерні дипломатичні візити на високому рівні та підписували двосторонні угоди про торгівлю та співробітництво, осо­ бливо з країнами «Боліваріанського альянсу для народів Америки», Болівією, Венесуелою та Нікарагуа (Болівія покинула групу у 2019 році; Іран мав статус спостерігача в з перших 98 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 років союзу). У 2009 році під час свого візиту Авігдор Ліберман, крім зміцнення існуючих двосторонніх відносин у різних сферах, праг­ нув пом’якшити все більшу присутність Іра­ ну. Він порушив такі питання, як зростаюча участь терористичної організації «Хезболла» у торгівлі наркотиками у Латинській Америці та серйозні наслідки, які можуть бути резуль­ татом поглиблення зв’язків Ірану з Венесуе­ лою та Болівією. І також повторив прохання Ізраїлю до Аргентини щодо розслідування ви­ бухів у Буенос-Айресі. Напруженість, спри­ чинена цими проханнями та подальшою реак­ цією уряду президента Крістіни Фернандес де Кіршнер, не зменшилася відразу після візиту Авігдора Лібермана. Однак ізраїльсько-ар­ гентинські відносини набули нового оберту у наступні роки та після виборів 2015 року правоцентристського кандидата у президенти Маурісіо Макрі (колишній мер Буенос-Айре­ са). У січні 2020 року новообраний лівий пре­ зидент Альберто Фернандес відвідав Ізраїль з метою участі у церемонії в меморіальному комплексі Голокосту «Яд-Вашем», в якій взя­ ли участь багато світових лідерів, присвяченій вшануванню пам’яті жертв Голокосту та 75-ї річниці звільнення концентраційного табору Аушвіц-Біркенау. Та зустрівся з прем’єр-мі­ ністром Бен’яміном Нетан’яху, обговоривши можливість поліпшення двосторонніх відно­ син. років союзу). У 2009 році під час свого візиту Авігдор Ліберман, крім зміцнення існуючих двосторонніх відносин у різних сферах, праг­ нув пом’якшити все більшу присутність Іра­ ну. Зміни політичних умов Таким чином, у 2000-х роках під час «Рожевої хвилі», незва­ жаючи на вигідні економічні відносини Ізра­ їлю з багатьма країнами регіону, ліві лідери, такі як колишній президент Бразилії Луїс Іна­ сіо Лула да Сілва та аргентинський президент Нестор Карлос Кіршнер, демонстрували силь­ ну солідарність з палестинцями на диплома­ Обидві сторони все ще працюють над взаємовигідною угодою не лише щодо поліп­ шення торгівлі та інвестицій, але і для надан­ ня обмежених можливостей для тимчасового, вільного обігу робочої сили. Ізраїль також підписав двосторонні торгові угоди з Колум­ бією (2013 рік) та Панамою (2018 рік), які ще не діють [IMF 2018]. Проте, за останні два де­ сятиліття, за винятком Колумбії, латиноаме­ риканські країни визнали державу Палестина. Протягом останніх двох років, після «Рожевої хвилі», унікальна комбінація факторів рап­ тово створила політичний клімат, який, без­ перечно, був сприятливим для спроб Ізраїлю отримати латиноамериканську дипломатичну підтримку на міжнародній арені. По-перше, відверта підтримка з боку американського 99 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 уряду щодо ізраїльських територіальних пре­ тензій, по-друге, поява правих президентів у Латинській Америці, які прагнуть розвивати тісні зв’язки з США. Цей клімат сприяв до­ сягненню, хоча і з невеликим запізненням, ці­ лей Ізраїлю, викладених у декларації від трав­ ня 2014 року, в якій зазначено про прагнення зміцнити економічні зв’язки з Латинською Америкою протягом наступних трьох років, особливо з Тихоокеанським союзом, в якому було надано статус спостерігача у лютому 2014 року [IMFA 2014]. 2019 році був четвертим з 2007 року, три з них відбулись між 2017-2019 роками. У контексті того, що Ізраїль намагався скористатися ос­ танніми подіями у континентальній політиці, у деяких випадках досягалися цілі без прямих запитів. Наприклад, переїзд американського посольства з Тель-Авіва до Єрусалиму у 2018 році спонукав Гватемалу, Парагвай та Гонду­ рас заявити, що їх посольства також змінять адреси. Гватемала та Гондурас, крім Коста-Рі­ ки з залежною від Сполучених Штатів еконо­ мікою, також є основними імпортерами ізра­ їльської зброї та складних систем оборони. У 2017 році Ізраїль уклав угоду з Гондурасом на 300 мільйонів доларів про надання йому зброї, кораблів та послуг з кібербезпеки. Ще одним яскравим прикладом є Бразилія. У 1990–2009 роках Ізраїль був сьомим за величиною екс­ портером військової техніки до цієї країни. Під час президенства Луїса да Сілви, Ділми Русефф та Мішеля Темера, після опубліку­ вання Національної стратегії оборони у 2008 році, Бразилія розширила співпрацю з ізра­ їльською оборонною промисловістю. Зміни політичних умов Євангелісти у Північній та Пів­ денній Америці очікують визнання Єрусали­ му як столиці Ізраїлю, згідно з пророцтвами диспенсаціоналізму, тому не дивно, що вони закликають своїх політичних лідерів офіцій­ но оголосити її такою. Країни Латинської Америки та Ізраїль зацікавлені у поглибленні вже існуючої співпраці, що базується голов­ ним чином на закупівлі високотехнологічних оборонних виробів та зброї. Як підкреслюєть­ ся у ізраїльській щоденній газеті «Гаарец», ізраїльський експорт зброї у 2017 році досяг рекордного рівня - понад 9 мільярдів доларів. Згідно з аналізом «Стокгольмського міжна­ родного інституту досліджень миру» (SIPRI), про який повідомляє ізраїльське видавництво «The Times of Israel», єврейська держава була «8-м найбільшим експортером зброї у світі» між 2014 та 2018 роками. Звичайно, за цим є низка причин. Як правильно підкреслюють бразильський професор міжнародних відно­ син Рафаель Дуарте Вілла та Джуліана Віджа­ но, «на південноамериканському ринку зброї Сполучені Штати більше не домінують». Вій­ ськова промисловість Ізраїлю багато в чому перевершує свою конкуренцію завдяки своїм інноваційним можливостям, передовим тех­ нологіям та людському капіталу. Ця перевага, роках, а бразильська дочірня компанія «Ares» ізраїльського оборонного підрядника «Elbit Systems», отримала рамковий контракт вар­ тістю приблизно 100 мільйонів доларів на постачання дистанційного керування. Ізраїль – другий за величиною постачальник зброї до Колумбії (після США), включаючи зброю, таку як протитанкові та ракети «земля-земля». Ізраїль також продавав шпигунське програмне забезпечення Колумбії у 2015 році для вико­ ристання у моніторингу діяльності «Револю­ ційних збройних сил Колумбії», з яким уряд Колумбії здійснював мирну угоду. Ізраїльська оборонна промисловість також розвивала міц­ ні стосунки з Мексикою у 2000-х роках. роках, а бразильська дочірня компанія «Ares» ізраїльського оборонного підрядника «Elbit Systems», отримала рамковий контракт вар­ тістю приблизно 100 мільйонів доларів на постачання дистанційного керування. Ізраїль – другий за величиною постачальник зброї до Колумбії (після США), включаючи зброю, таку як протитанкові та ракети «земля-земля». Ізраїль також продавав шпигунське програмне забезпечення Колумбії у 2015 році для вико­ ристання у моніторингу діяльності «Револю­ ційних збройних сил Колумбії», з яким уряд Колумбії здійснював мирну угоду. Ізраїльська оборонна промисловість також розвивала міц­ ні стосунки з Мексикою у 2000-х роках. – другий за величиною постачальник зброї до Колумбії (після США), включаючи зброю, таку як протитанкові та ракети «земля-земля». Ізраїль також продавав шпигунське програмне забезпечення Колумбії у 2015 році для вико­ ристання у моніторингу діяльності «Револю­ ційних збройних сил Колумбії», з яким уряд Колумбії здійснював мирну угоду. Ізраїльська оборонна промисловість також розвивала міц­ ні стосунки з Мексикою у 2000-х роках. Зміни політичних умов Голов­ ною метою Бразилії було пожвавлення своїх оборонних систем з особливим акцентом на збільшення потенціалу досліджень та розро­ бок як державного, так і приватного секторів, що пропонують супутні товари. На дипломатичній арені Ізраїль прагне переконати країни Латинської Америки вчи­ нити певні дії, зокрема, проголосувати за про­ позиції Ізраїлю у різних міжнародних органі­ заціях, що включає: розрив зв’язків з Іраном, терористичною організацією «Хезболла» та Палестинською автономією; підтримку пере­ несення посольств з Тель-Авіва до Єрусали­ му. З іншого боку, Ізраїль не вимагає однако­ вого рівня згоди від кожної країни, швидше, воліє задовольнятися тим, що реалістично на даний момент. Досяжність конкретних цілей залежить від субрегіону країни-партнера Ла­ тинської Америки, її економічного становища та бажання підтримати Ізраїль у міжнародних організаціях. Відносини Ізраїль–Уругвай мають свої особливості. Ізраїльські дипломати в Уругваї, країні-члені МЕРКОСУР, не пришвидшують питання перенесення посольства, оскільки це наразі нездійсненно, але все ж працюють, щоб підтримувати добрі стосунки. Поточ­ ні та попередні посли намагалися просувати зв’язки між країнами-членами МЕРКОСУР та Ізраїлем, внести зміни до угоди про Віль­ ну торгівлю та прихильність до боротьби з антисемітизмом. Вони також запропонували співпрацю у галузі кібербезпеки, в якій ізра­ їльські компанії мають високу конкуренто­ спроможність, та підтримку у голосуваннях міжнародних організацій, таких як Всесвітня організація охорони здоров’я (ВООЗ), щоб не допустити міжнародного визнання Палести­ ни [Radio Uruguay 2019]. Бен’ямін Нетан’яху намагався скористатись зростанням правих урядів Латинської Америки, здійснивши кіль­ ка візитів до регіону. Останній його візит у Деякі країни мають численні контакти з із­ раїльським військовим сектором. Хоча даних про продаж військових товарів з відкритим ко­ дом небагато, «Стокгольмський міжнародний інститут досліджень миру» (SIPRI) надає таку інформацію. Згідно з даними, Бразилія та Ко­ лумбія є одними з основних споживачів висо­ котехнологічної ізраїльської зброї; авіаційних радіолокаційних систем; систем повітря-по­ вітря, повітря-земля та протитанкові ракетні системи; та БПЛА (безпілотні літальні апара­ ти), що продаються як основна зброя [SIPRI 2019]. Крім цих військових систем, Ізраїль продає програмне забезпечення для спостере­ ження багатьом країнам Латинської Америки. Поглиблюючи зв’язки цих країн із ізра­ їльською індустрією безпеки, очевидно, що Бразилія була одним з найважливіших торго­ вих партнерів Ізраїлю. Бразилія стала голов­ ним споживачем ізраїльської зброї у 2000-х 100 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 ньої та зовнішньої політики. Хоча наслідком проізраїльської політики Дональда Трампа не можна нехтувати, було б занадто спрощеним пояснювати перебіг дій лише результатом бажання наслідувати прикладу Сполучених Штатів. Зміни політичних умов Дійсно, політична мета новообраних правих урядів стерти те, що зробили попе­ редні ліві лідери, включаючи встановлення тісних зв’язків з деякими мусульманськими країнами, відіграє важливу роль. Ці зв’язки не тільки передбачали дипломатичну підтримку палестинців, але також дозволили відкрити Латинську Америку таким країнам, як Іран та Сирія. Хоча зростання євангельського хри­ стиянства у Латинській Америці не є новим явищем, безумовно, це спонукає правих по­ літиків наблизитися до США та підтримати Ізраїль. Крім того, на рішення щодо зміцнен­ ня відносин з Ізраїлем, особливо у Бразилії, Гондурасі, Гватемалі та Болівії, впливає від­ носна політична сила, яку мають євангельські члени уряду . Євангелісти у Північній та Пів­ денній Америці очікують визнання Єрусали­ му як столиці Ізраїлю, згідно з пророцтвами диспенсаціоналізму, тому не дивно, що вони закликають своїх політичних лідерів офіцій­ но оголосити її такою. Країни Латинської Америки та Ізраїль зацікавлені у поглибленні вже існуючої співпраці, що базується голов­ ним чином на закупівлі високотехнологічних оборонних виробів та зброї. Як підкреслюєть­ ся у ізраїльській щоденній газеті «Гаарец», ізраїльський експорт зброї у 2017 році досяг рекордного рівня - понад 9 мільярдів доларів. Згідно з аналізом «Стокгольмського міжна­ родного інституту досліджень миру» (SIPRI), про який повідомляє ізраїльське видавництво «The Times of Israel», єврейська держава була «8-м найбільшим експортером зброї у світі» між 2014 та 2018 роками. Звичайно, за цим є низка причин. Як правильно підкреслюють бразильський професор міжнародних відно­ син Рафаель Дуарте Вілла та Джуліана Віджа­ но, «на південноамериканському ринку зброї Сполучені Штати більше не домінують». Вій­ ськова промисловість Ізраїлю багато в чому 101 ньої та зовнішньої політики. Хоча наслідком проізраїльської політики Дональда Трампа не можна нехтувати, було б занадто спрощеним пояснювати перебіг дій лише результатом бажання наслідувати прикладу Сполучених Штатів. Дійсно, політична мета новообраних правих урядів стерти те, що зробили попе­ редні ліві лідери, включаючи встановлення тісних зв’язків з деякими мусульманськими країнами, відіграє важливу роль. Ці зв’язки не тільки передбачали дипломатичну підтримку палестинців, але також дозволили відкрити Латинську Америку таким країнам, як Іран та Сирія. Хоча зростання євангельського хри­ стиянства у Латинській Америці не є новим явищем, безумовно, це спонукає правих по­ літиків наблизитися до США та підтримати Ізраїль. Крім того, на рішення щодо зміцнен­ ня відносин з Ізраїлем, особливо у Бразилії, Гондурасі, Гватемалі та Болівії, впливає від­ носна політична сила, яку мають євангельські члени уряду . Зміни політичних умов Разом з цим, триваючий судовий процес над Бен’яміном Нетан’яху може ще більше по­ гіршити ситуацію та пригальмувати прогрес, досягнутий за його перебування на посаді. Ці внутрішні лінії розломів можуть попогірши­ ти відносини. Довговічність чинних правих урядів у Латинській Америці є ще одним фак­ тором, що визначає майбутнє відносин з Ізра­ їлем. Поглиблені політичні зміни в столицях Латинської Америки можуть призвести до негативної реакції, яка вимагатиме перезаван­ таження дипломатичних відносин. Незважа­ ючи на все це, нинішні ізраїльсько-латиноа­ мериканські зв’язки заслуговують на увагу як приклад успішної багатогранної дипломатії у світовій політиці. «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 ків, посилена участь Єрусалиму в регіоні – тема, яка не отримала належного наукового висвітлення. Поява правих партій у Латин­ ській Америці переорієнтувала дипломатію на єврейську державу. Однак нещодавнє поліп­ шення ізраїльської зовнішньої політики щодо латиноамериканських держав не може бути пояснене виключно політичною трансформа­ цією континентальної політики. Для сприяння ізраїльській дипломатичній діяльності у Ла­ тинській Америці збіглися численні фактори. Сюди входять регіональна ізоляція єврейської держави, підписання торгових договорів, ін­ тереси зростаючої оборонної промисловості Ізраїлю та культурні зв’язки з діаспорою. Із­ раїльсько-латиноамериканські відносини до­ сягли нової фази, яка характеризується спри­ ятливим політичним, економічним та соціаль­ ним середовищем як в Ізраїлі, так і у країнах Латинської Америки. Крім того, не можна не помітити вплив унікальних характеристик американсько-ізраїльських відносин за ча­ сів Дональда Трампа. На додаток до згаданої вище динаміки, немає сумнівів, що зовнішня політика Ізраїлю щодо латиноамериканських держав втратила оберти після політичного «глухого кута» внаслідок проведення трьох раундів послідовних національних виборів у 2019–2020 роках. Нестабільність політичної системи Ізраїлю негативно вплинула на про­ цес прийняття зовнішньополітичних рішень. Разом з цим, триваючий судовий процес над Бен’яміном Нетан’яху може ще більше по­ гіршити ситуацію та пригальмувати прогрес, досягнутий за його перебування на посаді. Ці внутрішні лінії розломів можуть попогірши­ ти відносини. Довговічність чинних правих урядів у Латинській Америці є ще одним фак­ тором, що визначає майбутнє відносин з Ізра­ їлем. Поглиблені політичні зміни в столицях Латинської Америки можуть призвести до негативної реакції, яка вимагатиме перезаван­ таження дипломатичних відносин Незважа безумовно, робить його більш конкуренто­ спроможним на світових ринках, включаю­ чи ринки Латинської Америки. Більше того, певний час в Ізраїлі постійно підтримується державна підтримка військових підрядників. Більше того, що стосується попиту, слід вра­ ховувати геополітичну чутливість латиноаме­ риканських держав. Зміни політичних умов Незважаючи на те, що у наш час на континенті не було повномасштаб­ ної війни, це не означає, що у регіоні не було міждержавних мілітаризованих прикордон­ них конфліктів . З першого десятиліття тися­ чоліття з’явилася значна кількість літератури, яка підкреслює триваючу гонку озброєнь у Південній Америці, яка залежить від багатьох факторів, включаючи, але не обмежуючись цим, стратегічні розрахунки, рівень загрози та обсяг бюджету. Крім того, з огляду на виник­ нення громадянських заворушень, особливо, як це спостерігається в сутичках між правими та лівими фракціями, які були поширеними у країнах Латинської Америки в останні роки [ICBS 2010], багато правих урядів відчувають потребу у збільшенні своїх можливостей вну­ трішньої безпеки з великим арсеналом. безумовно, робить його більш конкуренто­ спроможним на світових ринках, включаю­ чи ринки Латинської Америки. Більше того, певний час в Ізраїлі постійно підтримується державна підтримка військових підрядників. Більше того, що стосується попиту, слід вра­ ховувати геополітичну чутливість латиноаме­ риканських держав. Незважаючи на те, що у наш час на континенті не було повномасштаб­ ної війни, це не означає, що у регіоні не було міждержавних мілітаризованих прикордон­ них конфліктів . З першого десятиліття тися­ чоліття з’явилася значна кількість літератури, яка підкреслює триваючу гонку озброєнь у Південній Америці, яка залежить від багатьох факторів, включаючи, але не обмежуючись цим, стратегічні розрахунки, рівень загрози та обсяг бюджету. Крім того, з огляду на виник­ нення громадянських заворушень, особливо, як це спостерігається в сутичках між правими та лівими фракціями, які були поширеними у країнах Латинської Америки в останні роки [ICBS 2010], багато правих урядів відчувають потребу у збільшенні своїх можливостей вну­ трішньої безпеки з великим арсеналом. Зміни політичних умов У той час як Болівія за президента Ево Моралеса розірвала свої дипломатичні зв’яз­ ки з Ізраїлем у 2009 році, нові члени уряду Бо­ лівії вирішили відновити відносини у грудні 2019 року після державного перевороту, який змусив Ево Моралеса покинути країну. Од­ нак найбільші зміни відбулися під час прези­ дентської виборчої кампанії 2018 року у Бра­ зилії, коли кандидат у президенти Жаїр Бол­ сонару заявив, що ось-ось почнеться період зближення з єврейською державою. Справді, його прихід до влади, здавалося, активізував відносини між Ізраїлем та Бразилією. На від­ міну від попередніх керівників лівих урядів, Жаїр Болсонару не висловлював застережень щодо Ізраїлю і дуже прагнув розвивати зв’яз­ ки у кількох напрямах – насамперед стосовно економіки та безпеки. Бразилія навіть заяви­ ла, що перенесе своє посольство з Тель-Аві­ ва до Єрусалиму. Однак після вступу на по­ саду Жаїр Болсонару відступив, мабуть, тому, що не хотів розривати економічні відносини з Лігою арабських держав, більшість з яких закуповують бразильське м’ясо та інші хар­ чові продукти. Щоб компенсувати невико­ нану обіцянку, Жаїр Болсонару організував швидкий дипломатичний візит до Ізраїлю у третьому місяці свого президентства та від­ крив комерційний офіс в Єрусалимі. На сьо­ годнішній день лише Гватемала реалізувала намір перенести посольство. Причини, що лежать в основі загальної позитивної реак­ ції Латинської Америки на спроби Ізраїлю зблизитися, зумовлені поєднанням внутріш­ 101 культури», 2020, Т. 12, № 2 ків, посилена участь Єрусалиму в регіоні – тема, яка не отримала належного наукового висвітлення. Поява правих партій у Латин­ ській Америці переорієнтувала дипломатію на єврейську державу. Однак нещодавнє поліп­ шення ізраїльської зовнішньої політики щодо латиноамериканських держав не може бути пояснене виключно політичною трансформа­ цією континентальної політики. Для сприяння ізраїльській дипломатичній діяльності у Ла­ тинській Америці збіглися численні фактори. Сюди входять регіональна ізоляція єврейської держави, підписання торгових договорів, ін­ тереси зростаючої оборонної промисловості Ізраїлю та культурні зв’язки з діаспорою. Із­ раїльсько-латиноамериканські відносини до­ сягли нової фази, яка характеризується спри­ ятливим політичним, економічним та соціаль­ ним середовищем як в Ізраїлі, так і у країнах Латинської Америки. Крім того, не можна не помітити вплив унікальних характеристик американсько-ізраїльських відносин за ча­ сів Дональда Трампа. На додаток до згаданої вище динаміки, немає сумнівів, що зовнішня політика Ізраїлю щодо латиноамериканських держав втратила оберти після політичного «глухого кута» внаслідок проведення трьох раундів послідовних національних виборів у 2019–2020 роках. Нестабільність політичної системи Ізраїлю негативно вплинула на про­ цес прийняття зовнішньополітичних рішень. Бібліографічні посилання / References р ф Azran, E. (2019). Israeli Government Fund to Direct Investment toward Latin America. Retrieved August 15, 2020 from https://www.haaretz.com/israel-news/business/israeli governmentfund-to-direct- investment-toward-latin-america-1.6995588. David, S.R. (2008). Existential Threats to Israel, Contemporary Israel: Domestic Politics, Foreign Policy, and Security Challenges, Robert O. Freedman (ed.)f Dimant, M. (2020). The“Mobileye Effect” in Latin America-Israel Relations, 2009-2019. Retrieved September 29, 2020 from https://strategicassessment.inss.org.il/en/articles/the-mobileye-effect-in-latin-america- israel-relations-2009-2019/ Israeli Central Bureau of Statistics. (2010). Israel’s Foreign Trade: 2000–2010, Statistilite 115. Retrieved August 15, 2020 from https://www.cbs.gov.il/en/Statistical/trade_115_e.pdf. Israeli Ministry of Finance. (2019). Bilateral Investment Treaties Retrieved August 15, 2020 from: https://mof. gov.il/en/InternationalAffairs/TradeAgreements/Pages/BIT.aspx. Israeli Ministry of Finance. (2018). Free Trade Area Agreements (FTAs). Retrieved August 15, 2020 from https://mof.gov.il/en/InternationalAffairs/TradeAgreements/Pages/FreeTradeArea.aspx.f Israeli Ministry of Foreign Affairs (2014), Israel to strengthen economic ties with Latin America and Pacific Alliance, Retrieved August 18, 2020 from https://mfa.gov.il/MFA/PressRoom/2014/Pages/ Government-approves-program-to-strengthen-economic-ties-with-Latin-American-countries.aspx. Kacowicz, A.M. (2017). Triangular Relations: Israel, Latin American Jewry, and Latin American Countries in a Changing International Context, 1967-2017. The Israel Journal of Foreign Affairs, XI:2 (2017), 203.i Kacowicz, A. M., Bar-Siman-Tov, Y. (2000) Stable Peace Among Nations. Rowman & Littlefield Publishersm. Kacowicz, A. M., Bar-Siman-Tov, Y. (2000) Stable Peace Among Nations. Rowman & Littlefield Publishersm. Katz, Y. (2017). Why Israel has the most technologically advanced military on Earth, Retrieved August 17 2020 from https://nypost com/2017/01/29/why israel has themost technologically advanced Kacowicz, A. M., Bar-Siman-Tov, Y. (2000) Stable Peace Among Nations. Rowman & Littlefield Publishersm. Katz, Y. (2017). Why Israel has the most technologically advanced military on Earth, Retrieved August 17, 2020 from https://nypost.com/2017/01/29/why-israel-has-themost-technologically-advanced- military-on-earth. Landau, N. (2019). Netanyahu Welcomes Brazil’s Bolsonaro to Israel, Days Before Election, Retrieved August 15, 2020 from https://www.haaretz.com/israel-news/.premiumbrazil-s-bolsonaro-arrives-in-israel- days-before-election-1.7067601.f Lazaroff, T. (2019). Israel to attend Expo 2020 Dubai, an Arab State with whom it has no Ties. Retrieved August 31, 2020 from https://www.jpost.com/Arab-Israeli-Conflict/Israelis-permitted-to-come-to- 2020-World-Expo-in-UAE-607376. Oster, M. (2019). Brazilian President Jair Bolsonaro walks back embassy move promise, Retrieved from https://www.jpost.com/Israel-News/Brazilian-President-Jair-Bolsonaro-walks-back-embassy-move- promise-585160. p Radio Uruguay. (2019). El embajador de Israel se entrevistó con Lacalle Pou, Retrieved August 22, 2020 from https://radiouruguay.uy/embajador-de-israel-se-entrevisto-con-lacalle-pou/. Ran, A. & Cahan J.A. (2012). Introduction: Rethinking Jewish Identity in Latin America. Returning to Babel: Jewish Latin American Experiences, Representations, and Identity (eds.), 6-7. SIPRI (2019). Arms Transfers Database. Retrieved from: http://armstrade.sipri.org/armstrade/page/trade_ register.php. The Times of Israel. (2019). Israel named world’s 8th largest arms exporter. Retrieved August 17, 2020 from https://www.timesofisrael.com/israel-named-worlds-8th-largest-arms-exporter/i Vysotskyi, O.Y. (2017). Technologies of legitimation in international relations. Scientific and Theoretical Almanac Grani, 20(10), 98-104. https://doi.org/10.15421/1717138. Waltz, K. (2001). Висновки. Отже, можна виокремити такі технології [Vysotskyi 2017] зовнішньої політики Ізраїлю, які він реалізовував на латиноамериканському напрямі: укладання торгових угод, обіцянка підтримки під час голосування у міжнарод­ них організаціях, офіційні візити ізраїльских високопосадовців до латиноамериканських країн, укладання договорів з латиноамерикан­ ськими державами, спрямованих на розвиток науки, технологій та інновацій. У результаті ефективного застосування зовнішньополітичних технологій Ізраїлем були досягнуті такі цілі: зміцнення позицій у регіоні, ослаблення впливу Ірану на латино­ американські країни, виключення «палестин­ ського питання» з порядку денного, зміна розстановки сил щодо голосування в ООН по відношенню до Ізраїлю, покращення еко­ номічних зв’язків через експорт ізраїльської продукції, програмного забезпечення та зброї. Хоча між Ізраїлем та державами Латин­ ської Америки існують відносини багато ро­ 102 «Філософія та політологія в контексті сучасної культури», 2020, Т. 12, № 2 Бібліографічні посилання / References Man, the State, and War: A Theoretical Analysis. New York, Columbia University Press, 80-123. Waxman, D (2003). Between Isolation and Integration: The Jewish Dimension in Israeli Foreign Policy, Israel Studies Forum, XIX:1. Wermenbol, G. (2019). Israel’s Latin America Push. Retrieved August 25, 2020 from https://www. atlanticcouncil.org/blogs/new-atlanticist/israel-s-latin-america-push/ 103
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Obstacles facing rural women development in the Palestinian society: Nablus Governorate as a Case Study
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Abstract Women constitute 49 percent of the Palestinian population, but the participation of Palestinian women in economic and social development in Palestinian society is low. The low participation of women is due to many obstacles and constraints preventing them from contributing to the economic and social development of Palestinian society. This study aims to address the most important obstacles facing Palestinian women in achieving development, focusing on the problems and constraints facing rural women in Nablus Governorate. The study used the descriptive, analytical, inductive, and historical approach based on references, books, periodicals, and field work. The data were collected through personal interviews and questionnaires. One hundred questionnaires were distributed to obtain scientific results in an objective manner. The study found that there are a number of factors preventing Palestinian women from contributing to the development process, most importantly social, economic, political, security, media, and personal factors. The study concluded with a number of important recommendations and proposals necessary to increase the role of rural women as well as the economic and social development of Palestinian society. Keywords: Development, Rural Women, Palestinian Women Keywords: Development, Rural Women, Palestinian Women Journal of Culture and Values in Education Volume 4 Issue 1, 2021 Journal of Culture and Values in Education Volume 4 Issue 1, 2021 88 L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study Case Study Loai Mahmoud Aburaida* An-Najah National University *Corresponding Author: laburaida@najah.edu Received : 2019-08-27 Rev. Req. : 2019-12-10 Accepted : 2020-02-05 How to cite this paper: Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study. Journal of Culture and Values in Education, 4(1), 88-99, https://doi.org/10.46303/jcve.2020.1 This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) 10.46303/jcve.2020.1 Loai Mahmoud Aburaida* An-Najah National University *Corresponding Author: laburaida@najah.edu How to cite this paper: Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study. Journal of Culture and Values in Education, 4(1), 88-99, https://doi.org/10.46303/jcve.2020.1 This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org Introduction How can rural women be empowered to play an active role in the Palestinian society and to increase their participation in overall development? The importance of this research stems from the fact that it studies an important segment of the society. Future generations will depend on this segment to reach a comprehensive and sustainable development in the countryside. In order to identify the obstacles preventing Palestinian rural women from development in society, it was necessary to know the role of rural women in development. The researcher considered conducting a field study that reflects this reality through a questionnaire designed for this purpose. The questionnaire included questions related to study objectives and to answer study questions from the following aspects: First: General information about rural women in Nablus Governorate. Second: Activities practiced by rural women in Nablus Governorate First: General information about rural women in Nablus Governorate. First: General information about rural women in Nablus Governorate. Second: Activities practiced by rural women in Nablus Governorate. Third: Obstacles and restrictions leading to non-participation in various development activities. Fourth: Recommendations and proposals to activate the role of rural women in real development. Literature Review Introduction It is recognized that the participation of Palestinian women in social and economic life in the West Bank is low. Moreover, rural women's activity is still ineffective in rural development (Shteih, 2018). The Palestinian Central Bureau of Statistics shows that 85.4 percent of the women in the West Bank are unemployed (PCBS, 2017a). According to the published report by 2021 Journal of Culture and Values in Education Volume 4 Issue 1, 2021 89 L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study the Palestinian Central Bureau of Statistics, women constituted 49 percent of the Palestinian population in 2019. Palestinian women’s participation in the labor force is 21 percent (Awad, 2018). In addition, there is a large gap between the rural and urban communities in Palestine. This leads to the absence of qualified cadres who can lead and develop rural communities. the Palestinian Central Bureau of Statistics, women constituted 49 percent of the Palestinian population in 2019. Palestinian women’s participation in the labor force is 21 percent (Awad, 2018). In addition, there is a large gap between the rural and urban communities in Palestine. This leads to the absence of qualified cadres who can lead and develop rural communities. Based on secondary sources of books, periodicals, and related reports, the study followed the analytical, inductive, historical, and descriptive method. In addition, the study depends on primary sources represented by field data collected through personal interviews and questionnaires. The questionnaires were distributed randomly in Nablus Governorate, targeting 100 Palestinian women ages 15-65. This study aims at identifying the economic activities practiced by Palestinian rural women and their community participation. It also aims at identifying the most important challenges and constraints facing Palestinian rural women in achieving development. Finally, the study aims to provide opinions, ideas, and proposals for activating Palestinian rural women’s roles and performance in society through answering the following questions: 1. What are the social and educational characteristics of rural women? 1. What are the social and educational characteristics of rural women? 2. Is there a low participation in the development of Palestinian rural communities? Is this decline due to the vulnerability of rural women? . What are the obstacles that prevent rural women from participating in th development of Palestinian rural communities? 4. Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org Literature Review 2021 Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org Journal of Culture and Values in Education Volume 4 Issue 1, 2021 90 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Development is the exploitation of the available energies and possibilities to meet the required needs of community and development in accordance with community, cultural, social, and economic needs. It is a complex process encompassing all life aspects such as economic, social, intellectual, political, and ideological life (Pinot, 1972). Over the past few years, many definitions of development have emerged. One of these defines development as the investment in the development of human resources and development through education and training for members of society to participate positively in the community (Sarhan, 2014). Development is the exploitation of the available energies and possibilities to meet the required needs of community and development in accordance with community, cultural, social, and economic needs. It is a complex process encompassing all life aspects such as economic, social, intellectual, political, and ideological life (Pinot, 1972). Over the past few years, many definitions of development have emerged. One of these defines development as the investment in the development of human resources and development through education and training for members of society to participate positively in the community (Sarhan, 2014). There have been considerable efforts in rural development that have led to controversy about the starting point in rural development. Is it through achieving awareness or through achieving economic development? Should there be focus and attention on the community or the most vulnerable economic and social sectors in society? What can be done toward patterns of communal injustice? In this context, Gandhi’s ideas for rural development are the most important of these ideas in terms of influence and continuity. He is recognized for his emphasis on the fact that change does not come from violence but from persuasion (Hopkins, 1998). Women have a vital role in development. Their full participation is therefore necessary to achieve sustainable development. Sustainable development is achieved through equality between women and men in rights, opportunities, and responsibilities. Social justice is a precondition in this process (Lohani & Aburaida, 2017). Rural women have a major role in the development of the rural family. Figure 1: Participation in the labor force by women and men 15 years and older in Palestine, 2001-2018 Literature Review Women work in all social, economic, and political fields. Studies indicate that rural women contribute about four percent of the world's food. In fact, this ratio may reach 80 percent in some developing countries (UNDP, 1990). Studies also show that in many societies, such as in Africa and Asia, women work longer hours than men. Women’s weekly work increases by about 13 hours; on the other hand, women work in Eastern European and Latin American countries about 6-7 hours more than men (Sayed, 1996). It is worth mentioning that international efforts to mainstream the role of women in development have yielded positive results. Grassroots and non-governmental organizations have played an active role in improving women's access to welfare and ease the restrictions related to participation and control (Fonjong, 2001). However, overall rural development in general and the role of Palestinian women in particular have been severely neglected. They have been dismissed out of the economic and social development plans in the era of the Israeli occupation, even after the establishment of the Palestinian Authority in 1994. Despite the high participation of Palestinian women in the labor force during the past years, it is still very low compared with men. Palestinian women’s participation rate in the Palestinian labor force was 21.7 percent in 2018, compared with 10.3 percent in 2001 (Figure 1). 2021 Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org 91 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study Source: Awad, 2018 Source: Awad, 2018 As the previous figure shows, women’s role in economic and social development is a vital one. Tim and Nadi (2010) studied the extent to which Palestinian women participate in development; their findings show that women have an important role that can only be realized through justice and equality between men and women in society. Najm (2013) studied Palestinian university youth trends toward women's issues in education and work. The study concluded that youth attitudes are positive toward women’s education and work. Hamayel (2003) examined the attitudes of Palestinian university students toward the work of women. The researcher concluded that the society has a positive attitude toward women. Literature Review It also emphasizes the role of women in economic development within the Palestinian society. On the other hand, Jaber (2005) concluded, in research about obstacles facing Palestinian women working in the public sector in the northern governorates of the West Bank, that the most important obstacles are the Israeli security policies on the checkpoints between the cities and villages of the West Bank. This prevents Palestinian women from reaching their workplaces and delays their return home. The study by Mohamad (2011) found that there is no correlation between the educational curricula and the needs of the society, which leads to a lack of cultural awareness and high unemployment in Palestinian society. In addition, the Palestinian-Israeli conflict and the lack of Palestinian unity have had a significant impact on the limited funding, which is the core of economic activity. Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org Methodology This study crosses both quantitative and qualitative research tools to collect original data, which is analyzed in the framework of a case study methodological approach, studying the development of rural women in Palestinian society and its main constraints under an exploratory inductive approach. This study does not begin with a hypothesis, using instead research questions to narrow the scope of the study. 2021 Journal of Culture and Values in Education Volume 4 Issue 1, 2021 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study 92 Journal of Culture and Values in Education Volume 4 Issue 1, 2021 92 L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study The study of the obstacles facing rural women in Palestinian society benefits not only from secondary data such as books, articles, periodicals, and related reports; it also uses original primary data collected through questionnaires and interviews. The questionnaires were designed to obtain scientific results objectively from 100 Palestinian women in Nablus Governorate. The in-depth interviews were conducted with the heads of women's associations, trade union organizations, women workers, and unemployed women. The study of the obstacles facing rural women in Palestinian society benefits not only from secondary data such as books, articles, periodicals, and related reports; it also uses original primary data collected through questionnaires and interviews. The questionnaires were designed to obtain scientific results objectively from 100 Palestinian women in Nablus Governorate. The in-depth interviews were conducted with the heads of women's associations, trade union organizations, women workers, and unemployed women. Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org Dataset Nablus Governorate is located in the north of the West Bank, 53 kilometers from Jerusalem. It is located along 35.16 west and 32.13 north of the Equator (Figure 2). It covers an area of 605 square kilometers. Its population is 392,407. The governorate includes 52 rural communities in addition to the city of Nablus (PCBS, 2017b), according to the administrative division approved by the Palestinian Authority. Figure 2: Location of the study area Figure 2: Location of the study area According to PCBS (2017b), Palestinian society is characterized by a young generation; 38.9 percent of the total population in Palestine is under 15 years of age, and 39.1 percent are male and 38.7 percent are female. Youth ages 15-29 make up 29.7 percent of the total population, distributed as 43.9 percent male and 56.1 percent female. Figure 2: Location of the study area Figure 2: Location of the study area According to PCBS (2017b), Palestinian society is characterized by a young generation; 38.9 percent of the total population in Palestine is under 15 years of age, and 39.1 percent are male and 38.7 percent are female. Youth ages 15-29 make up 29.7 percent of the total population, distributed as 43.9 percent male and 56.1 percent female. 2021 Journal of Culture and Values in Education Volume 4 Issue 1, 2021 93 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorat Study The sample of this study consists of women in the rural areas in Nablus that contains 64 villages and towns. The questionnaires were distributed randomly to the women in these areas. This sample is characterized by the following characteristics, as shown in Figure 3. The sample of this study consists of women in the rural areas in Nablus that contains 64 villages and towns. The questionnaires were distributed randomly to the women in these areas. This sample is characterized by the following characteristics, as shown in Figure 3. Regarding the age of the sample, looking to Figure 3, it is clear that, on one hand, women aged 15-24 years constitute 40 percent of the population. This is a high percentage that can be relied upon in all future development activities. Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org Dataset On the other hand, women aged 25-34 constitute 26 percent, and women aged 35-44 years 13 percent. This is the age at which women can do all developmental activities in society. As for those who are older than 45-65 years, they represent 21 percent; this segment is effective to raise awareness and educate the rural community since they have life experiences. Figure 3: Age level of sample members Source: Field Study 2018 Regarding the social status of the sample members, Figure 4 explains that the percentage of single women is 58 percent of the total sample; undoubtedly this has a negative impact on rural women’s performance and activity. Rural women’s psychological instability, fear of obsession, and the society's attitude regarding spinsterhood are all reasons that expose them to convergence and inability to interact with the surrounding community. It also prevents rural women from carrying out any developmental role. Figure 4 explains also that the percentage of married women is 39 percent. In spite of the fact that married women are more stable psychologically, they are still inactive in performing their role in development. The inability of women to reconcile their home chores and their work or their societal role idles their energies, resulting in the absence of their developmental role. The presence of widows and divorced Figure 3: Age level of sample members Source: Field Study 2018 Figure 3: Age level of sample members Source: Field Study 2018 Regarding the social status of the sample members, Figure 4 explains that the percentage of single women is 58 percent of the total sample; undoubtedly this has a negative impact on rural women’s performance and activity. Rural women’s psychological instability, fear of obsession, and the society's attitude regarding spinsterhood are all reasons that expose them to convergence and inability to interact with the surrounding community. It also prevents rural women from carrying out any developmental role. Figure 4 explains also that the percentage of married women is 39 percent. In spite of the fact that married women are more stable psychologically, they are still inactive in performing their role in development. The inability of women to reconcile their home chores and their work or their societal role idles their energies, resulting in the absence of their developmental role. Dataset The presence of widows and divorced Regarding the social status of the sample members, Figure 4 explains that the percentage of single women is 58 percent of the total sample; undoubtedly this has a negative impact on rural women’s performance and activity. Rural women’s psychological instability, fear of obsession, and the society's attitude regarding spinsterhood are all reasons that expose them to convergence and inability to interact with the surrounding community. It also prevents rural women from carrying out any developmental role. Figure 4 explains also that the percentage of married women is 39 percent. In spite of the fact that married women are more stable psychologically, they are still inactive in performing their role in development. The inability of women to reconcile their home chores and their work or their societal role idles their energies, resulting in the absence of their developmental role. The presence of widows and divorced 2021 94 L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case women in the sample of the study was very low: two percent widowed and one percent divorced. Figure 4: Study sample social status Source: Field Study 2018 Regarding the sample educational level, which is an important factor in the development process: It affects all life aspects and social, economic, and political levels. The low level of women’s education in many societies is considered the general factor of underdevelopment and backwardness of society. This study shows that the educational level of rural women is one of the most important pillars in developing the society. Through these educated rural women, we can promote active participation in society. The percentage of those with a university degree was 59 percent, with one percent of them holding a high degree. On the other hand, women in the secondary school and those who attained this degree reached 39 percent. This is a clear indicator of rural women’s interest in education, especially after they moved from this stage to the university level; thus, their role contributes effectively in the future development. Figure 4: Study sample social status Figure 4: Study sample social status Source: Field Study 2018 Source: Field Study 2018 Source: Field Study 2018 Regarding the sample educational level, which is an important factor in the development process: It affects all life aspects and social, economic, and political levels. Dataset The low level of women’s education in many societies is considered the general factor of underdevelopment and backwardness of society. This study shows that the educational level of rural women is one of the most important pillars in developing the society. Through these educated rural women, we can promote active participation in society. The percentage of those with a university degree was 59 percent, with one percent of them holding a high degree. On the other hand, women in the secondary school and those who attained this degree reached 39 percent. This is a clear indicator of rural women’s interest in education, especially after they moved from this stage to the university level; thus, their role contributes effectively in the future development. Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org Economic conditions The researcher found that the Palestinian-Israeli conflict and the lack of Palestinian unity had a great impact on the limited funding, which is considered the mainstay of economic activity. Of the respondents, 39 percent attribute the prevailing economic conditions not only to the study area but to Palestinian women, which impedes the role of women in development, resulting from the lack of funding for development projects and the spread of poverty in these rural communities. Additionally, 35 percent of respondents said that there is a lack of services in rural areas, which leads to women's reluctance to interact in development work. Findings Despite rural women’s high level of education, their participation in economic activities is still very low. The percentage of female workers in the study sample was 6.3 percent, which is less than the percentage of women working in Palestine, 9.7 percent (Shteih, 2018). The study finds that the professions practiced by rural women in the countryside are still limited to traditional occupations. About 29 percent are engaged in handicrafts such as sewing and embroidery, while 26 percent work in agriculture; 23 percent work in education, and the rest work in 2021 Journal of Culture and Values in Education Volume 4 Issue 1, 2021 95 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case economic activities and social work such as literacy, charities, women's groups, rehabilitation centers, trade unions, etc. The study showed that 12 percent of the respondents were active in their societies, and this is a low percentage that hinders development. economic activities and social work such as literacy, charities, women's groups, rehabilitation centers, trade unions, etc. The study showed that 12 percent of the respondents were active in their societies, and this is a low percentage that hinders development. The study showed that there are many obstacles facing rural women in the Palestinian society development process. This includes social, economic, and political aspects, in addition to the lack of training and the institution and the women's collective form (Figure 5). Figure 5: The most important obstacles facing rural women in the development of the Palestinian society Figure 5: The most important obstacles facing rural women in the development of the Palestinian society Economic conditions Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org The structure of social systems and the cultural framework of society Economic life revolves around economic, social and political organizations in addition to the cultural framework of society (values, barriers, traditions, beliefs, moral qualities, attitudes, etc.). The existing framework indirectly affects women’s role in economic development. It also affects the level of comprehensive development (Abdul-Rahman, 2003). The study explains that 2021 Journal of Culture and Values in Education Volume 4 Issue 1, 2021 Journal of Culture and Values in Education Volume 4 Issue 1, 2021 96 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case reducing the role of women in development due to the contribution of the existing structure of social systems and the cultural framework of society is 29 percent. It should be noted that the dominant culture among women plays an important role in hindering their contribution to the overall development. The study revealed that 27 percent of women direct their available savings in many non-productive investments that do not benefit the beneficiary. Their saving is directed toward agriculture, gold hoarding, and acquisition of ornaments. In addition, cultural values and traditions result in spending on many consuming aspects, which do not contribute positively to raising the level of material well-being of individuals and thus impede the role of women in development. reducing the role of women in development due to the contribution of the existing structure of social systems and the cultural framework of society is 29 percent. It should be noted that the dominant culture among women plays an important role in hindering their contribution to the overall development. The study revealed that 27 percent of women direct their available savings in many non-productive investments that do not benefit the beneficiary. Their saving is directed toward agriculture, gold hoarding, and acquisition of ornaments. In addition, cultural values and traditions result in spending on many consuming aspects, which do not contribute positively to raising the level of material well-being of individuals and thus impede the role of women in development. The social systems, customs, and traditions prevailing in rural communities, lack of local council confidence among rural women, and social oppression all lead to the reluctance of rural women to participate in the various development activities. The structure of social systems and the cultural framework of society As a result, the study showed that 52 percent of the study sample believes that society does not give rural women the right of decision-making. This leads to imbalance, mistrust, and a permanent conflict between society and ambitions, and exposes rural women to the intransigence and inability to interact with the surrounding society. Israeli actions at military checkpoints The Israeli measures at the military checkpoints are the most important obstacles that prevent Palestinian women from taking part in their developmental role. These checkpoints, which are described by Palestinians as death gates, were increased to hundreds after the intifada in 2000. They are spread throughout the West Bank. Israel military checkpoints are spread along the entrances to cities and towns. Due to this abuse and humiliation, the lives of Palestinian citizens are very difficult. They are subjected to barriers in addition to the killings and arrests that take place at these checkpoints. Palestinians are no safer or freer when they pass a checkpoint. This is directly reflected on Palestinian women, who are afraid of passing through these barriers. Moreover, they are always late at work or in returning home, resulting in staying at home and waiting for a nearby job to avoid passing through these military barriers, which negatively affects and limits their role in development. Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org Absence of women's training center organizations In spite of the increased percentage of education in rural communities, 42 percent of the respondent’s members indicated that the lack of training centers and lack of women's organizations isolated rural women from their role in development; 11 percent mentioned that the absence of training and rehabilitation associations for rural women and the lack of women's societies in rural society is one of the important reasons that causes the absence of women from development roles. In addition, undermining rural women in administrative structures and local councils is one of the crucial aspects that led to rural women’s reluctance to interact in the development work. 2021 Journal of Culture and Values in Education Volume 4 Issue 1, 2021 Journal of Culture and Values in Education Volume 4 Issue 1, 2021 97 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Rural women are the main drivers of development, but limited access to credit, health care, and education are among the many challenges women face. This crisis is compounded by the global food and economic crisis and climate change. Therefore, empowerment is necessary, not only for the well-being of individuals, families, and rural communities, but also for overall economic productivity since the presence of women in the agricultural labor force is worldwide. Rural women are the main drivers of development, but limited access to credit, health care, and education are among the many challenges women face. This crisis is compounded by the global food and economic crisis and climate change. Therefore, empowerment is necessary, not only for the well-being of individuals, families, and rural communities, but also for overall economic productivity since the presence of women in the agricultural labor force is worldwide. Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org Conclusions and Recommendations Rural women have a significant and effective impact on the real development of rural society. They also play a catalytic role in achieving the economic, environmental, and social transformations that are necessary to achieve sustainable development. However, women in these societies are still unable to play a real and active role due to their social conditions and the clear discrimination against rural women. Lack of awareness, training, and rehabilitation, lack of qualified communities for qualified personnel, the absence of women's institutions, the weak role of government in rural areas, and the lack of service accessibility are all reasons for underdevelopment, as well as the lack of economic potential of rural communities and rural women where they do not have direct income, which prevents investment and makes them non-productive and consuming. Empowerment of rural women is therefore critical, not only for the welfare of individuals, families, and communities, but also for overall economic productivity due to the presence of rural women in the workforce throughout the world. The researcher, through the field study on the obstacles facing rural women in achieving development in Palestinian society, concluded with the following recommendations to activate the role of rural women to achieve real development within its society: The researcher, through the field study on the obstacles facing rural women in achieving development in Palestinian society, concluded with the following recommendations to activate the role of rural women to achieve real development within its society:  Promote the educational role of rural women to enable them to gain access to education that ensures equality and parity with men.  Promote the educational role of rural women to enable them to gain access to education that ensures equality and parity with men.  Work on improving and adjusting the image of rural women, combating stereotypical and mental concepts prevailing in the Palestinian society that consider women as housewives doing agricultural work only. All creative areas for rural women must be highlighted.  Conduct scientific studies on rural women in all aspects to identify needs and develop plans and programs to improve the efficiency of rural women, and liberate them from the economic and social controls imposed on them. It is also necessary to establish a training center in rural areas to serve rural women and raise their scientific and professional efficiency. E-ISSN: 2590-342X https://cultureandvalues.org Conclusions and Recommendations  Establish civil associations to eliminate illiteracy and introduce women to their rights in order to achieve their role in the development process.  Establish civil associations to eliminate illiteracy and introduce women to their rights in order to achieve their role in the development process.  Work to improve the image of women in Palestinian society in the media. Also, combat concepts and vulgar images that lead to discrimination against women. Support their work as a fundamental right to contribute to development.  Work to improve the image of women in Palestinian society in the media. Also, combat concepts and vulgar images that lead to discrimination against women. Support their work as a fundamental right to contribute to development. Activating the role of women within the family in the process of social upbringing has a great impact on the comprehensive development of society. It also has an effective role in eliminating Activating the role of women within the family in the process of social upbringing has a great impact on the comprehensive development of society. It also has an effective role in eliminating Journal of Culture and Values in Education 2021 E-ISSN: 2590-342X https://cultureandvalues.org 2021 Journal of Culture and Values in Education Volume 4 Issue 1, 2021 98 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study the negative social phenomena that limit the ability and contribution of women in development such as education, early marriage, and frequent reproduction, etc., in addition to raising the level of women's participation in public, political, and developmental life through their participation in decision-making. The underdevelopment of societies is due to the backwardness of their cultures. Therefore, it is necessary to create an effective and positive cultural balance. It is also important to liquidate the negative residues, including the details of the daily lives of individuals in the society, so that the continuous exchange between the individual's effective behavior and lifestyle achieves individual autonomy and active participation in society. References Abdul-Rahman, A. (2003). Development management: Development management in the Arab world and the new world order. Kingdom of Saudi Arabia: Center for Arab Unity Studies. Abdul-Rahman, A. (2003). Development management: Development management in the Arab world and the new world order. Kingdom of Saudi Arabia: Center for Arab Unity Studies. Awad, P. (2018). The situation of Palestinian women. Ramallah: Palestinian Central Bureau of Statistics. Fonjong, L. (2001). Fostering women’s participation in development through non‐ governmental efforts in Cameroon. Geographical Journal, 167(3), 223-234. Hamayel, S. (2003). Palestinian university students' attitudes towards the work of women. Nablus: An-Najah National University. Hopkins, N. (1998). Gandhi and the discourse of rural development in independent India. Journal of Comparative Poetics, 18, 205-236. Jaber, D. (2005). Difficulties facing Palestinian women working in the public sector in the northern governorates of the West Bank. Nablus: An-Najah National University. Lohani, M., & Aburaida, L. (2017). Women empowerment: A key to sustainable development. The Social ION, 6(2), 26-29. Mohamad, Y. (2011). The obstacles to development in Palestine. Khartoum: Sudan University of Science and Technology, Institute of Family and Community Development. Najm, M. (2013). Palestinian university youth attitudes towards women's education and work. IUG Journal of Educational and Psychological Studies, 21(1), 567-617. PCBS. (2017a). Preliminary results of the general census of population, housing and establishments. Ramallah: Palestinian Central Bureau of Statistics. Journal of Culture and Values in Education 2021 E-ISSN: 2590-342X https://cultureandvalues.org Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org 2021 Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org Journal of Culture and Values in Education Volume 4 Issue 1, 2021 99 Aburaida, L. M. (2021). Obstacles Facing Rural Women’s Development in Palestinian Society: Nablus Governorate as a Case Study y PCBS. (2017b). Women and men in Palestine issues and statistics. Ramallah: Palestinian Central Bureau of Statistics PCBS. (2017b). Women and men in Palestine issues and statistics. Ramallah: Palestinian Central Bureau of Statistics Pinot, E. (1972). What is development? Beirut: Dar Alhaqiqa. Sarhan, H. (2014). Sustainable human development and building a knowledge society. Ahl al- Bayt Journal, 1(16), 138-155. Sayed, P. (1996). Impact of the WTO agreement on agriculture on the role of women in rural development. Yemen: Ministry of Agriculture. Shteih, A. (2018). Problems of women in the economic life and the labor market in the West Bank, according to the data of the Palestinian labor force 2015. Nablus: An-Najah National University, unpublished thesis. Journal of Culture and Values in Education E-ISSN: 2590-342X https://cultureandvalues.org References Tim, H., & Anadi, E. (2010). The degree of Palestinian women's participation in development from the perspective of graduate students at An-Najah National University in Nablus. Nablus: An-Najah National University. UNDP. (1990). Rural women’s participation in development. New York, NY: UNDP. 2021
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Ensuring leadership at the operational level of a health system in protracted crisis context. A cross-sectional qualitative study covering 8 health districts in Eastern Democratic Republic of Congo
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Results The study has revealed deficiencies regarding Management and Organisation of the health zones, Internal collaboration within their management teams as well as collaboration between these teams and the health zone’s external partners. Communication and clinical and managerial capacities were identified as key factors to be strengthened in improving leadership within the districts. The findings have also highlighted the detrimental influence of vertical interventions from external partners and hierarchical supervisors in health zones on planning, human resource management and decision-making autonomy of district leaders, weakening their leadership. Research Article License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Additional Declarations: No competing interests reported. Additional Declarations: No competing interests reported. Page 1/22 Version of Record: A version of this preprint was published at BMC Health Services Research on December 6th, 2023. See the published version at https://doi.org/10.1186/s12913-023-10336-7. Version of Record: A version of this preprint was published at BMC Health Services Research on December 6th, 2023. See the published version at https://doi.org/10.1186/s12913-023-10336-7. Page 2/22 Background This study examines how leadership is provided at the operational level of a health system in a protracted crisis context. Despite advances in medical science and technology, health systems in low- and middle- income countries struggle to deliver quality care to all their citizens. The role of leadership in fostering resilience and positive transformation of a health system is established. However, there is little literature on this issue in Democratic Republic of the Congo (DRC). This study describes leadership as experienced and perceived by health managers in crisis affected health districts in Eastern DRC. Methods A qualitative cross-sectional study was conducted in eight rural health districts (corresponding to health zones, in DRC’s health system organization), in 2021. Data were collected through in-depth interviews and non-participatory observations. Participants were key health actors in each district. The study deductively explored six themes related to leadership, using an adapted version of the Leadership Framework conceptual approach to leadership from the United Kingdom National Health Service’s Leadership Academy. From these themes, an inductive analysis extracted emerging subthemes. Conclusions Despite their decentralized basic operating structure, which has withstood decades of crisis and insufficient government investment in healthcare, the districts still struggle to assert their leadership and autonomy. The authors suggest greater support for personal and professional development of the health workforce, coupled with increased government investment, to further strengthen health system capacities in these settings. Background Page 3/22 Page 3/22 Advances in medical science and technology continue to expand the strategic opportunities for curative and preventive interventions around the world to deliver better health for all and extend life (1). At the country level, these interventions should be implemented through the health system, which the World Health Organization (WHO) defines as a set of elements, structures, and individuals that interact in a coordinated manner to ensure holistic and integrated care of the health of populations (2). The fit between existing policy options and national health systems' capacity at delivering quality universal healthcare, however, varies in practice. This is especially true for low- and middle-income countries, whose health performance remains consistently subdued compared to that of high-income countries (3, 4). The 2020–2021 WHO Results Report (5) concludes that the Triple Billion Initiative has achieved relative success in achieving the Sustainable Development Goals. However, 80% of these achievements have occurred essentially in a handful of countries, leaving a rather worrisome health situation elsewhere, particularly in sub-Saharan Africa. The Covid-19 pandemic has undoubtedly contributed to this underperformance, as 90% of countries have acknowledged having experienced significant disruptions in organizing and delivering essential health services (5, 6). Nevertheless, the pandemic has demonstrated the importance of strong leadership, capable of ensuring multisectoral coordination in preparing the health system to address health emergencies during international crisis (7, 8), at both national and sub-national levels. Indeed, studies have reported the indirect effects of health emergencies and natural disasters on health systems. Beyond the associated morbidity and mortality, these emergencies usually induce disruptions in various health services across the health system’ six building blocks (6, 9, 10), including leadership and governance. Most health policy experts consider managers with strong leadership to be a critical component for health system development (1, 11), and a prerequisite for health system strengthening and overall progress (12). Several authors have demonstrated the key role of leadership in resilience and positive health system change in various contexts (13–15). Factors such as good governance, political commitment, effective management, and the ability to innovate and adapt to resource constraints or crises have been recognized as characteristics of the best-performing health systems (16). Eastern Democratic Republic of Congo has been facing crisis for more than three decades. Settings and study period This study was conducted in the mountainous province of South Kivu in Eastern DRC. The health system in the DRC is organized in three levels: (i) the Central level, where health policies, norms and strategies are elaborated in the Ministry of Health ; (ii) the intermediate level represented by the 26 provinces which plays a role of coordinating health interventions, planning and technical support (through the Provincial Health Division – PHD) and of control, audit and inspection (through the Provincial Health Inspection (PHI); (iii) and the operational level featuring 516 Health Zones (HZ – corresponding to health districts ) where health policies and strategies are implemented (26, 27). The HZ is managed by an autonomous Health Zone Management Team (HZMT) whose mission is to ensure the consistency of activities, including improving health coverage and quality of care, streamlining the operation of integrated health structures, This study was conducted in the mountainous province of South Kivu in Eastern DRC. The health system in the DRC is organized in three levels: (i) the Central level, where health policies, norms and strategies are elaborated in the Ministry of Health ; (ii) the intermediate level represented by the 26 provinces which plays a role of coordinating health interventions, planning and technical support (through the Provincial Health Division – PHD) and of control, audit and inspection (through the Provincial Health Inspection (PHI); (iii) and the operational level featuring 516 Health Zones (HZ – corresponding to health districts ) where health policies and strategies are implemented (26, 27). The HZ is managed by an autonomous Health Zone Management Team (HZMT) whose mission is to ensure the consistency of activities, including improving health coverage and quality of care, streamlining the operation of integrated health structures, management of human and financial resources, and organizing community participation. This team therefore represents the foundation for the leadership that contributes to strengthening the health system at the operational level (28, 29). This organization of the health system stems from the 1980s. it has been inspired by the Alma Ata (1978) recommendations regarding Primary Health Care’s organization, renewed through Astana Declaration (2018) (30, 31). Some authors consider it to be among the best designed and most robust health system organizations in sub-Saharan Africa. It has proven its resilience by surviving an environment of security, economic and governance crisis that has plagued the country throughout the 20 years following its independence in 1960. Settings and study period (32, 33). Private faith-based health care organizations play an important role in health care delivery and are co-managers with the Congolese State of several integrated health facilities. The health sector is poorly financed by the state. Therefore, it depends heavily on external Technical and Financial Partners (TPF) support, and a large part of the operating funds for the facilities and staff remuneration comes directly from households (34, 35). For the past three decades, the South- Kivu province has evolved in a context of instability and protracted humanitarian crisis linked to the recurrence of conflicts in the region (17, 36). The province is organized into a Provincial Health Division (PHD), with 34 health zones. Our study takes place in eight rural health zones covering 1 812 123 inhabitants and considers data and events for the year 2021. g q y , g p g , management of human and financial resources, and organizing community participation. This team therefore represents the foundation for the leadership that contributes to strengthening the health system at the operational level (28, 29). This organization of the health system stems from the 1980s. it has been inspired by the Alma Ata (1978) recommendations regarding Primary Health Care’s organization, renewed through Astana Declaration (2018) (30, 31). Some authors consider it to be among the best designed and most robust health system organizations in sub-Saharan Africa. It has proven its resilience by surviving an environment of security, economic and governance crisis that has plagued the country throughout the 20 years following its independence in 1960. (32, 33). Private faith-based health care organizations play an important role in health care delivery and are co-managers with the Congolese State of several integrated health facilities. The health sector is poorly financed by the state. Therefore, it depends heavily on external Technical and Financial Partners (TPF) support, and a large part of the operating funds for the facilities and staff remuneration comes directly from households (34, 35). For the past three decades, the South- Kivu province has evolved in a context of instability and protracted humanitarian crisis linked to the recurrence of conflicts in the region (17, 36). The province is organized into a Provincial Health Division (PHD), with 34 health zones. Our study takes place in eight rural health zones covering 1 812 123 inhabitants and considers data and events for the year 2021. Background This situation has strongly contributed to the deterioration of the population's socio-economic conditions, and has notably led to a weakened health system and a substantial lack of health care (17) for the vast majority of the population. As a result, along with the combined burden of infectious diseases and malnutrition, additional health problems directly related to crisis and armed conflict emerge, with major consequences for the overall health of the local population (18, 19). The province of South Kivu in Eastern DRC is one of the most affected provinces by these recurring conflicts (17, 20). Hence the need to promote the leadership necessary to achieve greater resilience of the health system (16). Very often, academic training programs for health workers do not include modules on leadership (21, 22). It is the same in DRC and little is known about leadership development in the Congolese health system (23). A few reports from the Ministry of Health mention a leadership training course focusing on the four functions (scan, focus, align and inspire) organized for the chief medical officers of health districts and Page 4/22 some Ministry of Health executives by Management Science for Health (MSH) more than ten years ago, without a clear follow-up program (24, 25). To date, there is no information on the proportion of managers who have completed this training and whether they are still working. In this study, we analyze the state of leadership at the health district level in South Kivu, Eastern DRC. some Ministry of Health executives by Management Science for Health (MSH) more than ten years ago, without a clear follow-up program (24, 25). To date, there is no information on the proportion of managers who have completed this training and whether they are still working. In this study, we analyze the state of leadership at the health district level in South Kivu, Eastern DRC. Selection of health zones Eight health zones were selected based on geographical and security accessibility. We targeted health zones benefiting from the support of a health system strengthening program funded by an international non-governmental organization, thus ensuring that all eight zones have at least a minimum level of functioning. International organizations are key partners in the survival of the Congolese health system in this protracted crisis environment. They are intended to provide collaborative support to the system, Page 5/22 integrating their interventions within the country's contextual priorities (28). Our study’s HZs are spread over five of the height territories that constitute the province, thus covering the province's different geographical areas: (i) Minova HZ, on the northern axis of the province (Kalehe Territory), (ii) 3 HZs (Kaziba, Mubumbano, Nyangezi) for the territory of Walungu located on the Central axis, (iii) Nyantede HZ for the territory of Kabare which forms a belt around the city of Bukavu, (iv) Mwana HZ for the territory of Mwenga located on the western axis of the province and (v) 2 HZs (Ruzizi and Uvira) for the territory of Uvira located on the southern axis. Study type We performed a qualitative phenomenological study to describe the opinions, perceptions, and attitudes of participants regarding leadership in their health zones. These participants were key leaders of the health zones, gathered in the Health Zone Management Team (HZMT): managers at the Health Zone General Referral Hospital and the Health Zone Central Office, and representatives of the local community involved in the Health Development Committee of the zone. Conceptual Approach to Leadership Leadership is a concept that still varies greatly among experts. Thus, multiple theories have been described, drawing on one or other of its underlying dimensions (37). For this study, we built our thematic framework inspired from the Leadership Framework conceptual approach to leadership of the United Kingdom’s National Health Service’s Leadership Academy (38, 39). We developed six themes, four of which derive from the definition of the seven constitutive dimensions of the NHS’s Leadership Framework related to the managerial functions recognized in a functional HZMT (Theme 1 to Theme 4) (Table 1): Page 6/22 Table 1 Leadership thematic framework deducted from the NHS’s Leadership Framework NHS’s Leadership Framework’s Leadership Dimensions Study deducted themes 1) Demonstrating personal qualities 1) Perspective about Leadership 2) Working with others 3) Creating the vision 2) Internal collaboration within the HZMTs 3) Collaboration between the HZMTs and the Technical and Financial Partners (TFPs) 4) Managing services 5) Improving services 6) Setting direction 7) Delivering the strategy 4) Management and organization of the HZs   5) Perception of the state of Leadership in the HZs 6) Leadership Strengthening Needs Data Collection: Table 1 In-depth interviews and non-participatory observations were used to collect data (Table 2). The data were collected by senior researchers from the Ecole Régionale de Santé Publique school of public health of the Université Catholique de Bukavu, all of whom have extensive experience in qualitative data collection. As the study took place while the barrier measures against the Covid-19 pandemic were still in effect, these were respected throughout the data collection. Interviews were conducted in French and interviewers and participants were all fluent in that language. The data collection tools were pre-tested on a small scale on a population estimated similar to the one targeted by the study. An interview guide exploring all six themes guided the individual discussions. Respondents matching the profiles were approached at their place of work, and the interview took place on the spot if the respondent gave consent and was available. Data collectors conducted an initial debriefing after each interview. The principle of saturation thus determined the number of interviews conducted in all eight HZs (Table 2). Structured non-participatory observations of activities that could provide an appreciation of leadership practices and attitudes among managers were conducted whenever possible. Conceptual Approach to Leadership The observations were of two types: observation of the managers in their work environment (clinical room rounds, team work sessions, supervisions) and observation of a routine work meeting of the members of the HZMT. The observation themes of interest were the technical settings of organizing the targeted activities, and the types of interactions during these activities. As attributes of the leadership dimensions "organization of work" and "communication" (39), these themes contributed to exploring two of the six themes of our thematic framework: Internal collaboration within the HZMT, and Management and organization of the HZ. The targeted activities were observed whenever they coincided with the interviewers' visit. The participants were not prepared beforehand about the observations. Their informed consent was obtained just before the onset of each observation. The average interview time was 45 minutes. The average length of a routine meeting observation was 1.5 hours, and that of observation of HZMT in their workplace was 8 hours. The average interview time was 45 minutes. The average length of a routine meeting observation was 1.5 hours, and that of observation of HZMT in their workplace was 8 hours. Page 7/22 Table 2 Summary of types of information collected. Collection method Profile Total Observations Observation of a routine work meeting of the HZMT Observation of managers in their work environment   05 06 11 Individual interviews CMO MD-GRH AM-HZCO HDCM MSC SN   03 07 02 09 01 03 25 CMO: Chief Medical Officer of the HZ; MD-GRH: Medical Director of the General Referral Hospital; AM- HZCO: Administrative Manager of the HZ Central Office; HDCM: member of Health Development Committee of the HZ; MCS: Medical Staff Chief of the GRH; SN: Supervising Nurse of the HZ. D t A l i Data Analysis: Interviews were transcribed into Word documents. We performed a thematic analysis (40) with deductive and inductive approaches. The six themes initially established allowed for initial coding of the data. Then, within each theme, an inductive in vivo analysis identified various emerging sub-themes. A triangulation between the information from the interviews and that from the observations made it possible to describe the state of leadership in the zones, as perceived and experienced by the HZMT. For the sake of anonymity, and to avoid any possibility of linking the identity of a respondent to a health zone, data were analyzed approaching all the height health zones as a whole. Ethical considerations: The research protocol was submitted to and validated by the ethics committee of the Université Catholique de Bukavu under the reference UCB/CIES/NC/019/2021. Informed consent was obtained from each participant prior to any interview or observation. Data were collected and analyzed in complete confidentiality. All methods were carried out in accordance with relevant guidelines and regulations. In analyzing this theme, two sub-themes emerged: In analyzing this theme, two sub-themes emerged: Governance: Respondents consider a leader as someone capable of effectively organizing resources to meet the community’ needs. This leader must furthermore have a good grasp of public health standards and be able to hold his/her institution accountable to such standards. P-4: "A leader is a person who is trained in the health system and is able to organize or lead the health zone to find solutions to identified problems with the least amount of cost..." P-10: "...In the health system, (leadership) is how to organize things as it should be, the need to meet the expectations or needs of the community very well and needs of the health system." P-16: "...I think leadership is a team that mentors, that ensures that public health is really respected and effective at the health zone level..." Vision/positive influence: Respondents also mentioned that a leader with a clear vision is one who able to meet the expectations of the community. A leader inspires confidence in his collaborators and the local community. He /she can positively influence his/her team and steer them towards the realization of this common ideal of integral well-being. Page 8/22 P-12: "Leadership, a leader is someone who leads a team, who leads a team for a common ideal or vision." P-18: "When we talk about leadership, we mainly see someone who has a vision and who has the ability to practically draw everyone towards him to bring them into that vision..." 2. Internal Collaboration within the HZMTs There is some variability in internal collaboration among the members of the HZMTs, with notable differences between zones. Three sub-themes emerged from this theme: Positive collaboration: Some respondents appreciate the teamwork within their zones. The planning of activities is good, tasks are clearly distributed, and work is decentralized in term of execution. Financial management is transparent and honest, and personnel management is adequate. P-5: "...When we even do the planning of activities, we do it together to say that the health zone is functional..." P-9: "I appreciate the way they work internally, because normally we work in a decentralized way, each one does his job according to his attributions. I see that even in the absence of the zone's chief medical officer, we organize the routine meetings of the management team; this already shows that there is delegation of power at the HZ level..." Conflict and division: Other respondents reported that there is conflict and division in their zones. Particularly when occasional activities generate dividends, some leaders step aside to share them without everyone's participation. Some respondents report that these divisions have an impact on the governance of the zone, leading to irregularities in the implementation of HZ activities. P-15: "... I see that apparently Chief Medical Officers of health zones do not collaborate well with the subordinates. For the most part of the Chief Medical Officers of the zones that I have already met. Because they are the ones who make decisions themselves, especially regarding collaboration with partners. Sometimes they don't give feedback on all the contacts they make with partners outside the team...". P-21: "... We do meetings together. We do all activities together. But when it comes to money, the management team is divided: “oh no, these people are from the hospital, and us we are from the zone…” and that sometimes causes problems. There are segregations when it comes to “war booty” ..." Communication: Our observations of meetings in some areas indicate poor communication. In some HZs, observers noted meetings with an ambiance of a passive stillness where few people speak up, yet the resolutions made in the meetings were not contested. However, in other zones, communication in the meetings was smooth, with active participation of all, and collegiality in decision making. 3. Collaboration between the HZMTs and the Technical and Financial Partners (TFPs) Page 9/22 By technical and financial partners (TFPs), we mean international non-governmental organizations and other partner institutions from multilateral collaboration engaged with the national health sector. By technical and financial partners (TFPs), we mean international non-governmental organizations and other partner institutions from multilateral collaboration engaged with the national health sector. In this theme too, two different positions are noted among respondents, through the following two sub- themes: Communication and Planning: Some respondents are satisfied with the quality of communication between the TFPs and their zones. Communication is two-way and planning of activities is collaborative. Elsewhere, other respondents criticized the fact that the TFPs plan their activities without prior consultation with the HZMT, which is the reason for the failure of these activities given their non-contextualization to the needs of the zone. P-12: "The collaboration is good because in the team meetings we have reports (from partners) in relation to everything and (feedback) on their different advocacies." P-12: "The collaboration is good because in the team meetings we have reports (from partners) in relation to everything and (feedback) on their different advocacies." P-4: "As I told you we, i.e the management team, are in conflict with the partner (name of the partner) for not working well together because of selfish interests. People don't collaborate; one hurts the other. Partnership is not respected." P-4: "As I told you we, i.e the management team, are in conflict with the partner (name of the partner) for not working well together because of selfish interests. People don't collaborate; one hurts the other. Partnership is not respected." Financial management: Some respondents report a lack of transparency and traceability in the management of funds that partners grant to zones but still decide how these funds shall be used, sometimes resulting in situations of financial mismanagement for which the HZMT considers these partners directly responsible. P-5: "I think the problem between the HZMT and the technical and financial partners is a planning problem. We have our operational action plan in the zone, which is where the TFPs should join. 3. Collaboration between the HZMTs and the Technical and Financial Partners (TFPs) But the TFPs plan activities outside this operational plan..." P-15: "...it's true that there are always small concerns among certain financial partners who are not clear in their degree of collaboration with the zone, and therefore the transparency and traceability in relation to the funds or in relation to the support they bring to the health zone are not always well traced. They are not really very clear in the transparency, in the management..." 4. Management and Organization of the Health Zones Three sub-themes emerged from this theme: Health Zone management: The management is not optimal. The issue of lack of internal cohesion within the teams and abuse of power by superiors is still noted in some HZ. This again takes the form of opaque management of funds, especially bonuses from extraordinary activities such as vaccination campaigns and large-scale campaigns of distribution of insecticide-treated bed nets. This mismanagement of the zone is also reflected in the administrative management of human resources, and delays in the payment of staffs’ salaries. Page 10/22 Page 10/22 P-4: "The management is not good, there is mismanagement of the HZ, the HZ Central Office is very badly managed. The chief himself manages the money, he himself is the cashier, the administrative manager, the accountant... So, everything is done in his office." P-18: "...there are several agents who do not receive (their remuneration), agents who are not matriculated, there are also many agents whose files are not complete, there are agents who do not have proper assignments and for whom regularization has not yet taken place..." Organization of the zone: A delay in carrying out the activities of the operational action plan of HZs is reported at all levels (health center, referral hospital or HZ central office) and is mainly the result of financial mismanagement or a failure to organize the work plan. This disorganization of the zone is also found in the organization of different healthcare packages at the first and second lines of care: in some HZs, there is no longer a clear demarcation between structures supposed to offer first- and second-line care packages; some front-line facilities anarchically offer services that are exclusive to second-line facilities. The lack of communication is also translating into tensions between facilities’ co-managers over staff assignment and other managerial decisions. P-3: "...In relation to the management of activities, I can say that there are times when the supervision schedule is not followed, for example, at the referral hospital in (name of the zone) and at the level of the primary structures, the health centers. Therefore, there is a lack of respect of the supervision schedule that was established for the activities”. P-18: "... A health center that doesn't respect its minimum package of activities; it does what it wants. Imagine a health center that performs blood transfusions..." P-5: "Here we have a general referral hospital which has a private manager that always poses the problem of co-management with the Ministry of Health... They can bring in someone who he is a teacher or an agronomist, they appoint him as the hospital's administrative manager. There is really no collaboration in the assignment of officers who manage the hospital..." Collaboration between the zones and the Provincial Health Division (PHD): Some respondents reported close collaboration between the zones and the PHD. However, others found that the management of this collaboration was not optimal. Page 10/22 In particular, they criticized the abuse of power by the PHD in the form of interference in the management of HZ staff and the planning of HZ activities. In addition, the zone's expectations in terms of capacity-building support from the PHD are not always met. P-2: "...PHD doesn't support the HZs like they used to when we had a lot of supervisions and that helped us. But now they're once or twice a year and if we got those supervisions once a quarter it would be fine..." P-18: "...there are still some irregularities when it comes to some activities that are practically the responsibility of the HZ Chief Medical Officer or the management team but are carried out by PHD managers... Examples of the opening of private health centers that do not meet any standards..." Page 11/22 Page 11/22 In addition to the results of the interviews, observations of the managers in their work environment reported an overall respect for the start and end times of work. However, of the average 8 hours spent at work, less than half (an average of 3 hours) is spent actually working, with time at work coexisting with untimely comings and goings, unscheduled private visits, and frequent and sometimes long breaks outside of work on the phone or in conversation with colleagues on site. Unlike meetings where the agenda is set in advance, in none of the observations made was there any prior preparation of the daily work plan, nor were there any specific time slots set aside for various tasks. 5. Perception of the state of Leadership in the Health Zones. The perception of the leadership of the HZMT varies among respondents. Some see effective leadership, with initiatives to bring together different local leaders, while others point to difficulties in managing unmotivated and resistant staff. In addition, issues of lack of cohesion within the HZMT, and the vertical approach of Technical and Financial Partners in their support to zones, were raised as factors that weaken the quality of leadership within the HZMT. P-1: "In the public health activities, leadership is conducted: the HZMT plans a meeting where it will call on all local community leaders, as well as influential leaders, to take certain (measures) together in the (management of) certain problems in society..." P-6: "It is not easy for (the zone leaders) to impose themselves on unmotivated staff. Often there is resistance, and they often have difficulty managing staff. This problem has a negative impact on the implementation of activities, but they do their best to keep us within the standards. P-18: "... And so instead of the different partners aligning themselves with the planning of the health zone, we feel at times that it's the health zone that practically aligns itself with partners objectives and planning. And so, that's kind of the big constraint in practice.” P-18: "... And so instead of the different partners aligning themselves with the planning of the health zone, we feel at times that it's the health zone that practically aligns itself with partners objectives and planning. And so, that's kind of the big constraint in practice.” Discussion Aiming to contribute to the strengthening of the DRC's health system through the integrated leadership of the HZ (28, 29), this study describes the state of leadership as experienced by operational-level health managers in rural areas in a context of crisis. The rural health zones in crisis in the DRC are similar in their organization and in the challenges they face (17, 20, 27, 29, 41), we believe that the results from these eight study areas will largely reflect the situation of all other areas in the same context. These results could represent one of the worst cases of the state of the DRC health system, with the crisis context playing as an aggravating factor (17, 41) on the rural context, which is even worse than the urban context (42–44). However, for this specific point, further studies are needed to confirm this assumption. 6. Leadership Strengthening Needs This theme explored respondents' views on the need for leadership development in the area. The following three sub-themes emerged: Communication and planning: Respondents emphasized improving communication and collaboration between the members of the HZMT, the PHD and technical and financial partners. This would restore cohesion and promote planning adapted to the realities of the zone. P-5: "I would recommend that when there is an activity, that the team organizing at the provincial level take into account the planning at the grassroots level." P-5: "I would recommend that when there is an activity, that the team organizing at the provincial level take into account the planning at the grassroots level." Autonomy and decision-making power: Respondents expressed the need for more autonomy in management and decision-making at the health zone level. Autonomy and decision-making power: Respondents expressed the need for more autonomy in management and decision-making at the health zone level. Page 12/22 Page 12/22 P-18: "The first recommendation is to give more responsibility to the HZ Medical Officers. They know what they have to do, but at times the PHD want to treat them like little children and that's something that doesn't go down well..." Capacity building: Respondents expressed a need to strengthen the clinical and managerial capacities of the various local actors to better manage the health zone, improve its performance and the health status of the local community. Some respondents emphasized that better work planning and organization skills would contribute to the achievement of the health zones' operational objectives. They felt that having a daily work plan to help manage time on the job would help them perform better. P-9: "you know you can't punish someone for what they don't know, I can say that trainings are always important because if you are trained in leadership and human resource management it can always build capacity." P-20: "Yes, it's the training. Especially training in primary health care management could help the zone to know how to apply or revitalize and sustain leadership in the health zone, but also the collaboration of partners." Perspective of leadership Several key words in the definitions of leadership most found in the literature were used by most respondents, suggesting that they had already been exposed to at least one update on the issue of leadership. In fact, the Ministry of Health, as part of its capacity building for human resources, regularly programs training for health zone managers that addresses, among other things, leadership and management issues (28, 29). However, one might question the success of these trainings, considering that most respondents seemed to equate leadership with simple respect for procedures, and to define it as the exclusive prerogative of the most senior officials in the zone. In general, leadership remains a concept with a rather changing definition, depending on the field and the understanding: It can be confused with management, rigor, knowledge, the courage to undertake, or the charisma that one person can exert on one or several others (37, 45). It can also be merged with governance, the two elements being presented by the WHO as a single pillar of the health system (1). All these descriptions are scattered components of this Page 13/22 Page 13/22 concept, which is so dense that several authors have given it different definitions and theoretical frameworks depending on their applications (37, 45, 46). By hypothesizing that a manager is more likely to apply a leadership style that is consistent with his understanding of this concept (47), we perceive a leadership style that is more transactional than transformational in these HZs. Transformational leadership aims to inspiring others to willingly follow, and requires a high level of coordination, communication, and cooperation. Transactional leadership is primarily based on processes and control and requires a strict management structure: rewards and punishment are used as a motivating basis. This style is much more concerned with short-term planning and execution than with the long-term vision of an institution and its innovation (48–51). Several authors studying the perception of leadership in Sub-Saharan Africa have reported a preferential application of the transformational style (52–54). According to some authors, in a turbulent and unstable environment, such as the one in our study, the best adapted leadership style would be transformational, whereas a well- established environment, where processes and practices are well established and the context is stable, can thrive with a transactional leader (48, 49). Yet, we find that the HZs in our study tend to adopt a transactional leadership style. Management, organization, and leadership in the HZ Government underfunding favors the development of a private informal sector (34, 55). Thus, in their search for alternative financing, facilities may be led to inflate their activities to increase their income. This represents a potential danger for patients because, faced with difficult living conditions, health workers may be more concerned with supplementing their income than providing quality care (59). Our observations revealed a poor level of organization and management of working time as a whole. Untimely visits, the use of cell phones for non-professional purposes, as well as the lack of a precise daily work plan are all factors that have contributed to an effective working time that is far below the theoretical working time. The use of cell phones and social networks in the workplace is becoming more and more widespread, sometimes with negative effects on performance. It is in particular by increasing the mental load by various cognitive solicitations, and by distracting the employees from their tasks, as it has been described by some authors (60, 61). However, since new communication technologies have found a place of choice in daily work, particularly by facilitating communication, some authors recommend that employers supervise the use of social media at work rather than simply banning them (61, 62). They suggest better human resource management, including drawing a well-defined daily work plan and tracking its execution, as a way to avoid delays in deliverables related to time wasted on social media or unplanned visits. Management, organization, and leadership in the HZ The issue of financial management of the HZ regularly came up as a point of contention among our respondents. The DRC's health system is designed in such a way that the health zones have all the management bodies necessary to ensure the ideally optimal management, operation and delivery of primary health care with high decision-making autonomy (28). But, in the DRC, as in most low-income countries (55), the government's contribution to health care spending remains insufficient, barely reaching 20%. In addition to increasing household expenditures, which account for up to 40% of current health expenditures, this situation has an impact on human resources in the sector, which are poorly supported by the State (34, 35). Thus, any opportunity to earn a salary bonus during extraordinary activities could prove to be a godsend for these regularly underpaid agents. The tendency of leaders to manage these occasional "windfalls" in a small circle, creating suspicion and frustration, affects the quality of collaboration among members of the HZMT and undermines the cohesion of the group, as several of our respondents complained. In such already divided communities, it is unlikely that the principles of good leadership can be achieved, since from the outset it is no longer possible to unite the whole team behind a common vision, which is the main essence of a good leader (12, 48). These frustrations, often downplayed, can have devastating indirect consequences. This is the case in our health zones where weekly board meetings become irregular and where we have observed meetings with such unbalanced power dynamics that the session becomes more a formal briefing than a participative discussion. The literature provides information on how interpersonal tensions between health care personnel have had negative impacts on patient care and on the management of institutions (56, 57). Without these board meetings, which provide the best frame for the realization of the zone's vision, all planning is doomed to failure in the short or long term. Without dialogue, there is no leadership. An appropriate leadership can create an organizational culture of good governance, and balance the power dynamics, which will result in improved system performance and help achieve system goals (1, 58). Page 14/22 Our study found disorganization in the delivery of primary and secondary health care. Beyond the simple observation of the disorganization of the health system, it is interesting to try to understand the underlying reasons for it. Collaboration with TFPs Each health zone elaborates its Operational Action Plan yearly, in collaboration with the PHD and with the support of the TFPs. TFPs are recognized as key contributors to the functioning of the DRC's health system, given the context of low government funding. It is during this activity that the priority interventions of the zones are planned, taking into account the context of each health zone. Our interviews revealed interference between these plans and the interventions of the TFPs. The latter also appear to be the main financiers of several activities, given the limited intervention of the State in covering the health expenses of the zones (34). This dependence on external aid is often the Achilles heel of health systems in developing countries (63–65). The prescriptive and unaligned nature of international partner interventions in low- income country health programs contributes somewhat to the status quo in empowerment and leadership development within health systems operating in these contexts (64, 65). This verticalization of aid has been commented on by the DRC’s Ministry of Health, which noted that "The establishment of mid-level structures by the Ministry of Health's partner institutions creates several problems for the already fragile health sector. These problems include (i) increasing conflict with the structures they are supposed to support, (ii) increasing verticalization of the system as a result of the intervention of these support structures, including health centers and the community, and (iii) inefficiency, (iv) a gradual shift from the support role that sector partners are supposed to play to that of providers.” (28) Respondents also felt that they lacked autonomy in their decisions, being stifled by interference from the provincial level in operational level decision-making. This could indirectly indicate a non-delegative leadership style on the part of provincial officials, which can lead to frustration and demotivation of HZMT Page 15/22 Page 15/22 members. Indeed, authors have shown a positive association between the degree of task delegation and provider motivation (58, 66). Strengthening leadership We analyzed respondents' views on the need for leadership development in their areas across the 7 domains of the NHS’s Leadership Framework (39). Thus, across the three sub-themes identified by the analysis of the results, respondents expressed needs for strengthening personal qualities (knowledge, skills, and attitudes), teamwork, service management, direction setting, and strategy delivering. While admittedly the DRC's Ministry of Public Health, in collaboration with certain TFPs, regularly provides capacity-building training to all health system agents, these trainings remain ad hoc unstructured briefings that often do not reach all agents at the various levels of the health system in a systematic manner (24, 25). Further study is needed to document the real impact of these trainings on improving the performance and functionality of the health zones. In several English-speaking countries in the same context, there is While admittedly the DRC's Ministry of Public Health, in collaboration with certain TFPs, regularly provides capacity-building training to all health system agents, these trainings remain ad hoc unstructured briefings that often do not reach all agents at the various levels of the health system in a systematic manner (24, 25). Further study is needed to document the real impact of these trainings on improving the performance and functionality of the health zones. In several English-speaking countries in the same context, there is evidence of structured and systematic capacity building programs at all levels of the health system (13, 14, 23). Researchers who have documented leadership development programs implemented in sub-Saharan Africa have broadly identified several leadership development needs. These include conceptual leadership, capacity building and theoretical knowledge from curricula and health policy; service, emergency planning and management; communication and advocacy; as well as experiential learning through internships with local mentors or Northern institutions (23, 67, 68). Conclusions Although leadership is recognized a key element in strengthening the health sector, we observe in our study that some aspects of leadership are sorely lacking in the day-to-day work and management in the health districts of eastern DRC. Management teams have a low level of cohesion, communication, and organization of work. The heavy dependence on aid from external international partners and the vertical nature of their interventions somewhat stifle the expression of leadership by local managers. Despite a well-designed decentralized structure that manages to keep the local health system functioning in the context of a protracted crisis and limited government investment in health care, this leadership deficit further compounds the development challenges encountered by these health zones. There is a definite urge to strengthen leadership. However, insufficient government contribution to health sector funding drastically hinders empowerment efforts. Therefore, alongside supporting the personal development of its human resources, the health sector should advocate for increased government investment in public health spending. HZMT: Health Zone Management Team NHS: National Health Service (of the United Kingdom) PHD: Provincial Health Division TFP: Technical and Financial Partners WHO: World Health Organization HZMT: Health Zone Management Team NHS: National Health Service (of the United Kingdom) PHD: Provincial Health Division TFP: Technical and Financial Partners WHO: World Health Organization Competing interests Competing interests The authors declare that they have no financial and non-financial competing interests. Funding This research didn’t benefit from any funding. This research didn’t benefit from any funding. Declarations Ethics approval and consent to participate Availability of data and materials Availability of data and materials Availability of data and materials Data generated and analyzed during the current study are not publicly available due to confidentiality restrictions, but anonymized transcripts and observation grids are available from the corresponding author upon reasonable request. Consent for publication Not applicable  Availability of data and materials Not applicable Abbreviations DRC: Democratic Republic of Congo DRC: Democratic Republic of Congo HZ: Health Zone Page 16/22 Ethics approval and consent to participate The research protocol was submitted to and validated by the ethics committee of the Université Catholique de Bukavu under the reference UCB/CIES/NC/019/2021. Informed consent was obtained from each participant prior to any interview or observation. Data were collected and analyzed in complete confidentiality. All methods were carried out in accordance with relevant guidelines and regulations. Authors' contributions "R.B., G.B. and A.M. conceived the study design and data collection tools. M.M. supported design of methods. R.B. led the data collection and analyzis. C.C. assisted in data analysis. P.S. and C.C. assisted R.B. in manuscript preparation. G.B. and D.P. have substantively revised the manuscript. S.M., P.M., P.S., and M.M. provided critical feedback. All authors read and approved the final manuscript." Acknowledgements Page 17/22 References 1. World Health Organisation. Everybody’s business, Strengthening health system to improve health outcomes, WHO’s framework for action. 2007; 2. World Health Organization. Key Components of a Well-Functioning Health System. World Health Organization; 2010. 3. Organisation Mondiale de la Santé. Rapport mondial 2020 sur la capacité des pays à produire des données sanitaires [Internet]. 2021. 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Primary health care: report of the International Conference on primary health care, Alma-Ata, USSR, 6-12 September 1978. World Health Organization; 1978. 30. World Health Organization. Primary health care: report of the International Conference on primary health care, Alma-Ata, USSR, 6-12 September 1978. World Health Organization; 1978. 31. World Health Organization. Report of the Global conference on primary health care: from Alma-Ata towards universal health coverage and the Sustainable Development Goals. World Health Organization; 2019. 31. World Health Organization. Report of the Global conference on primary health care: from Alma-Ata towards universal health coverage and the Sustainable Development Goals. World Health Organization; 2019. 32. Porignon D, Porignon D, Mugisho Soron‘Gane E, Elongo Lokombe T, Katulanya Isu D, and Van Lerberghe W. How robust are district health systems? Coping with crisis and disasters in Rutshuru, Democratic Republic of Congo. Trop Med Int Health. 1998;3(7):559–65. 32. Porignon D, Porignon D, Mugisho Soron‘Gane E, Elongo Lokombe T, Katulanya Isu D, and Van Lerberghe W. How robust are district health systems? Coping with crisis and disasters in Rutshuru, Democratic Republic of Congo. Trop Med Int Health. 1998;3(7):559–65. 33. Rajan D, Kalambay H, Mossoko M, Kwete D, Bulakali J, Lokonga JP, et al. References Health service planning contributes to policy dialogue around strengthening district health systems: an example from DR Congo 2008-2013. BMC Health Serv Res. 2014 Oct 31;14(1):522. 34. Ministère de la Santé Publique de la République Démocratique du Congo. Rapport sur les comptes de la santé 2020. 2021. 35. World Health Organization. Improving health system efficiency: Democratic Republic of the Congo: improving aid coordination in the health sector. World Health Organization; 2015. 36. Stearns J, Vogel C. The Landscape of Armed Groups in the Eastern Congo. Stearns Jason Vogel Christoph 2015 Landsc Armed Groups East Congo N Y Congo Res Group N Y Univ CIC [Internet]. 2015 Dec [cited 2022 Apr 7]; Available from: http://congoresearchgroup.org/essay-the-landscape-of-armed- groups-in-eastern-congo-2/ 37. Komives SR, Dugan JP, Owen JE, Slack C, Wagner W, Programs (NCLP) NC of L. The Handbook for Student Leadership Development. John Wiley & Sons; 2011. 448 p. 37. Komives SR, Dugan JP, Owen JE, Slack C, Wagner W, Programs (NCLP) NC of L. The Handbook for Student Leadership Development. John Wiley & Sons; 2011. 448 p. 38. Chapman ALN, Giri P. Learning to Lead: Tools for Self Assessment of Leadership Skills and Styles. In: Godbole P, Burke D, Aylott J, editors. Why Hospitals Fail [Internet]. Cham: Springer International Publishing; 2017 [cited 2022 Apr 8]. p. 137–48. Available from: http://link.springer.com/10.1007/978- 3-319-56224-7_14 38. Chapman ALN, Giri P. Learning to Lead: Tools for Self Assessment of Leadership Skills and Styles. In: Godbole P, Burke D, Aylott J, editors. Why Hospitals Fail [Internet]. Cham: Springer International Publishing; 2017 [cited 2022 Apr 8]. p. 137–48. Available from: http://link.springer.com/10.1007/978- 3-319-56224-7_14 39. NHS Institute for Innovation and Improvement. Leadership Framework [Internet]. NHS Institute for Innovation and Improvement, Coventry House, University of Warwick Campus, Coventry, CV4 7AL.; 2011 [cited 2023 Apr 18]. Available from: https://www.leadershipacademy.nhs.uk/wp- content/uploads/2012/11/NHSLeadership-Framework-LeadershipFramework.pdf 39. NHS Institute for Innovation and Improvement. Leadership Framework [Internet]. NHS Institute for Innovation and Improvement, Coventry House, University of Warwick Campus, Coventry, CV4 7AL.; 2011 [cited 2023 Apr 18]. Available from: https://www.leadershipacademy.nhs.uk/wp- content/uploads/2012/11/NHSLeadership-Framework-LeadershipFramework.pdf Page 20/22 40. Clarke V, Braun V, Hayfield N. Thematic analysis. Qual Psychol Pract Guide Res Methods. 2015;3:222– 48. 41. Malembaka EB, Altare C, Bigirinama RN, Bisimwa G, Banywesize R, Tabbal N, et al. The use of health facility data to assess the effects of armed conflicts on maternal and child health: experience from the Kivu, DR Congo. BMC Health Serv Res. 2021 Sep 13;21(1):195. 41. References Malembaka EB, Altare C, Bigirinama RN, Bisimwa G, Banywesize R, Tabbal N, et al. The use of health facility data to assess the effects of armed conflicts on maternal and child health: experience from the Kivu, DR Congo. BMC Health Serv Res. 2021 Sep 13;21(1):195. 42. Chenge F. De la nécessité d’adapter le modèle de district sanitaire au contexte urbain: exemple de la ville de Lubumbashi en RD Congo. Antwerp: ITGPress; 2013. 132 p. ([SHSOP]). 42. Chenge F. De la nécessité d’adapter le modèle de district sanitaire au contexte urbain: exemple de la ville de Lubumbashi en RD Congo. Antwerp: ITGPress; 2013. 132 p. ([SHSOP]). 43. Fraze TK, Lewis VA, Wood A, Newton H, Colla CH. Configuration and Delivery of Primary Care in Rural and Urban Settings. J Gen Intern Med. 2022 Sep;37(12):3045–53. 43. Fraze TK, Lewis VA, Wood A, Newton H, Colla CH. Configuration and Delivery of Primary Care in Rural and Urban Settings. J Gen Intern Med. 2022 Sep;37(12):3045–53. 44. Didier CK, Criel B. Investir dans les Equipes-cadres des Zones de Santé : une priorité conditionnelle pour le renforcement du système de santé. CCSC [Internet]. 2020;(8). Available from: https://www.ccsc-rdc.net/doc/ccsc_note_de_politique_08_web.pdf 45. Winston BE, Patterson K. An integrative definition of leadership. Int J Leadersh Stud. 2006 Jan 1;1:6– 66. 45. Winston BE, Patterson K. An integrative definition of leadership. Int J Leadersh Stud. 2006 Jan 1;1:6– 66. 46. Vecchio RP. Leadership: Understanding the Dynamics of Power and Influence in Organizations, Second Edition. University of Notre Dame Pess; 2007. 565 p. 47. Aarons GA. Transformational and transactional leadership: Association with attitudes toward evidence-based practice. Psychiatr Serv. 2006;57(8):1162–9. 48. Burns JM. Leadership. Open Road Media; 2012. 48. Burns JM. Leadership. Open Road Media; 2012. 49. McCall Jr. MW. Leadership and performance beyond expectations, by Bernard M. Bass. New York: The Free Press, 1985, 191 pp. Hum Resour Manage. 1986;25(3):481–4. 50. Bass BM, Avolio BJ. Transformational leadership and organizational culture. Public Adm Q. 1993;112–21. 51. Odumeru JA, Ogbonna IG. Transformational vs. transactional leadership theories: Evidence in literature. Int Rev Manag Bus Res. 2013;2(2):355. Page 21/22 athole T, Lembani M, Jackson D, Zarowsky C, Bijlmakers L, Sanders D. Leadership and the unctioning of maternal health services in two rural district hospitals in South Africa. Health Policy an. 2018 Jul 1;33(suppl_2):ii5–15. urry L, Taylor L, Chen PGC, Bradley E. Experiences of leadership in health care in sub-Saharan Africa. um Resour Health. 2012 Sep 13;10(1):33. References usinguzi C, Namale L, Rutebemberwa E, Dahal A, Nahirya-Ntege P, Kekitiinwa A. The relationship etween leadership style and health worker motivation, job satisfaction and teamwork in Uganda. J ealthc Leadersh. 2018 Dec 31;10:21–32. ills A. Health Care Systems in Low- and Middle-Income Countries. N Engl J Med. 2014 Feb 370(6):552–7. m S, Bochatay N, Relyea-Chew A, Buttrick E, Amdahl C, Kim L, et al. Individual, interpersonal, and rganisational factors of healthcare conflict: A scoping review. J Interprof Care. 2017 May 31(3):282–90. 52. Mathole T, Lembani M, Jackson D, Zarowsky C, Bijlmakers L, Sanders D. Leadership and the functioning of maternal health services in two rural district hospitals in South Africa. Health Policy Plan. 2018 Jul 1;33(suppl_2):ii5–15. 53. Curry L, Taylor L, Chen PGC, Bradley E. Experiences of leadership in health care in sub-Saharan Africa. Hum Resour Health. 2012 Sep 13;10(1):33. 54. Musinguzi C, Namale L, Rutebemberwa E, Dahal A, Nahirya-Ntege P, Kekitiinwa A. The relationship between leadership style and health worker motivation, job satisfaction and teamwork in Uganda. J Healthc Leadersh. 2018 Dec 31;10:21–32. 55. Mills A. Health Care Systems in Low- and Middle-Income Countries. N Engl J Med. 2014 Feb 6;370(6):552–7. 56. Kim S, Bochatay N, Relyea-Chew A, Buttrick E, Amdahl C, Kim L, et al. Individual, interpersonal, and organisational factors of healthcare conflict: A scoping review. J Interprof Care. 2017 May 4;31(3):282–90. Page 21/22 Page 21/22 57. Cullati S, Bochatay N, Maître F, Laroche T, Muller-Juge V, Blondon KS, et al. When Team Conflicts Threaten Quality of Care: A Study of Health Care Professionals’ Experiences and Perceptions. Mayo Clin Proc Innov Qual Outcomes. 2019 Mar 1;3(1):43–51. 57. Cullati S, Bochatay N, Maître F, Laroche T, Muller-Juge V, Blondon KS, et al. When Team Conflicts Threaten Quality of Care: A Study of Health Care Professionals’ Experiences and Perceptions. Mayo Clin Proc Innov Qual Outcomes. 2019 Mar 1;3(1):43–51. 58. Mosadeghrad AM, Ferdosi M. Leadership, Job Satisfaction and Organizational Commitment in Healthcare Sector: Proposing and Testing a Model. Mater Socio-Medica. 2013;25(2):121–6. 58. Mosadeghrad AM, Ferdosi M. Leadership, Job Satisfaction and Organizational Commitment in Healthcare Sector: Proposing and Testing a Model. Mater Socio-Medica. 2013;25(2):121–6. 59. Ferrinho P, Lerberghe W van. Providing health care under adverse conditions: health personnel performance & individual coping strategies [Internet]. Antwerp: ITG Press; 2000. 247 p. (Studies in health services organisation & policy). Available from: https://www.hrhresourcecenter.org/node/1405.html 59. Ferrinho P, Lerberghe W van. References Providing health care under adverse conditions: health personnel performance & individual coping strategies [Internet]. Antwerp: ITG Press; 2000. 247 p. (Studies in health services organisation & policy). Available from: https://www.hrhresourcecenter.org/node/1405.html 60. Zahmat Doost E, Zhang W. Mental workload variations during different cognitive office tasks with social media interruptions. Ergonomics. 2022 Jul 20;0(0):1–17. 60. Zahmat Doost E, Zhang W. Mental workload variations during different cognitive office tasks with social media interruptions. Ergonomics. 2022 Jul 20;0(0):1–17. 61. Wushe T, Shenje J. The relationship between social media usage in the workplace and employee productivity in the public sector : case study of government departments in Harare. SA J Hum Resour Manag. 2019 Jan;17(1):1–10. 61. Wushe T, Shenje J. The relationship between social media usage in the workplace and employee productivity in the public sector : case study of government departments in Harare. SA J Hum Resour Manag. 2019 Jan;17(1):1–10. 62. Tulu DT. Should online social Medias (OSMs) be banned at work? The impact of social Medias on employee productivity in Ambo University, a case study. Res Int Bus Finance. 2017 Dec 1;42:1096– 102. 62. Tulu DT. Should online social Medias (OSMs) be banned at work? The impact of social Medias on employee productivity in Ambo University, a case study. Res Int Bus Finance. 2017 Dec 1;42:1096– 102. 63. Ifeagwu SC, Yang JC, Parkes-Ratanshi R, Brayne C. Health financing for universal health coverage in Sub-Saharan Africa: a systematic review. Glob Health Res Policy. 2021 Dec;6(1):8. 64. Moss TJ, Pettersson Gelander G, van de Walle N. An Aid-Institutions Paradox? A Review Essay on Aid Dependency and State Building in Sub-Saharan Africa [Internet]. Rochester, NY; 2006 [cited 2023 Feb 23]. Available from: https://hdl.handle.net/1813/55015 65. Bräutigam D. Aid dependence and governance. Vol. 1. Almqvist & Wiksell International Stockholm; 2000. 66. Riisgaard H, Søndergaard J, Munch M, Le JV, Ledderer L, Pedersen LB, et al. Associations between degrees of task delegation and job satisfaction of general practitioners and their staff: a cross- sectional study. BMC Health Serv Res. 2017 Jan 17;17:44. 66. Riisgaard H, Søndergaard J, Munch M, Le JV, Ledderer L, Pedersen LB, et al. Associations between degrees of task delegation and job satisfaction of general practitioners and their staff: a cross- sectional study. BMC Health Serv Res. 2017 Jan 17;17:44. 67. Kimball AM, Harper D, Creamer K, Adeyemi A, Yates R, Lillywhite L, et al. Strengthening Public Health Leadership in Africa: An Innovative Fellowship Program. References Acad Med. 2019 Aug;94(8):1146. 67. Kimball AM, Harper D, Creamer K, Adeyemi A, Yates R, Lillywhite L, et al. Strengthening Public Health Leadership in Africa: An Innovative Fellowship Program. Acad Med. 2019 Aug;94(8):1146. 68. Evans D, Bolden R, Jarvis C, Mann R, Patterson M, Thompson E. How do you develop systems leadership in public health? Insights from a scoping study. Public Health. 2021 Jul 1;196:24–8. 68. Evans D, Bolden R, Jarvis C, Mann R, Patterson M, Thompson E. How do you develop systems leadership in public health? Insights from a scoping study. Public Health. 2021 Jul 1;196:24–8. Page 22/22
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Adaptation of the Mohr Volumetric Method to General Determinations of Chlorine.
˜The œjournal of industrial and engineering chemistry/Journal of industrial and engineering chemistry
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Aug., 1919 T H E J O U R N A L OF I N D U S T R I A L ADAPTATION OF THE MOHR VOLUMETRIC METHOD TO GENERAL DETERMlNATIONS OF CHLORINE A N D ENGINEERING C H E M I S T R Y Mohr titration must provide for the bonates and phosphates, calcium acet Two ignitions with- organic materials have not failed in our work to give clear and colorless solutions. Fair examples of the results obtained in the above procedure are reported in the table. Votocek4 recently reported a method in which the chlorides are titrated in about 2 5 0 cc. of slightly acid solution with mercuric nitrate solution using 0.06 g. of sodizm nitroprusside crystals as the indicator. In this method nitrites and sulfites interfere. The well-known method of Mohr in which alkaline or alkaline-earth chlorides react with silver nitrate in the presence of a few drops of potassium chromate solution as indicator is as simple, direct. and fully as accurate as the method of Votocek, provided the proper conditions for the titration are as easily attained. The conditions necessary for an accurate titration appear numerous and exacting because (I) the solu- tion must be neutral, (2) no carbonates or phosphates may be present since the silver salts of these acids are less solable than the red silver chromate indicator and would therefore be titrated as well as the chlo- rides, and (3) the solution of the chlorides must have &' proper concentration to produce the most definite color change. Calculated Weight Weight of Error of Chlorine or Chlorine Found Difference ~ ~ ~ ~ * ~ / K ' ~ I H C 1 1 . . . . . . , . . . . . . 0.0472 0.0469 -0.0003 Feces No 19 2 g.. . . . . . . . . . . . . 0.0037 0.0035 -0.0002 0.0048 -0,0003 0.0049 * 0.0000 0.0022 +0.0002 0.0063 +0.0002 0,0015 -0.0003 Feces No: 23' 2 g.. . . . . . . . . . . . . . 0.0051 Alfalfa Hay No. 2, 3 g.. . . . . . . . . . 0.0061 0.0018 Feces No. 27' 2 g.. . . . . . . . . . . . . . 0.0049 Mixed Grain: No. 1 , 3 g.. . . . . . . . 0.0020 Mixed Grain No. 5, 3 g . , . , . . , . . . Aug., 1919 T H E J O U R N A L OF I N D U S T R I A L ADAPTATION OF THE MOHR VOLUMETRIC METHOD TO GENERAL DETERMlNATIONS OF CHLORINE A N D ENGINEERING C H E M I S T R Y Mohr titration must provide for the bonates and phosphates, calcium acet Aug., 1919 755 Mohr titration must provide for the removal of car- bonates and phosphates, calcium acetate solution was substituted for the solution of sodium carbonate and ferric acetate solution was subsequently added to the ignited residue. Mohr titration must provide for the removal of car- bonates and phosphates, calcium acetate solution was substituted for the solution of sodium carbonate and ferric acetate solution was subsequently added to the ignited residue. By LESTER YODER Received April 1 1 , 1919 By LESTER YODER Received April 1 1 , 1919 By the proper preliminary preparation of the chloride solutions many determinations of chlorine as usually carried out may be simplified and shortened by the use of Mohr's volumetric method. Other volumetric methods are less satisfactory as the fol- lowing brief r&sum& will show: g The following procedure gave the best results: To the sample is added 5 cc. of a 30 per cent solution of calcium acetate with sufficient distilled water to thoroughly saturate the material. The mixture is evaporated to dryness at 120' C. and ignited at a temperature not over 450° C. The cooled residue is thoroughly moistened with a few cubic centimeters of a IO per cent solution of ferric acetate, and again evaporated to dryness and ignited below 450' C. The residue is triturated with hot water, filtered, and washed until free from chlorides. The filtrate is evaporated to dryness or nearly to dryness and taken up with just sufficient hot water to insure complete solution of the chlorides, when cooled. After the addition of z or 3 drops of potassium chromate, the solution is titrated with 0.05 N silver nitrate. The original Volhard method has been modified by Drechsel,' Rothmund and Burgstaller,2 and Alefeld,3 to a short and accurate process. Excess of standard- ized silver nitrate solution is added to the chloride solution and the excess titrated with standardized thiocyanate. The precipitate of silver chloride must be rendered either more insoluble by flocculation with heat or reagents or filtered from the excess of silver nitrate for the titration with the thiocyanate. The calcium acetate fixes free chlorine and during the extraction of the ignited residue precipitates car- bonates and neutralizes the filtrate for the titration. The ferric acetate precipitates the phosphates and is itself converted into the insoluble oxide and also re- moved by the one filtration. 1 Z . anal. Chem., 16 (1877), 351. 2 2. anorg. Chem., 63 (1909), 330. * Z . anal. Chem., 48 (1909), 79. ' Chem.-Ztg., 4'2 (1918), 257-60. Since the modifications necessary for the use of the Aug., 1919 T H E J O U R N A L OF I N D U S T R I A L ADAPTATION OF THE MOHR VOLUMETRIC METHOD TO GENERAL DETERMlNATIONS OF CHLORINE A N D ENGINEERING C H E M I S T R Y Mohr titration must provide for the bonates and phosphates, calcium acet The object of the work herein presented was to develop and test modifications of procedure to meet these conditions so that the Mohr method would be applicable to rapid determinations of chlorine in various materials and particularly in organic products con- taining small amounts of the element. The modified method was applied to two solutions, one containing known amounts of free hydrochloric acid and its potassium salt, and another containing in addition added soluble phosphate. These were evapo- rated and ignited twice and subjected to a temper- ature of 4joo C. in one of the ignitions. The results show no loss of chlorine and only a negligible difference from the calculated weight of chlorine in the samples. Determinations of chlorine were also made in different kinds of cow feces and mixed grain and in alfalfa hay. The results differ only slightly from those of deter- minations made gravimetrically and are well within the limits of experimental error although the percentage error in the weights of chlorine found is large by reason of the low chlorine content of the materials. With the procedure outlined and from the results In the preparation of a titratable solution of the material in which chlorine is to be determined the sample must be ignited (in the case of organic products, at a low heat), and provision made for the fixation of free chlorine. An excess of sodium carbonate is usually added with the result that the sodium salts fuse and thereby prevent even after repeated ignitions, the complete oxidation of the carbonaceous matter which will pass through the filter in the subsequent filtration. A large amount of carbonates will also be present in the solution and the removal of any excess of phos- phates IS not assured. With the procedure outlined and from the results obtained by its use it seems that the Mohr direct titration method could be used for determinations of total chlorine in most instances. Since the modifications necessary for the use of the CHEMISTRY SECTION IOWA AGRICULTURAL EXPERIMENT STATION AMES, IOWA
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Individual Parental Leave for Fathers: Promoting Gender Equality in Norway
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Individual Parental Leave for Fathers: Promoting Gender Equality in Norway Elin Kvande E. Kvande (*) Department of Sociology and Political Science, Norwegian University of Science and Technology, Trondheim, Norway e-mail: elin.kvande@ntnu.no © The Author(s) 2022 M. Grau Grau et al. (eds.), Engaged Fatherhood for Men, Families and Gender Equality, Contributions to Management Science, https://doi.org/10.1007/978-3-030-75645-1_8 1 Introduction How to increase fathers’ use of parental leave is a relevant question for countries that want to promote men’s involvement in childrearing and gender equality more broadly. As countries are searching for instruments that can effectively promote a greater involvement of fathers in care work, the Nordic parental leave experiences may be useful. The Nordic countries, Denmark, Finland, Iceland, Norway and Sweden, have followed similar trajectories of development, not exactly following the same timeline, but clearly inspired by each other. All of them have introduced special incentives for fathers to use leave after having experienced that simply offering shared parental leave was not enough to get fathers to use it. Norway was the first country to introduce a fathers’ quota in 1993, followed by Sweden 2 years later, Denmark in 1998 (until 2002 when it was discontinued) and Iceland in 2000. Finland had a bonus system providing fathers with 12 extra days if they used 12 days of the shared parental leave. This was changed to an individual, non-transferable right, a father’s quota in 2013. In comparative research on gender equality, the Nordic welfare states are analysed as including regulations that support both working mothers and fathers (Pascall 2012). Equality between men and women is encouraged through an indi- vidual earner-carer regime (Sainsbury 1999). Important policy measures in this regime include publicly funded parental leave schemes, universal, high quality daycare, and access to reduced work hours. These are the same social arrangements 153 154 E. Kvande as Gornick and Meyers (2009) pinpoint as important in order to create a dual-earner/ dual-caregiver society. A comprehensive research literature on parental leave has evolved during the last 20 years. In fact, the study of parental leave is in the forefront of comparative social policy research focusing on gender equality (Ray et al. 2010). This strong interest in parental leave policies must be understood on the basis of these policies having the potential to change women’s position in employment and engaging men in caregiv- ing. Parental leave policy rights and designs vary substantially across countries (Blum et al. 2018) and the effect of the different leave systems on gender equality is also debated (Morgan 2008; Moss and Deven 1999; Moss et al. 2019). 1 Introduction In their analysis of what is needed to achieve “strong gender equality” in family and working life, Brighouse and Wright (2008) distinguish between three types of policies: (1) equality-impeding policies (e.g., unpaid caregiving leaves), (2) equality- enabling policies (e.g., paid caregiving leaves given to families), and (3) equality- promoting policies (e.g., paid caregiving leaves given to individuals rather than families). According to them, shared parental leave granted to the family enables parents to adopt egalitarian strategies, but do not represent strong incentives for fathers to use the leave rights. Leave policies that promote equality are exemplified by paid leave granted to individual parents, which lapses if it is not used. Brighouse and Wright find that this type of leave is necessary for breaking down the cultural barriers to gender equality in family and working life. Using this as a point of departure, this paper will describe the design elements of the Norwegian parental leave system for fathers and examine how it works as a regulatory measure to promote equality in care work. The paper will thus address the request put forward by Ray et al. (2010), in which they point out that surprisingly little research has been carried out that links the design of leave policies to their outcomes. There are especially few empirical studies assessing which parental leave schemes are gender egalitarian by design (Bartel et al. 2018; Dearing 2016), and this has left a gap in cross-national literature on leave policies. 2 Designing Individualized Parental Leave for Fathers Research on social policy in European welfare states has increasingly focused on the norm of individualization, thus indicating a social policy that treats women and men as individual workers (Lewis 2015). Similarly Daly (2011) suggests applying the concept of “individualization processes” in order to capture change in family policies which implies a shift away from policy assumptions based on the male breadwinner/female carer model and, instead, expecting all adults to be both bread- winners and carers. Individualistic policy designs, however, do not necessarily include gender equality (Ray et al. 2010). Therefore, how social policies relate to this parameter dictates whether they are classified as supporting an individualistic or familistic model according to Daly (2011). 155 Individual Parental Leave for Fathers: Promoting Gender Equality in Norway Research has documented that to give parental leave rights to individuals, rather than to families, is more effective when it comes to getting fathers to take leave (Duvander and Lammi-Taskula 2012; Haas and Rostgaard 2011; Eydal and Gíslason 2013). In their analyses of institutions that support gender equality in parenthood and employment, Gornick and Meyers (2009) point to the importance of individualized parental leave, as well as the principle of non-transferability, as in the fathers’ quota. They suggest a period of 6 months leave to each parent, which cannot be transferred to the other parent. This is also what was suggested in a white paper produced by an expert committee for the Norwegian government in 2017 (NOU 2017). The international literature on specific policy provisions for parental leave is expanding (McKay and Doucet 2010), particularly concerning fathers. Within research based on Nordic experiences, there is a consensus that parental leave rights given to individuals, rather than to families, are most likely to get fathers to take leave (Rostgaard 2002; Duvander and Lammi-Taskula 2012; Haas and Rostgaard 2011; Eydal et al. 2015). The father’s quota in Nordic countries has been successful in involving fathers in taking care of their young babies (Haas and Rostgaard 2011; Brandth and Kvande 1998, 2018). These results are also found internationally (Moss and Kamerman 2009; Gornick and Meyers 2009; Miller 2013; Harvey and Tremblay 2019). Documented findings from a number of countries have shown that the shared parental leave (and thus optional for fathers) is mostly used by mothers (O’Brien and Wall 2017; Ray et al. 2010; Fougner 2012; Gíslason and Eydal 2013). 3 The Norwegian Parental Leave System for Fathers In 1978 the leave rights in Norway were changed so that most of the leave could be shared between the parents, moving away from the idea of maternity leave as a special right only for women. By granting fathers the right to shared leave, legisla- tion signaled a new view of men’s responsibilities and participation in caregiving. In the years to come, fathers, however, rarely used shared parental leave so the policy did not promote more equal parenting. To advance that goal, an earmarked, non-transferable leave of 4 weeks for fathers was introduced in 1993. At the same time the total leave period was extended from 35 to 42 weeks with 100% wage compensation. Proponents argued that a quota would give a strong signal to parents as well as to employers that men as well as women are parents with obligations and rights as caregivers. Children’s need for their fathers was also emphasized in the debate. Since then the father’s quota has developed gradually, extended to 14 weeks and then reduced to 10 weeks in 2014 following the politics of the parties in power. Both mothers and fathers have individual, non-transferable leave rights in addi- tion to shared leave rights. Currently, mothers have an earmarked period of 13 weeks, of which 3 must be taken before the child’s birth. Beginning in 2014, 26 weeks are sharable between mothers and fathers. If the parents choose lower pay (80% of wages), the leave is extended by 10 weeks. The fathers’ quota is now 10 weeks. In addition to parental leave, fathers have 2 weeks of paternity leave to be taken after the birth of the child to assist the mother. There are no public records of the usage of paternity leave, as wage compensation is based on collective agreements and paid by employers. The fathers’ quota gives male employees the right and obligation to provide care during the child’s early years of life. The principal aim of this leave is to break away from the norm that men serve as breadwinners and women as caregivers even if they, too, are employed outside the home. The system is based on the principle that parents “earn” the right through participation in working life. To qualify for parental leave, both mothers and fathers have to be in the workforce for 6 of the last 10 months prior to the birth. 2 Designing Individualized Parental Leave for Fathers Fathers taking leave challenge the traditional gender norm that mothers are the primary caregivers of small children. This chapter explores fathers’ understandings and experiences with the father’s quota (i.e., the leave programs), which, according to Brighouse and Wright (2008), may promote equality. Studies of the Norwegian leave programme comparing the father’s quota to the more optional schemes of shared parental leave and cash allowances were conducted some years after the introduction of the father’s quota (Brandth and Kvande 2009) This research documented that mandatory leave for fathers made it easier for them to use the father’s quota to set boundaries against the demands of work, thus reserving uninterrupted father-child time. It was also pointed out that a statutory earmarking of the father’s quota lifts the decision of who should take leave from the family up to the institutional level, where it would apply to “all” fathers. The father’s quota became a pre-negotiated right for men also in terms of the workplace, and it was supposed to eliminate the need to negotiate individually with the employer over the use of the father’s quota. This chapter examines the impact of the expansion and maturation of the father’s quota. Using Brighouse and Wright’s conceptual framework the chapter explores how the Norwegian leave policies which are an individual right are experienced by the fathers in our latest study. E. Kvande 156 3 The Norwegian Parental Leave System for Fathers 4 Data and Method The analysis is based on a qualitative study in which 22 fathers who had taken parental leave were interviewed in 2012 and 2013. The interviews were carried out during the second year after the child’s birth. Thus, the fathers in the sample had rights to 10 or 12 weeks of individual leave and 27 or 26 weeks of shared leave if they chose 100% compensation. If they chose the 80% compensation option, the leave would have been prolonged accordingly. The fathers were recruited by contact with various workplaces and then snowballing. The interviewees had to have become fathers after the fathers’ quota was expanded to 10 weeks in 2009, as we were interested in their experiences of relatively long leaves. The length of the leave taken by the sample varied; most fathers had taken the father’s quota of 10 or 12 weeks, but 8 had also taken all or part of the shared parental leave. The research team endeavoured to find interviewees with varied social back- grounds. Half had higher education (masters level), while the other half either had a medium level education at the bachelor level (6) or no education beyond high school (5). The fathers had a wide range of occupations, including engineers, artisans, teachers, office workers, consultants, and administrative, healthcare, and technical staff. They worked in organizations of various sizes and composition. As Norwegian leave rights are employment based (i.e., accrued by the participa- tion of both parents in working life), all the fathers and most of their children’s mothers (except for three) were in paid employment prior to the birth of their child and had a right to parental leave. Half of the fathers were employed by private companies, but only one was self-employed, and one, a student, was temporarily employed. Except for this father, all worked full time. All the fathers lived together with the mother and their child, and the child who triggered the interview could be the father’s first, second, or third child. Most fathers were in their 30s, though they ranged between 27 and 43. Eight of the fathers (36%) had taken shared parental leave. Two of them had taken all the shared parental leave available, as the mothers were not eligible due either to having returned to work or school. The interviews were semi-structured and lasted between 1 and 2 h. 3 The Norwegian Parental Leave System for Fathers If the mother is not eligible, the father loses his right to the fathers’ quota but not to the shared leave if the mother returns to studies or takes on employment. This type of eligibility encourages both parents to combine work and family obligations as it is built on a model in which both mothers and fathers are employed. Since its introduction, the fathers’ quota has been widely used, and more than 90% of eligible fathers use all or part of this leave (Kitterød et al. 2017). Mothers take most of the shared leave days, and, for most couples, mothers’ leave is considerably longer than fathers’. 157 Individual Parental Leave for Fathers: Promoting Gender Equality in Norway 5.1 The Fathers’ Quota as a Norm The fathers’ quota enjoys a high degree of support among fathers in Norway (Hamre 2017), and studies on fathers’ quota usage have pointed out that it has become a norm among men in Norway to take leave when they have become fathers (Halrynjo and Kitterød 2016; Naz 2010). Our findings also support this claim. “There was no doubt that I should take the fathers’ quota,” said Steinar, an engineer with two daughters. According to Ivar, “For fathers to have 12 weeks is quite natural in a way.. . . It has become incorporated.” Their viewpoints illustrate that the fathers’ quota is a matter of fact. Twenty-five years after it was introduced, taking leave seems to be taken for granted among fathers in Norway. That it is based in law, earmarked, and non-transferable identifies this leave with fathers and defines it as their right and ‘property.’ It is also interpreted as an obligation and seen as a signal from the welfare state that fathers are expected to engage in taking care of small children. “Society reacts if you don’t take it, right,” Harold said. Lars, an engineer, claimed that the quota “feels like something you ought to . . . that it’s something you should take, really.. . . It feels like there’s pressure on you to take it. That . . . if you want to be a good parent, or a good father, then you have to take the daddy leave.” Several fathers indicated that if they had not taken the fathers’ quota, they would have to explain themselves to others. Fathers’ leave-taking is supported by social norms of good fatherhood that these fathers seem to have incorporated into their identities. As the next section shows, fatherhood has also been incorporated into their practices as employees. 4 Data and Method The data was collected by a research team, in which the author participated. To preserve anonym- ity, the full name and contact details of the interviewees were not recorded, and fictitious names have been used. The fathers were mostly interviewed in their homes. The fathers’ understandings were based on their own experiences and what they observed with colleagues and friends. The recorded transcripts were examined to identify each father’s stories about their experiences at their respective workplaces. We also asked hypothetical questions about what would have happened if there were no father’s quota. The next stage was interpreting these themes in a dialogue with the literature. The findings are illustrated by quotations. E. Kvande E. Kvande 158 5.2 Employers’ Support of Fathers’ Caregiving Responsibilities Many of the fathers in the sample strongly felt that having a quota given to them as employees was an unconditional strength in relation to work, and that it would have been much more difficult to gain support from employers if it were not for their legal right to the fathers’ leave. “It makes your position stronger when the quota is based in law,” said Geir. Kristoffer and many others believed that if the father’s quota was not retained as a father-specific right, they would fail in their negotiations over leave with their employer. Since the fathers’ quota is statutory, employers have little leeway to adopt discriminatory practices. The fathers’ sense of entitlement becomes explicit when Steinar reflects on how he would have had to argue in his previous job as a consulting engineer with a small company. “It was very intense with a call on us to work 80 h a week and perform all we could with lots of pressure and bonuses. In this place, taking leave would have Individual Parental Leave for Fathers: Promoting Gender Equality in Norway 159 been frowned upon. But still, should you have to fight for your rights?” Moreover, the fathers’ leave is paid by the state rather than the employer. Comparing his right to the fathers’ quota with his right to paid holidays, Steiner said that if he did not take his “3 months ‘holiday’ with pay,” he would lose it. Entitlements to paid time off are acceptable in working life. To have to argue with his employer about his childcare responsibilities would not work as well, Steinar claimed. None of the fathers in the study reported that they had experienced any serious problems with their current employers when planning to use their entitlement (Brandth and Kvande 2019a, b). Indeed, men seem to be expected to take the fathers’ leave by their employers and colleagues. Harold, a schoolteacher, said: “It was all right, and it was expected! It would have been more of an issue if I hadn’t taken it. Public workplaces have to play by the rules.” For fathers, it seems inevitable that working life must adapt to the regulations of the welfare state. Christian, a senior advisor in the municipal administration, pointed out that even though the fathers’ quota might sometimes represent challenges for workplaces, organizations do adapt to this legislation. 5.2 Employers’ Support of Fathers’ Caregiving Responsibilities The fathers’ quota has existed for a quarter century, which means that men who have advanced to management positions in some organizations have taken fathers’ leave themselves. That experience influences what is considered fair and feasible. Tore, a doctor in a large hospital, described how his leave-taking was received by his director, a 60-year-old chief physician: “He is up to date on the father’s quota.. . . He has had young children himself. . . . And I am not the first father to be in this situation.” Steinar, too, explained that his bosses are fathers: “They are 54 and 62, and both were home with their children at a time when it was much less common than now. So, they pushed me, saying ‘Steinar, it is clear that you must stay home,’ and ‘Are you sure you won’t take a bit longer leave?’ They said so even if it was bad for the job.” Likewise, Sivert described his boss as very positive: “He understood me very well. I suppose he is 50 years, so he is very up to date.” His boss was eager to help him find out about the regulations concerning the father’s quota and the rest of the parental leave system. Sivert considered him a “modern” man who regarded fathers’ involvement with children as important. Another father interviewed, Hans, said: I think most employers today live in the modern world and understand that they must live up to that. This is how it is. They need employees who are happy with their job and have a good family life. Now, we see that both managers and middle managers in companies, 35 to 40 years old, experience the same tensions concerning career, childcare, parental leaves and work hours. I have a mate who is manager of marketing, only a few years older than me in a top job; he had four months daddy leave, so that says a lot. Fathers are more likely to take up family friendly working practices if they can “compare themselves with other fathers and realize that it is feasible to do so” (Lewis and Stumbitz 2017: 230). The fathers we interviewed reported that as leave takers they did not stand out in any way. 5.3 Empowered as Caregivers The fathers communicated an identity as competent caregivers and attributed this to their time on leave when they had gotten to know the child well. They thought that children benefit from close contact with fathers, and that fathers are significant caregivers for children. Erlend said: “It is quite unfair that only mothers are regarded as important for the children. Speaking as a man I think this is a new situation for gender equality.. . . I have been able to prove that I can be just as good a carer as the mother. I think it is super important! It increases men’s self- confidence and society’s confidence in men as caregivers.” “It is quite unfair that only mothers are regarded as important for the children. Speaking as a man I think this is a new situation for gender equality.. . . I have been able to prove that I can be just as good a carer as the mother. I think it is super important! It increases men’s self- confidence and society’s confidence in men as caregivers.” Regarding it as unfair that only mothers are given support as caregivers, these men see the fathers’ quota as remedying this injustice. They justify their entitlement to leave as based on their ability to care for their small children and think the fathers’ quota contributes to their being seen as needed and important caregiving parents. They feel entitled to both the joys and burdens of childcare, and they stress that the fathers’ quota represents an opportunity to develop an autonomous relationship with their children. “Being home on leave has in a way laid the foundation for the contact we [father and child] have today. A lot will happen later in life, but this is the basis,” Didrik said. The quota as a father-specific right simplifies negotiations with the mother. Sivert realized that this was the point of earmarking it: “This is why they designed it like that. If not, nothing would have come of it. Then the mother would have taken the whole leave.” He thought that to many people it is still not obvious that the father will choose to stay home with the child. 5.2 Employers’ Support of Fathers’ Caregiving Responsibilities Hans, a communications advisor in a transport company, told us that at his workplace “many of my male colleagues had a child at about the same time as me, which was great! We were about three or four who had kids within a 2- or 3-month span. In addition, many employees here have small 160 E. Kvande children.” The norms that are produced by these practices make it easy for fathers to take leave and for organizations to plan for it. Dahl et al. (2014), who studied the peer effect of father quota usage, found that fathers are even more likely to take the quota if their colleagues did. The effect was greatest if a manager at a higher level in the organization had taken the fathers’ leave. Many of the fathers confidently portrayed the quota as their leave. In so doing, they conveyed a sense of entitlement and beliefs about what is right and fair. Hobson and Morgan (2002: 14) hold that family friendly policies provide men with discur- sive resources with which they can make claims upon their employers. For instance, Ivar communicated that it was he who controlled how much and when he would work, and he was not afraid to insist on his priorities. 5.3 Empowered as Caregivers To avoid making parental leave only mothers’ leave, he said, it was important that things were not “made completely flexible.” Employed fathers view the fathers’ quota as an entitlement, a support from the welfare state for them to be active caregivers. There are strong moral obligations for fathers to take the father’s quota and for employers to accept it. This finding seems important in understanding the high use of the quota among fathers in Norway. 161 Individual Parental Leave for Fathers: Promoting Gender Equality in Norway 6 Practical Recommendations These findings illustrate that the design of the father’s quota as a statutory, earmarked, and non-transferrable right for fathers promotes the fathers’ use of leave and hence equality. The earmarking, and the fact that it cannot be transferred to the mother, renders it unnecessary for fathers to negotiate with the mother about this leave. The father’s quota is also an important bargaining chip in relation to the job. Even if fathers have stories about situations where the employers do not want the father to take leave, employers are most often described as positive towards the father’s leave, and the interviews include few personally experienced stories about employers impeding the fathers from taking leave. We interpret this as a sign that the father’s quota as a legal earmarked right may have contributed to making visible and promoting the fact that employed men are also fathers and “encumbered” with caregiving responsibilities as much as employed mothers. Thus, in order to promote gender equality, policy makers should choose paid parental leave given to individ- uals rather than to families. These policies help the equality processes in work organizations through normalizing that both female and male employees are parents. Much of the evidence indicates that if there were no earmarked and non-transferrable leave for the father that was based in law, reluctant fathers would not have taken any leave and mothers may have been unwilling to give up leave to share with them. There are ambivalent and hesitant fathers who would then choose differently. This also shows that leave for many fathers is not something that is fully in place as an accepted and taken-for-granted practice. These findings thus support other research on fathers’ use of leave which have shown that the design character- istics of father’s quota represents a strong incentive for greater involvement on the part of fathers. Considering these findings, it is interesting that the EU Commission in 2019 introduced a new package on work-life balance to ensure better leave provisions and care facilities for working parents in all EU member states. The existing EU Directives on maternity and parental leave are regarded as outdated as they have largely failed to improve gender equality, neither expanding women’s participation in the labour market, nor encouraging men to use leave provisions and take a greater share of caring responsibilities. Blum S, Koslowski A, Macht A, Moss P (2018) 14th annual international review of leave policies and research 2018. International network on leave policies & research. https://www. leavenetwork.org/annual-review-reports/archive-reviews/ B d h B K d E (1998) M li i d hild h i f f h i S i l R Bartel AP, Rossin-Slater M, Ruhm CJ, Stearns J, Waldfogel J (2018) Paid family leave, fathers’ leave-taking, and leave-sharing in dual-earner households. J Policy Anal Manage 37(1):10–37 Brandth B, Kvande E (1998) Masculinity and child care: the reconstruction of fathering. Sociol Rev 46(2):293–313 Bartel AP, Rossin-Slater M, Ruhm CJ, Stearns J, Waldfogel J (2018) Paid family leave, fathers’ leave-taking, and leave-sharing in dual-earner households. J Policy Anal Manage 37(1):10–37 Blum S, Koslowski A, Macht A, Moss P (2018) 14th annual international review of leave policies and research 2018. International network on leave policies & research. https://www. leavenetwork.org/annual-review-reports/archive-reviews/ Brandth B, Kvande E (1998) Masculinity and child care: the reconstruction of fathering. Sociol Rev 46(2):293–313 References Bartel AP, Rossin-Slater M, Ruhm CJ, Stearns J, Waldfogel J (2018) Paid family leave, fathers’ leave-taking, and leave-sharing in dual-earner households. J Policy Anal Manage 37(1):10–37 Blum S, Koslowski A, Macht A, Moss P (2018) 14th annual international review of leave policies and research 2018. International network on leave policies & research. https://www. leavenetwork.org/annual-review-reports/archive-reviews/ Brandth B, Kvande E (1998) Masculinity and child care: the reconstruction of fathering. Sociol Rev 46(2):293–313 162 E. Kvande Brandth B, Kvande E (2009) Gendered or gender neutral care policies for fathers? Ann Am Acad Polit Social Sci 624(1):177–189 Brandth B, Kvande E (2018) Masculinity and fathering alone. Men Masculinities 21(1):72–90 Brandth B, Kvande E (2019a) Fathers’ sense of entitlement to ear-marked and shared parental leave Sociol Rev 67(5):1154–1169 Brandth B, Kvande E (2019b) Workplace support of fathers’ parental leave use in Norway Community Work Fam 22:43–57 Brighouse H, Wright EO (2008) Strong gender egalitarianism. Polit Soc 36(3):360–372 Dahl GB, Løken KV, Mogstad M (2014) Peer effects in program participation. Am Econ Rev 104 (7):2049–2074 Daly M (2011) What adult worker model? A critical look at recent social policy reform in Europe from a gender and family perspective. Soc Polit 18(19):1–24 Dearing H (2016) Gender equality in the division of work: how to assess European leave policies regarding their compliance with an ideal leave model. J Eur Soc Policy 26(3):234–247 Dearing H (2016) Gender equality in the division of work: how to assess European leave policies di th i li ith id l l d l J E S P li 26(3) 234 247 regarding their compliance with an ideal leave model. J Eur Soc Policy 26(3):234–247 Duvander A-Z, Lammi-Taskula J (2012) Parental leave. In: Gíslason IV, Eydal GB (eds) Parental leave, childcare and gender equality in the Nordic countries. Nordic Council of Ministers, Copenhagen, pp 31–64 Eydal GB, Gíslason IV (2013) Tredelt permisjon og lang fedrekvote: Erfaringer fra Island. In: Brandth B, Kvande E (eds) Fedrekvoten og den farsvennlige velferdsstaten. 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On kernel-based estimation of conditional Kendall’s tau: finite-distance bounds and asymptotic behavior
Dependence Modeling
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cc-by
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Depend. Model. 2019; 7:292–321 Research Article Open Access Alexis Derumigny* and Jean-David Fermanian On kernel-based estimation of conditional Kendall’s tau: finite-distance bounds and asymptotic behavior https://doi.org/10.1515/demo-2019-0016 Received May 29, 2019; accepted August 31, 2019 Abstract: We study nonparametric estimators of conditional Kendall’s tau, a measure of concordance between two random variables given some covariates. We prove non-asymptotic pointwise and uniform bounds, that hold with high probabilities. We provide “direct proofs” of the consistency and the asymptotic law of conditional Kendall’s tau. A simulation study evaluates the numerical performance of such nonparametric estimators. An application to the dependence between energy consumption and temperature conditionally to calendar days is finally provided. Keywords: conditional dependence measures, kernel smoothing, conditional Kendall’s tau MSC: 62H20, 62G05, 62G08, 62G20 1 Introduction In the field of dependence modeling, it is common to work with dependence measures. Contrary to usual linear correlations, most of them have the advantage of being defined without any condition on moments, and of being invariant to changes in the underlying marginal distributions. Such summaries of information are very popular and can be explicitly written as functionals of the underlying copulas: Kendall’s tau, Spearman’s rho, Blomqvist’s coefficient... See Nelsen [30] for an introduction. In particular, for more than a century (Spearman (1904), Kendall (1938)), Kendall’s tau has become a popular dependence measure in [−1, 1]. It quantifies the positive or negative dependence between two random variables X1 and X2 . Denoting by C1,2 the unique underlying copula of (X1 , X2 ) that is assumed to be continuous, their Kendall’s tau can be directly defined as Z τ1,2 := 4 C1,2 (u1 , u2 ) C1,2 (du1 , du2 ) − 1 (1) [0,1]2   = IP (X1,1 − X2,1 )(X1,2 − X2,2 ) > 0 − IP (X1,1 − X2,1 )(X1,2 − X2,2 ) < 0 , where (X i,1 , X i,2 )i=1,2 are two independent versions of X := (X1 , X2 ). This measure is then interpreted as the probability of observing a concordant pair minus the probability of observing a discordant pair. See [22] for an historical perspective on Kendall’s tau. Its inference is discussed in many textbooks (see [18] or [24], e.g.). Its links with copulas and other dependence measures can be found in [30] or [20]. Similar dependence measures can be introduced in a conditional setup, when a p-dimensional covariate Z is available. When hundreds of papers refer to Kendall’s tau, only a few of them have considered conditional Kendall’s tau (as defined below) until now. The goal is now to model the dependence between the two *Corresponding Author: Alexis Derumigny: CREST-ENSAE and University of Twente, 5 Drienerlolaan, 7522 NB Enschede, Netherlands, E-mail: a.f.f.derumigny@utwente.nl. Jean-David Fermanian: CREST-ENSAE, 5, avenue Henry Le Chatelier, 91764 Palaiseau cedex, France, E-mail: jean-david.fermanian@ensae.fr. Open Access. © 2019 Alexis Derumigny and Jean-David Fermanian, published by De Gruyter. This work is licensed under the Creative Commons Attribution alone 4.0 License. On kernel-based estimation of conditional Kendall’s tau | 293 components X1 and X2 , given the vector of covariates Z. Logically, we can invoke the conditional copula¹ C1,2|Z=z of (X1 , X2 ) given Z = z for any point z ∈ Rp , and the corresponding conditional Kendall’s tau would be simply defined as Z τ1,2|Z=z := 4 C1,2|Z=z (u1 , u2 ) C1,2|Z=z (du1 , du2 ) − 1 [0,1]2   = IP (X1,1 − X2,1 )(X1,2 − X2,2 ) > 0 Z1 = Z2 = z − IP (X1,1 − X2,1 )(X1,2 − X2,2 ) < 0 Z1 = Z2 = z , where (X i,1 , X i,2 , Zi )i=1,2 are two independent versions of (X1 , X2 , Z). As above, this is the probability of observing a concordant pair minus the probability of observing a discordant pair, conditionally on Z1 and Z2 being both equal to z. Note that, as conditional copulas themselves, conditional Kendall’s taus are invariant w.r.t. increasing transformations of the conditional margins X1 and X2 , given Z. Of course, if Z is independent of (X1 , X2 ) then, for every z ∈ Rp , the conditional Kendall’s tau τ1,2|Z=z is equal to the (unconditional) Kendall’s tau τ1,2 . Conditional Kendall’s tau, and more generally conditional dependence measures, are of interest per se because they allow to summarize the evolution of the dependence between X1 and X2 , when the covariate Z is changing. Surprisingly, their nonparametric estimates have been introduced in the literature only a few years ago ([15],[40],[13]) and their properties have not yet been fully studied in depth. Indeed, until now and to the best of our knowledge, the theoretical properties of nonparametric conditional Kendall’s tau estimates have been obtained “in passing” in the literature, as a sub-product of the weak-convergence of conditional copula processes ([40]) or as intermediate quantities that will be “plugged-in” ([12]). Therefore, such properties have been stated under too demanding assumptions. In particular, some assumptions were related to the estimation of conditional margins, while this is not required because Kendall’s tau are based on ranks. In this paper, we directly study nonparametric estimates τ̂1,2|z without relying on the theory/inference of copulas. Therefore, we will state their main usual statistical properties: exponential bounds in probability, consistency, asymptotic normality. Our τ1,2|Z=z has not to be confused with the so-called “conditional Kendall’s tau” in the case of truncated data ([39], [28]), in the case of semi-competing risk models ([23], [19]), or for other partial information schemes ([6], [21], among others). Indeed, particularly in biostatistics or reliability, the inference of dependence models under truncation/censoring can be led by considering some types of conditional Kendall’s tau, given some algebraic relationships among the underlying random variables. This would induce conditioning by subsets. At the opposite, we will consider only pointwise conditioning events in this paper, under a nonparametric point-of-view. Nonetheless, such pointwise events can be found in the literature, but in some parametric or semi-parametric particular frameworks, as for the identifiability of frailty distributions in bivariate proportional models ([31], [27]). Other related papers are [3] or [25], that are dealing with extreme co-movements (bivariate extreme-value theory). There, the tail conditioning events of Kendall’s tau have probabilities that go to zero with the sample size. In Section 2, different kernel-based estimators of the conditional Kendall’s tau are discussed. Moreover, we propose a cross-validation criterion to select the associated bandwidth. In Section 3, numerous original theoretical properties of the latter estimators are proved: at first, finite distance exponential bounds in probability (pointwise and uniformly w.r.t. z); then, under an asymptotic point-of-view, pointwise and uniform consistency; and finally the asymptotic normality of conditional Kendall’s tau under unrestrictive assumptions (see below) and with an explicit limiting law. A short simulation study is provided in Section 4. Proofs are postponed into the appendix. 1 The conditional copula of X1 and X2 given Z = z can be defined almost surely as the unique copula of the conditional c.d.f. F X1 ,X2 |Z=z by Sklar’s theorem. It was introduced by Patton [33, 34]. 294 | Alexis Derumigny and Jean-David Fermanian 2 Definition of several kernel-based estimators of τ1,2|z Let (X i,1 , X i,2 , Zi ), i = 1, . . . , n be an i.i.d. sample distributed as (X1 , X2 , Z), and n ≥ 2. Assuming continuous underlying distributions, there are several equivalent ways of defining the conditional Kendall’s tau:  τ1,2|Z=z = 4 IP X1,1 > X2,1 , X1,2 > X2,2 Z1 = Z2 = z − 1  = 1 − 4 IP X1,1 > X2,1 , X1,2 < X2,2 Z1 = Z2 = z   = IP (X1,1 − X2,1 )(X1,2 − X2,2 ) > 0 Z1 = Z2 = z − IP (X1,1 − X2,1 )(X1,2 − X2,2 ) < 0 Z1 = Z2 = z . Motivated by each of the latter expressions, we introduce several kernel-based estimators of τ1,2|Z=z : τ̂(1) := 4 1,2|Z=z n X n X  w i,n (z)w j,n (z)1 X i,1 < X j,1 , X i,2 < X j,2 − 1, i=1 j=1 τ̂(2) := 1,2|Z=z n X n X     w i,n (z)w j,n (z) 1 (X i,1 − X j,1 )(X i,2 − X j,2 ) > 0 − 1 (X i,1 − X j,1 )(X i,2 − X j,2 ) < 0 , i=1 j=1 τ̂(3) := 1 − 4 1,2|Z=z n X n X  w i,n (z)w j,n (z)1 X i,1 < X j,1 , X i,2 > X j,2 , i=1 j=1 where 1 denotes the indicator function, w i,n is a sequence of weights given by K (Z − z) , w i,n (z) = Pn h i j=1 K h (Zj − z) (2) with K h (·) := h−p K(·/h) for some kernel K on Rp , and h = h(n) denotes a usual bandwidth sequence that tends to zero when n → ∞. In this paper, we have chosen usual Nadaraya-Watson weights. Obviously, there are alternatives (local linear, Priestley-Chao, Gasser-Müller, etc., weight), that would lead to different theoretical results. , τ̂(2) and τ̂(3) look similar, but they are nevertheless different, as shown in The estimators τ̂(1) 1,2|Z=z 1,2|Z=z 1,2|Z=z Proposition 1. These differences are due to the fact that all the τ̂(k) , k = 1, 2, 3 are affine transformations 1,2|Z=z of a double-indexed sum, on every pair (i, j), including the diagonal terms where i = j. The treatment of these P diagonal terms is different for each of the three estimators defined above. Indeed, setting s n := ni=1 w2i,n (z), takes values in the interval [−1 , 1 − 2s n ], τ̂(2) in [−1 + s n , 1 − s n ], and it can be easily proved that τ̂(1) 1,2|Z=z 1,2|Z=z τ̂(3) in [−1 + 2s n , 1]. Moreover, there exists a direct relationship between these estimators, given by the 1,2|Z=z following proposition. Proposition 1. Almost surely, τ̂(1) + s n = τ̂(2) = τ̂(3) − s n , where s n := 1,2|Z=z 1,2|Z=z 1,2|Z=z Pn i=1 w2i,n (z). This proposition is proved in A.2. As a consequence, we can easily rescale the previous estimators so that the new estimator will take values in the whole interval [−1, 1]. This would yield τ̃1,2|Z=z := τ̂(1) 1,2|Z=z 1 − sn τ̂(2) τ̂(3) sn sn 1,2|Z=z 1,2|Z=z + = = − · 1 − sn 1 − sn 1 − sn 1 − sn Note that none of the latter estimators depends on any estimation of conditional marginal distributions. In other words, we only have to conveniently choose the weights w i,n to obtain an estimator of the conditional Kendall’s tau. This is coherent with the fact that conditional Kendall’s taus are invariant with respect to conditional marginal distributions. Moreover, note that, in the definition of our estimators, the inequalities are strict (there are no terms corresponding to the cases i = j). This is inline with the definition of (conditional) Kendall’s tau itself through concordant/discordant pairs of observations. On kernel-based estimation of conditional Kendall’s tau | 295 The definition of τ̂(1) can be motivated as follows. For j = 1, 2, let F̂ j|Z (·|Z = z) be an estimator of the 1,2|Z=z conditional cdf of X j given Z = z. Then, a usual estimator of the conditional copula of X1 and X2 given Z = z is n X  Ĉ1,2|Z (u1 , u2 |Z = z) := w i,n (z)1 F̂1|Z (X i,1 |Z = z) ≤ u1 , F̂2|Z (X i,2 |Z = z) ≤ u2 . i=1 See [40] or [13], e.g. The latter estimator of the conditional copula can be plugged into (1) to define an estimator of the conditional Kendall’s tau itself: Z τ̂1,2|Z=z := 4 Ĉ1,2|Z (u1 , u2 |Z = z) Ĉ1,2|Z (du1 , du2 |Z = z) − 1 (3) =4 n X  w j,n (z)Ĉ1,2|Z F̂1|Z (X j,1 |Z = z), F̂2|Z (X j,2 |Z = z) Z = z − 1. j=1 Since the functions F̂ j|Z (·|Z = z) are non-decreasing, this reduces to τ̂1,2|Z=z = 4 n X n X  w i,n (z)w j,n (z)1 X i,1 ≤ X j,1 , X i,2 ≤ X j,2 − 1 i=1 j=1 = 4 n X n X  w i,n (z)w j,n (z)1 X i,1 < X j,1 , X i,2 < X j,2 − 1 + o P (1) = τ̂(1) + o P (1). 1,2|Z=z i=1 j=1 Veraverbeke et al. [40], Subsection 3.2, introduced their estimator of τ1,2|Z=z by (3) for a univariate conditioning variable. Note that this estimator is the same as the one studied in [15, p.4], i.e. τ̂1,2|Z=z . By the functional Delta-Method, they deduced its asymptotic normality as a sub-product of the weak convergence of the process √  nh Ĉ1,2|Z (·, ·|z) − C1,2|Z (·, ·|z) when Z is univariate. In our case, we will obtain more and stronger theoreti- cal properties of τ̂(1) under weaker conditions by a more direct analysis based on ranks. In particular, we 1,2|Z=z will not require any regularity condition on the conditional marginal distributions, contrary to [40]. Indeed, in the latter paper, it is required that F j|Z (·|Z = z) has to be two times continuously differentiable (assumption (R̃3)) and its inverse has to be continuous (assumption (R1)). This is not satisfied for some simple univariate cdf as F j (t) = t1(t ∈ [0, 1])/2 + 1(t ∈ (1, 2])/2 + t1(t ∈ (2, 4])/4 + 1(t > 4), for instance. Note that we could justify τ̂(3) in a similar way by considering conditional survival copulas. 1,2|Z=z Let us define g1 , g2 , g3 by  g1 (Xi , Xj ) := 41 X i,1 < X j,1 , X i,2 < X j,2 − 1,   g2 (Xi , Xj ) := 1 (X i,1 − X j,1 ) × (X i,2 − X j,2 ) > 0 − 1 (X i,1 − X j,1 ) × (X i,2 − X j,2 ) < 0 ,  g3 (Xi , Xj ) := 1 − 41 X i,1 < X j,1 , X i,2 > X j,2 , where, for i = 1, . . . , n, we set Xi := (X i,1 , X i,2 ). Clearly, τ̂(k) is a smoothed estimator of E[g k (X1 , X2 )|Z1 = 1,2|z Z2 = z], k = 1, 2, 3. Note that such dependence measures are of interest for the purpose of estimating (conditional or unconditional) copula models too. Indeed, several popular parametric families of copulas have a simple one-to-one mapping between their parameter and the associated Kendall’s tau (or Spearman’s rho): Gaussian, Student with a fixed degree of freedom, Clayton, Gumbel and Frank copulas, etc. Then, assume for instance that the conditional copula C1,2|Z=z is a Gaussian copula with a parameter ρ(z). Then, by estimating its conditional Kendall’s tau τ1,2|Z=z , we get an estimate of the corresponding parameter ρ(z), and finally of the conditional copula itself. See [36], e.g. The choice of the bandwidth h could be done in a data-driven way, following the general conditional U-statistics framework detailed in Dony and Mason [10, Section 2]. Indeed, for any k ∈ {1, 2, 3} and z ∈ Rp , k) denote by τ̂(h, the estimator τ̂(k) that is made with the smoothing parameter h and our dataset, 1,2|Z=z −(i,j), 1,2|Z=z (h, k) when the i-th and j-th observations have been removed. As a consequence, the random function τ̂−(i,j), 1,2|Z=· 296 | Alexis Derumigny and Jean-David Fermanian  is independent of (Xi , Zi ), (Xj , Zj ) . As usual with kernel methods, it would be tempting to propose h as the minimizer of the cross-validation criterion CV DM (h) := n  2 X 2 (h, k) g k (Xi , Xj ) − τ̂−(i,j), K h (Zi − Zj ), 1,2|Z=(Z +Z )/2 i j n(n − 1) i,j=1 for k = 1, 2, 3 or for τ̃1,2|Z=· . The latter criterion would be a “naively localized” version of the usual crossvalidation method. Unfortunately, we observe that the function h 7→ CV DM (h) is most often decreasing in the range of realistic bandwidth values. If we remove the weight K h (Zi − Zj ), then there is no reason why g k (Xi , Xj ) should be equal to τ̂(k) (on average), and we are not interested in the prediction of −(i,j), 1,2|Z=(Z +Z )/2 i j concordance/discordance pairs for which the Z i and Z j are far apart. Therefore, a modification of this criteria k) is necessary. We propose to separate the choice of h for the terms g k (Xi , Xj ) − τ̂(h, and the −(i,j), 1,2|Z=(Z +Z )/2 selection of the “convenient pairs” of observations (i, j). This leads to the new criterion CV h˜ (h) := n  2 X 2 (h, k) g k (Xi , Xj ) − τ̂−(i,j), K̃ h˜ (Zi − Zj ), 1,2|Z=(Z +Z )/2 i j n(n − 1) i j (4) i,j=1 ˜ Even if more complex procedures with a potentially different kernel K̃ and a new fixed tuning parameter h. ˜ so that only a fraction of the are possible, we suggest to simply choose K̃(z) := 1{|z|∞ ≤ 1} and to calibrate h ˜ as the empirical quantile of {|Zi − Zj |∞ : 1 ≤ i < j ≠ n} of pairs (i, j) has non-zero weights. In practice, set h order 2N pairs /(n(n − 1)), where N pairs is the number of pairs we want to keep. 3 Theoretical results 3.1 Finite distance bounds Hereafter, we will consider the behavior of conditional Kendall’s tau estimates given Z = z belongs to some fixed open and bounded subset Z in Rp . For the moment, let us state an instrumental result that is of interest P per se. Let ˆfZ (z) := n−1 nj=1 K h (Zj − z) be the usual kernel estimator of the density fZ of the conditioning variable Z. Note that the estimators τ̂(k) , k = 1, . . . , 3 are well-behaved only whenever ˆfZ (z) > 0. Denote 1,2|Z=z the joint density of (X, Z) by fX,Z . In our study, we need some usual conditions of regularity. Assumption 3.1. (a) The kernel K is bounded, and set kK k∞ =: C K . (b) It is symmetrical in the sense that R R R K(u) = K(−u) for every u ∈ Rp and satisfies K = 1, |K | < ∞, K 2 < ∞. (c) This kernel is of order α for some R integer α > 1: for all j = 1, . . . , α − 1 and every indices i1 , . . . , i j in {1, . . . , p}, K(u)u i1 . . . u i j du = 0. (d) R Moreover, E[K h (Z − z)] > 0 for every z ∈ Z and h > 0. Set K̃(·) := K 2 (·)/ K 2 and kK̃ k∞ =: C K̃ . Assumption 3.2. fZ is α-times continuously differentiable on Z ² and there exists a constant C K,α > 0 s.t., for all z ∈ Z, Z p X ∂ α fZ (z + thu) du ≤ C K,α . |u i1 . . . u i α | sup |K |(u) t∈[0,1] ∂z i1 . . . ∂z i α i1 ,...,i α =1 Moreover, C K̃,2 denotes a similar constant replacing K by K̃ and α by two. Assumption 3.3. There exist two positive constants fZ,min and fZ,max such that, for every z ∈ Z, fZ,min ≤ fZ (z) ≤ fZ,max . 2 This means that the partial derivatives ∂ k f Z (z)/∂z i1 · · · ∂z i k exist and are continuous for every z ∈ Z and every k-uplet (i1 , . . . , i k ) of integers in {1, . . . , p}, k ≤ α. On kernel-based estimation of conditional Kendall’s tau | 297 Since Z is bounded, Assumption 3.3 is most often satisfied with the commonly met continuous distribution. Proposition 2. Under Assumptions 3.1-3.3 and if C K,α h α /α! < fZ,min , for any z ∈ Z, the estimator ˆfZ (z) is strictly positive with a probability larger than Z   2 1 − 2 exp − nh p fZ,min − C K,α h α /α! / 2fZ,max K 2 + (2/3)C K (fZ,min − C K,α h α /α!) . The latter proposition is proved in A.3. It guarantees that our estimators τ̂(k) , k = 1, . . . , 3, are well-behaved 1,2|z with a probability close to one. The next regularity assumption is necessary to explicitly control the bias of τ̂1,2|Z=z . Assumption 3.4. For every x ∈ R2 , z 7→ fX,Z (x, z) is differentiable on Z almost everywhere up to the order α. For every 0 ≤ k ≤ α and every 1 ≤ i1 , . . . , i α ≤ p, let H k,~ι (u, v, x1 , x2 , z) := sup t∈[0,1]  ∂ α−k f   ∂ k fX,Z  X,Z x1 , z + thu x2 , z + thv , ∂z i1 . . . ∂z i k ∂z i k+1 . . . ∂z i α denoting~ι = (i1 , . . . , i α ). Assume that H k,~ι (u, v, x1 , x2 , z) is integrable and there exists a finite constant CXZ,α > 0 such that, for every z ∈ Z and every h < 1, ! Z p α X X α |K |(u)|K |(v) H k,~ι (u, v, x1 , x2 , z)|u i1 . . . u i k v i k+1 . . . v i α | du dv dx1 dx2 k k=0 i1 ,...,i α =1 is less than CXZ,α . Assumptions 3.2 and 3.4 are satisfied when the density of Z is α-times continuously differentiable in a (strictly larger) neighborhood of Z and K is compactly supported, for n sufficiently large. Indeed, the vectors thu and thv will then be arbitrary small uniformly w.r.t. t ∈ [0, 1] and u (resp. v) in the support of K ³. If K is not compactly supported, these assumptions are most often satisfied when the tails of fZ and its derivatives do not exhibit pathological patterns. For instance, if fZ is a Gaussian density, this is the case because this density and its derivatives are bounded on Rp . The next three propositions state pointwise and uniform exponential inequalities for the estimators τ̂(k) , when k = 1, 2, 3. They are proved in Sections A.4, A.5 and A.6. We will denote c1 := c3 := 4 and 1,2|Z=z c2 := 2. Proposition 3 (Exponential bound with explicit constants). Under Assumptions 3.1-3.4, for every t > 0 such that C K,α h α /α! + t ≤ fZ,min /2 and every t0 > 0, if C K̃,2 h2 < fz (z), we have ! R    16fZ2 (z)  C K,α h α c k  CXZ,α h α 3fz (z) K 2 0 (k) + +t × 1+ 3 +t IP |τ̂1,2|Z=z − τ1,2|Z=z | > 2 α! 2nh p α! fz (z) fZ,min     nh p t2 (n − 1)h2p t02 R R + 2 exp − 2 ≤ 2 exp − 2 2 2 2 0 2fZ,max K + (2/3)C K t 4fZ,max ( K ) + (8/3)C K t   p 2 2 nh (fz (z) − C K̃,2 h ) + 2 exp − , R 8fZ,max K̃ 2 + 4C K̃ (fz (z) − C K̃,2 h2 )/3 for any z ∈ Z and every k = 1, 2, 3. Alternatively, we can apply Theorem 1 in Major [26] instead of the Bernstein-type inequality that has been used in the proof of Proposition 3. 3 Then, all the terms that involve fZ and its derivatives are uniformly bounded. And invoke the α-order property of K to check the validity of such assumptions. 298 | Alexis Derumigny and Jean-David Fermanian Proposition 4 (Alternative exponential bound without explicit constants). Under Assumptions 3.1-3.4, for R 3 every t > 0 such that C K,α h α /α! + t ≤ fZ,min /2 and every t0 > 0 s.t. t0 ≤ 2h p ( K 2 )3 fZ,max /C4K , there exist some universal constants C2 and α2 s.t. ! R    16fZ2 (z)  C K,α h α c k  CXZ,α h α 3fz (z) K 2 (k) 0 IP |τ̂1,2|Z=z − τ1,2|Z=z | > 2 + +t +t × 1+ 3 α! 2nh p α! fz (z) fZ,min     nh p (fz (z) − C K̃,2 h2 )2 nh p t2 R + 2 exp − ≤ 2 exp − R 2fZ,max K 2 + (2/3)C K t 8fZ,max K̃ 2 + 4C K̃ (fz (z) − C K̃,2 h2 )/3     α2 nh p t0 nh p t2 R R R R + C2 exp − , + 2 exp 3 8fZ,max ( K 2 ) 32 K 2 ( |K |)2 fZ,max + 8C K |K |fZ,max t/3 for any z ∈ Z and every k = 1, 2, 3, if C K̃,2 h2 < fZ (z) and 6h p R |K | 2 fz,max < R K2. Remark 5. In Propositions 2, 3 and 4, when the support of K is included in [−c, c]p for some c > 0, fZ,max can be replaced by a local bound supz̃∈V(z,ϵ) fZ (z̃), denoting by V(z, ϵ) a closed ball of center z and any radius ϵ > 0, when h c < ϵ. Propositions 3 and 4 look similar. Nonetheless, only the upper bound in the former case can be explicitly calculated because this bound involves constants that can be numerically evaluated. But, on the other side, Proposition 4 provides better rates of convergence. Indeed, by choosing t0 of the order h p , the latter result can   − τ1,2|Z=z | > ϵh p  exp − Cnh2p ϵ , for some constants ϵ > 0 and C > 0. At the be summarized as IP |τ̂(k) 1,2|Z=z   opposite, the bound obtained in Proposition 3 is of the type IP |τ̂(k) − τ1,2|Z=z | > ϵ  exp − C0 nh2p ϵ , 1,2|Z=z C0 > 0, what is clearly weaker. As a corollary, the two latter results yield the weak consistency of τ̂(k) for every z ∈ Z, when nh2p → ∞ 1,2|Z=z (choose the constants t and t0 ∼ h p sufficiently small, in Proposition 4, e.g.). It is possible to obtain uniform bounds, by slightly strengthening our assumptions. Note that this next result will be true if n is sufficiently large, when Proposition 4 was true for every n. Assumption 3.5. The kernel K is Lipschitz on (Z, k · k∞ ), with a constant λ K and Z is a subset of an hypercube in Rp whose volume is denoted by V. Moreover, K and K 2 are regular in the sense of [16] or [11]. Proposition 6 (Uniform exponential bound). Under the assumptions 3.1-3.5, there exist some constants L K and C K (resp. L K̃ and C K̃ ) that depend only on the VC characteristics of K (resp. K̃), s.t., for every µ ∈ (0, 1) such R R that µfz,min < CXZ,α h α /α! + b K K 2 fZ,max /C K , if fZ,max < C̃XZ,2 h2 /2 + b K̃ K̃ 2 fZ,max /C K̃ , R  ! CXZ,α h α 3fz,max K 2 ck (k) IP sup |τ̂1,2|Z=z − τ1,2|Z=z | > 2 + +t α! 2nh p fz,min (1 − µ)2 z∈Z    C h α 2 ≤ L K exp − C f ,K nh p µfz,min − XZ,α α!     p α2 nth p 2 2 R + C2 D exp − + L exp − C nh f − C̃ h /4 z,max XZ,2 K̃ f , K̃ 8fZ,max ( K 2 )     A2 nh p t2 C−4 A nh p t + 2 exp − 2 2 R 2 3 K R + 2 exp − 2 2 , 2 16C K A1 16 A1 K fz,max ( |K |) R 3 for n sufficiently large, k = 1, 2, 3, and for every t > 0 s.t. t ≤ 2h p ( K 2 )3 fZ,max /C4K , Z Z Z Z 3 3 −16A1 C2K A g K 2 fz,max ( |K |)2 ln(h p K 2 fz,max ( |K |)2 ) < n1/2 h p/2 t, and nh p t ≥ Z   K 2 fz,max M2 (p + β)3/2 log 4C2K hp f z,max  R K2 , β = max 0, log D  4C K λ K p , D := dV e, log n h for some universal constants C2 , α2 , M2 , A1 , A2 and a constant A g that depends on K and fz,max . On kernel-based estimation of conditional Kendall’s tau | 299 R We have denoted C f ,K := log(1 + b K /(4L K ))/(L K b K fz,max K 2 ), for any arbitrarily chosen constant b K ≥ C K . R Similarly, C f , K̃ := log(1 + b K̃ /(4L K̃ ))/(L K̃ b K̃ fz,max K̃ 2 ), b K̃ ≥ C K̃ . 3.2 Asymptotic behavior The previous exponential inequalities are not optimal to prove usual asymptotic results. Indeed, they directly or indirectly rely on upper bounds of estimates, as in Hoeffding or Bernstein-type inequalities. In the case of kernel estimates, this implies the necessary condition nh2p → ∞, at least. By a direct approach, it is possible to state the consistency of τ̂(k) , k = 1, 2, 3, and then of τ̃1,2|Z=z , under the weaker condition nh p → ∞. 1,2|Z=z Proposition 7 (Consistency). Under Assumption 3.1, if nh pn → ∞, lim K(t)|t|p = 0 when |t| → ∞, fZ and z 7→ τ1,2|Z=z are continuous on Z, then τ̂(k) tends to τ1,2|Z=z in probability, when n → ∞ for any k = 1, 2, 3. 1,2|Z=z This property is proved in A.7. Moreover, Proposition 6 does not allow to state the strong uniform consistency of τ̂(k) because the threshold t has to be of order h p at most. Here again, a direct approach is possible, 1,2|Z=z nonetheless. p Proposition 8 (Uniform consistency). Under Assumption 3.1, assume that nh2p n / log n → ∞, lim K(t)|t| = 0 when |t| → ∞, K is Lipschitz, fZ and z 7→ τ1,2|Z=z are continuous on a bounded set Z, and there exists a lower − τ1,2|Z=z → 0 almost surely, when n → ∞ bound fZ,min s.t. fZ,min ≤ fZ (z) for any z ∈ Z. Then supz∈Z τ̂(k) 1,2|Z=z for any k = 1, 2, 3. This property is proved in A.8. To derive the asymptotic law of this estimator, we will assume: Assumption 3.6. (i) nh pn → ∞ and nh p+2α → 0; (ii) K( · ) is compactly supported. n Proposition 9 (Joint asymptotic normality at different points). Let z01 , . . . , z0n0 be fixed points in a set Z ⊂ Rp . Assume 3.1, 3.4, 3.6, that the z0i are distinct and that fZ and z 7→ fX,Z (x, z) are continuous on Z, for every x. Then, as n → ∞,   D (nh pn )1/2 τ̂1,2|Z=z0i − τ1,2|Z=z0i −→ N(0, H(k) ), k = 1, 2, 3, i=1,...,n0 , τ̂(k) 1,2|Z=z k = 1, 2, 3 or τ̃1,2|Z=z , and H is the n0 × n0 diagonal real where τ̂1,2|Z=z denotes any of the estimators matrix defined by R 4 K 2 1{i=j}  (k) E[g k (X1 , X)g k (X2 , X)|Z = Z1 = Z2 = z0i ] − τ21,2|Z=z0 , [H ]i,j = i fZ (z0i ) for every 1 ≤ i, j ≤ n0 , and (X, Z), (X1 , Z1 ), (X2 , Z2 ) are independent versions. This proposition is proved in A.9. Remark 10. The latter results will provide some simple tests of the constancy of the function z 7→ τ1,2|z , and then of the constancy of the associated conditional copula itself. This would test the famous “simplifying assumption” (“H0 : C1,2|Z=z does not depend on the choice of z”), a key assumption for vine modeling in particular: see [1] or [17] for a discussion, [8] for a review and a presentation of formal tests for this hypothesis. 4 Simulation study In this simulation study, we draw i.i.d. random samples (X i,1 , X i,2 , Z i ), i = 1, . . . , n, with univariate explanatory variables (p = 1). We consider two settings, that correspond to bounded and/or unbounded explanatory variables respectively: 300 | Alexis Derumigny and Jean-David Fermanian 1. Z =]0, 1[ and the law of Z is uniform on ]0, 1[. Conditionally on Z = z, X1 |Z = z and X2 |Z = z both follow a Gaussian distribution N(z, 1). Their associated conditional copula is Gaussian and their conditional Kendall’s tau is given by τ1,2|Z=z = 2z − 1. 2. Z =]−2, 2[ and the law of Z is N(0, 1). Conditionally on Z = z, X1 |Z = z and X2 |Z = z both follow a Gaussian distribution N(Φ(z), 1), where Φ(·) is the cdf of the Z. Their associated conditional copula is Gaussian and their conditional Kendall’s tau is given by τ1,2|Z=z = 2Φ(z) − 1. These simple frameworks allow us to compare the numerical properties of our different estimators in different parts of the space, in particular when Z is close to zero or one, i.e. when the conditional Kendall’s tau is close to −1 or to 1. Note that these distributions are continuous, with infinitely differentiable densities. We will use the Epanechnikov kernel. Therefore, they will satisfy Assumptions 3.1-3.6. We compute the different estimators τ̂(k) for k = 1, 2, 3, and the symmetrically rescaled version τ̃1,2|z . The bandwidth h is chosen 1,2|Z=z as proportional to the usual “rule-of-thumb” for kernel density estimation, i.e. h = α h σ̂(Z)n−1/5 with α h ∈ {0.5, 0.75, 1, 1.5, 2} and n ∈ {100, 500, 1000, 2000}. For each setting, we consider three local measures of goodness-of-fit: for a given z and for any Kendall’s tau estimate (say τ̂1,2|Z=z ), let • the (local) bias: Bias(z) := E[τ̂1,2|Z=z ] − τ1,2|Z=z , h 2 i1/2 , • the (local) standard deviation: Sd(z) := E τ̂1,2|Z=z − E[τ̂1,2|Z=z ] h 2 i • the (local) mean square-error: MSE(z) := E τ̂1,2|Z=z − τ1,2|Z=z . We also consider their integrated version w.r.t the usual Lebesgue measure on the whole support of z, respectively denoted by IBias, ISd and IMSE. Some results concerning these integrated measures are given in Table 1 (resp. Table 2) for Setting 1 (resp. Setting 2), and for different choices of α h and n. For the sake of effective calculations of these measures, all the theoretical previous expectations are replaced by their empirical counterparts based on 500 simulations. For every n, the best results seem to be obtained with α h = 1.5 and the fourth (rescaled) estimator, particularly in terms of bias. This is not so surprising, because the estimators τ̂(k) , k = 1, 2, 3, do not have the right support at a finite distance. Note that this comparative advantage of τ̃ in terms of bias decreases with n, as expected. In terms of integrated variance, all the considered estimators behave more or less similarly, particularly when n ≥ 500. To illustrate our results for Setting 1 (resp. Setting 2), the functions z 7→ Bias(z), Sd(z) and MSE(z) have been plotted on Figures 1-2 (resp. Figures 3-4), both with our empirically optimal choice α h = 1.5. We can note that, considering the bias, the estimator τ̃ behaves similarly as τ̂(1) when the true τ is close to −1, and similarly as τ̂(3) when the true Kendall’s tau is close to 1. But globally, the best pointwise estimator is clearly obtained with the rescaled version τ̃1,2|Z=· , after a quick inspection of MSE levels, and even if the differences between our four estimators weaken for large sample sizes. The comparative advantage of τ̃1,2|z more clearly appears with Setting 2 than with Setting 1. Indeed, in the former case, the support of Z’s distribution is the whole line. Then ˆfZ does not suffer any more from the boundary bias phenomenon, contrary to what happened with Setting 1. As a consequence, the biases induced by the definitions of τ̂(k) , k = 1, 3, appear more strikingly 1,2|z in Figure 3, for instance: when z is close to (−1) (resp. 1), the biases of τ̂(1) (resp. τ̂(3) ) and τ̃1,2|z are close, 1,2|z 1,2|z when the bias τ̂(3) (resp. τ̂(1) ) is a lot larger. Since the squared biases are here significantly larger than the 1,2|z 1,2|z variances in the tails, τ̃1,2|z provides the best estimator globally considering “both sides” together. But even in the center of Z’s distribution, the latter estimator behaves very well. In Setting 2 where there is no boundary problem, we also try to estimate the conditional Kendall’s tau using our cross-validation criterion (4), with N pairs = 1000. More precisely, denoting by h CV the minimizer of the cross-validation criterion, we try different choices h = α h ×h CV with α h ∈ {0.5, 0.75, 1, 1.5, 2}. The results in terms of integrated bias, standard deviation and MSE are given in Table 3. We do not find any substantial improvements compared to the previous Table 2, where the bandwidth was chosen “roughly”. In Table 4, On kernel-based estimation of conditional Kendall’s tau | 301 we compare the average h CV with the previous choice of h. The expectation of h CV is always higher than the “rule-of-thumb” h ref , but the difference between both decreases when the sample size n increases. The standard deviation of h CV is quite high for low values of n, but decreases as a function of n. This may be seen as quite surprising given the fact that the number of pairs N pairs used in the computation of the criterion stays constant. Nevertheless, when the sample size increases, the selected pairs are better in the sense that the differences |Z i − Z j | can become smaller as more replications of Z i are available. Table 1: Results of the simulation in Setting 1. All values have been multiplied by 1000. Bold values indicate optimal choices for the chosen measure of performance. These results are integrated measures of performance over the whole space Z; the corresponding local measures of performance are displayed in Figures 1 and 2. αh = 2 α h = 1.5 αh = 1 α h = 0.75 α h = 0.5 n = 100 n = 500 n = 1000 n = 2000 IBias ISd IMSE IBias ISd IMSE IBias ISd IMSE IBias ISd IMSE -133 197 66.5 -34.5 84.9 9.86 -18.2 61.6 4.85 -10.9 46 2.65 -12.9 187 43.7 -4.08 84.4 8.58 -0.9 61.5 4.49 -1.07 46 2.53 107 190 56.6 26.4 84.5 9.26 16.4 61.5 4.76 8.8 46 2.6 τ̃1,2|Z=· -0.91 213 48.2 -1.18 86.9 8.55 0.733 62.4 4.46 -0.149 46.4 2.5 τ̂(1) 1,2|Z=· τ̂(2) 1,2|Z=· τ̂(3) 1,2|Z=· -88 150 35.8 -26.3 68 6.32 -13.9 50.7 3.33 -7.98 37.6 1.8 -10.4 145 26.3 -5.97 67.9 5.6 -2.33 50.6 3.12 -1.39 37.5 1.74 67.2 146 30.6 14.3 67.9 5.75 9.2 50.6 3.19 5.2 37.5 1.76 τ̃1,2|Z=· -2.06 157 26.7 -3.99 69.2 5.49 -1.21 51.2 3.05 -0.76 37.8 1.69 τ̂(1) 1,2|Z=· τ̂(2) 1,2|Z=· τ̂(3) 1,2|Z=· -67.8 123 24.5 -19.2 58.7 4.8 -11 43.1 2.52 -6.34 33 1.44 -9.99 121 19 -3.95 58.6 4.39 -2.35 43.1 2.39 -1.39 33 1.4 47.8 122 20.9 11.3 58.7 4.47 6.34 43.1 2.41 3.57 33 1.41 τ̃1,2|Z=· -3.48 128 18.1 -2.34 59.5 4.18 -1.46 43.4 2.29 -0.897 33.2 1.35 τ̂(1) 1,2|Z=· -44.6 101 17.5 -15.9 50.4 4.12 -9.7 35.9 2.13 -5.52 27.6 1.28 τ̂(2) 1,2|Z=· τ̂(3) 1,2|Z=· -5.81 100 14.9 -5.68 50.3 3.84 -3.84 35.9 2.02 -2.18 27.6 1.24 33 101 15.5 4.58 50.3 3.77 2.01 35.9 1.99 1.15 27.6 1.23 τ̃1,2|Z=· -1.09 104 13.4 -4.55 50.8 3.57 -3.19 36.1 1.9 -1.83 27.7 1.18 τ̂(1) 1,2|Z=· τ̂(2) 1,2|Z=· τ̂(3) 1,2|Z=· -37.8 91.4 17.3 -11.8 43.8 4.14 -7.2 31.2 2.35 -5.97 23.7 1.43 -8.03 91.4 15.4 -3.93 43.8 3.94 -2.75 31.2 2.28 -3.44 23.7 1.39 21.7 91.7 15.4 3.91 43.8 3.87 1.7 31.2 2.24 -0.912 23.7 1.37 τ̃1,2|Z=· -4.5 94.2 13.5 -3.01 44.1 3.62 -2.24 31.3 2.12 -3.16 23.8 1.32 τ̂(1) 1,2|Z=· τ̂(2) 1,2|Z=· τ̂(3) 1,2|Z=· 5 Application to real data In this section, we present an application of this methodology to the dependence between electricity consumption and temperature. The first paper on this topic dates back to 1958 ([7]). Using UK data, they show that a decrease in temperature increases the electricity demand. Moreover, they show that the marginal effect of temperature levels on electricity consumption differs depending on the time of the day. Numerous other 302 | Alexis Derumigny and Jean-David Fermanian Sd, alpha_h = 1.5 , n = 100 MSE, alpha_h = 1.5 , n = 100 0.06 MSE at point z 0.02 0.04 0.10 0.08 0.0 −0.3 −0.2 −0.1 Bias at point z 0.1 Standard deviation at point z 0.12 0.2 0.08 0.3 Bias, alpha_h = 1.5 , n = 100 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 z 0.6 0.8 1.0 0.0 0.2 0.4 z 0.6 0.8 1.0 z Figure 1: Local bias, standard deviation and MSE for the estimators τ̂(1) (red) , τ̂(2) (blue), τ̂(3) (green), τ̃ (orange), with n = 100 and α h = 1.5 in Setting 1. The dotted line on the first figure is the reference at 0. Sd, alpha_h = 1.5 , n = 500 −0.15 0.020 0.015 0.005 0.010 MSE at point z 0.05 0.02 −0.10 0.03 0.04 Standard deviation at point z 0.06 0.10 0.05 0.00 −0.05 Bias at point z MSE, alpha_h = 1.5 , n = 500 0.07 0.15 Bias, alpha_h = 1.5 , n = 500 0.0 0.2 0.4 0.6 z 0.8 1.0 0.0 0.2 0.4 0.6 z 0.8 1.0 0.0 0.2 0.4 0.6 0.8 z Figure 2: Local bias, standard deviation and MSE for the estimators τ̂(1) (red) , τ̂(2) (blue), τ̂(3) (green), τ̃ (orange), with n = 500 and α h = 1.5 in Setting 1. The dotted line on the first figure is the reference at 0. 1.0 On kernel-based estimation of conditional Kendall’s tau Sd, alpha_h = 1.5 , n = 100 MSE, alpha_h = 1.5 , n = 100 MSE at point z 0.10 0.15 0.20 0.15 Standard deviation at point z 0.0 0.00 −0.4 0.10 0.05 −0.2 Bias at point z 0.2 0.20 0.4 0.25 Bias, alpha_h = 1.5 , n = 100 | 303 −2 −1 0 1 2 −2 −1 z 0 1 2 −2 −1 z 0 1 2 z Figure 3: Local bias, standard deviation and MSE for the estimators τ̂(1) (red) , τ̂(2) (blue), τ̂(3) (green), τ̃ (orange), with n = 100 and α h = 1.5 in Setting 2. The dotted line on the first figure is the reference at 0. 0.012 0.055 MSE at point z 0.035 0.006 0.008 0.010 0.050 0.045 0.040 Standard deviation at point z 0.05 0.00 0.025 −0.10 0.002 0.030 0.004 −0.05 Bias at point z MSE, alpha_h = 1.5 , n = 500 0.014 Sd, alpha_h = 1.5 , n = 500 0.10 Bias, alpha_h = 1.5 , n = 500 −2 −1 0 z 1 2 −2 −1 0 z 1 2 −2 −1 0 z Figure 4: Local bias, standard deviation and MSE for the estimators τ̂(1) (red) , τ̂(2) (blue), τ̂(3) (green), τ̃ (orange), with n = 500 and α h = 1.5 in Setting 2. The dotted line on the first figure is the reference at 0. 1 2 304 | Alexis Derumigny and Jean-David Fermanian Table 2: Results of the simulation in Setting 2. All values have been multiplied by 1000. Bold values indicate optimal choices for the chosen measure of performance. These results are integrated measures of performance over the whole space Z; the corresponding local measures of performance are displayed in Figures 3 and 4. αh = 2 α h = 1.5 αh = 1 α h = 0.75 α h = 0.5 n = 100 n = 500 n = 1000 n = 2000 IBias ISd IMSE IBias ISd IMSE IBias ISd IMSE IBias ISd IMSE τ̂(1) 1,2|Z=· τ̂(2) 1,2|Z=· τ̂(3) 1,2|Z=· -207 227 180 -54.1 83.9 16.9 -29.6 55.3 5.81 -16.9 38.9 2.49 1.15 207 97 0.845 80.5 10.8 0.557 54.4 4.35 0.145 38.6 2.04 210 228 181 55.7 83.2 16.4 30.7 55.4 5.9 17.2 38.9 2.5 τ̃1,2|Z=· 1.4 225 51.9 0.987 81.4 6.86 0.456 55 3.22 0.175 38.9 1.66 τ̂(1) 1,2|Z=· τ̂(2) 1,2|Z=· τ̂(3) 1,2|Z=· -144 175 98.6 -33.3 60.6 7.5 -19.8 41.9 3.12 -10.6 30.5 1.42 -2.33 163 56.2 1.73 59.4 5.56 -0.0619 41.7 2.51 0.665 30.4 1.24 140 176 99.2 36.8 60.7 7.73 19.7 42.1 3.12 11.9 30.5 1.45 τ̃1,2|Z=· -3.15 170 30.3 1.69 60.2 3.85 -0.093 42.1 1.95 0.645 30.5 1.05 τ̂(1) 1,2|Z=· τ̂(2) 1,2|Z=· τ̂(3) 1,2|Z=· -99.8 143 57.7 -24.9 50.9 5.06 -13.5 36.6 2.28 -6.92 26.6 1.09 1.17 132 34.6 0.903 50.4 4.02 1.16 36.5 1.97 1.46 26.6 0.994 102 139 54.4 26.7 51 5.13 15.8 36.6 2.33 9.83 26.6 1.11 τ̃1,2|Z=· 2.51 138 20.1 0.897 50.9 2.89 1.16 36.7 1.56 1.48 26.7 0.847 τ̂(1) 1,2|Z=· τ̂(2) 1,2|Z=· τ̂(3) 1,2|Z=· -59.1 104 28.1 -14.7 42.3 3.87 -7.56 29.7 1.86 -4.17 21.8 0.932 4.34 99.7 21.4 2.05 42.1 3.48 2.07 29.6 1.75 1.35 21.8 0.899 67.8 103 29.6 18.8 42.3 3.96 11.7 29.6 1.92 6.87 21.8 0.957 τ̃1,2|Z=· 3.34 103 13.4 2.08 42.5 2.6 2.08 29.7 1.39 1.35 21.8 0.755 τ̂(1) 1,2|Z=· -37.2 88.2 23.9 -9.57 38.2 4.6 -3.75 26.2 2.34 -1.09 19.8 1.32 τ̂(2) 1,2|Z=· τ̂(3) 1,2|Z=· 8.17 85.9 21.2 2.69 38 4.45 3.32 26.1 2.3 2.99 19.8 1.32 53.5 87.4 25.3 14.9 38.1 4.74 10.4 26.2 2.41 7.08 19.8 1.36 τ̃1,2|Z=· 8.47 88.5 15 2.69 38.4 3.59 3.33 26.3 1.93 3 19.9 1.15 articles have studied the dependence between these two variables, see for instance [4, 29, 32]. Generally, in winter, electricity consumption increases when temperature decreases, because of the demand for heating. On the contrary, high temperatures in summer would cause an increased electricity demand for cooling homes, offices and so on. Formally, we study the dependence between the following two variables: • Power t , the French electricity consumption⁴ in MW at time t; • Temp t , the temperature in Celsius degree at the Orly Airport weather station (France)⁵. These two variables are observed every 30 minutes from 01/01/1996 to 31/03/2019. The final dataset has got n = 329, 756 rows. The unconditional Kendall’s tau between these two variables is −0.397, computed using the fast Kendall’s tau algorithm [14]. In other words, on average, lower temperatures are associated to higher electricity consumption. 4 downloaded from http://clients.rte-france.com/lang/an/visiteurs/vie/vie_stats_conso_inst.jsp 5 downloaded from https://gis.ncdc.noaa.gov/maps/ncei/cdo/hourly On kernel-based estimation of conditional Kendall’s tau | 305 Table 3: Results of the simulation in Setting 2 using h = α h × h CV where h CV has been chosen by cross-validation. All values have been multiplied by 1000. Bold values indicate optimal choices for the chosen measure of performance. α h = 1.5 αh = 1 α h = 0.75 α h = 0.5 n = 100 n = 500 n = 1000 n = 2000 IBias ISd IMSE IBias ISd IMSE IBias ISd IMSE IBias ISd IMSE -111 154 66.2 -36.9 66.8 9.01 -22.4 48.2 4.06 -12.9 36.1 2.04 0.0488 137 36.3 0.236 64.2 6.45 0.546 46.8 3.14 1.29 35.7 1.78 111 151 60.6 37.4 66.3 8.88 23.5 47.2 4.07 15.5 36.2 2.18 τ̃1,2|Z=· 1.38 132 18.3 0.27 64.5 4.49 0.61 46.8 2.36 1.29 35.6 1.49 τ̂(1) 1,2|Z=· -67.4 117 35.7 -23.3 52.1 5.27 -13.9 37.8 2.4 -7.6 29 1.3 τ̂(2) 1,2|Z=· τ̂(3) 1,2|Z=· 4.32 108 23.5 0.809 50.7 4.21 1.03 37.2 2.07 1.78 28.8 1.21 76.1 119 35.4 24.9 51.6 5.12 16 37.6 2.49 11.2 29.1 1.39 τ̃1,2|Z=· 4.98 106 13.3 0.86 51.6 3.13 1.03 37.5 1.63 1.81 28.9 1.02 τ̂(1) 1,2|Z=· -43 101 28 -15.8 45.7 4.44 -9.51 33.1 2.04 -4.68 25.1 1.07 τ̂(2) 1,2|Z=· τ̂(3) 1,2|Z=· 7.87 93.1 22.4 2.01 44.8 3.91 1.57 32.7 1.87 2.29 24.9 1.03 58.8 97.6 27.2 19.8 45.3 4.41 12.7 32.9 2.1 9.27 25.1 1.14 τ̃1,2|Z=· 8.51 98 15.7 2.05 46 3.01 1.57 33.1 1.5 2.33 25.1 0.871 τ̂(1) 1,2|Z=· (2) τ̂1,2|Z=· τ̂(3) 1,2|Z=· -16.1 95.6 41.7 -6.36 43 6.35 -4.04 30.6 2.87 -1.11 22.1 1.34 14.9 92.6 40.4 5.08 42.6 6.2 3.17 30.4 2.83 3.47 22 1.34 46 92.8 42.2 16.5 42.6 6.45 10.4 30.4 2.94 8.06 22.1 1.4 τ̃1,2|Z=· 15.6 100 35.2 5.11 44 5.31 3.17 31 2.45 3.5 22.4 1.17 τ̂(1) 1,2|Z=· τ̂(2) 1,2|Z=· τ̂(3) 1,2|Z=· Table 4: Expectation and standard deviation of the bandwidth selected by cross-validation as a function of the sample size n, and comparison with bandwidth h ref chosen by the rule-of-thumb. n E[h CV ] Sd[h CV ] ref h = n−1/5 100 0.77 0.17 0.40 500 0.43 0.091 0.29 1000 0.34 0.060 0.25 2000 0.27 0.057 0.22 To have a more precise investigation about the dependence between these two variables, we decided to use a usual “detrending method”: we fit a linear trend on both variables and consider only the dependence between the two series of residuals. Formally, our model assumption is Power t = a0, power + a1, power × t + ε1,t , (5) Temp t = a0, temp + a1, temp × t + ε2,t , (6) where t is the the number of half-hours since 01/01/1996, for some unknown coefficients a0, power , a1, power , a0, temp , a1, temp . And the couple of series (ε1,t , ε2,t ) is assumed to be stationary. We estimate these two linear regressions separately using ordinary least squares (OLS). The results are reported in Table 5. All the coefficients are significant. Indeed, because of economic and technological growth, the electricity consumption increases on average by 0.0044 MW each hour. At the same time, temperature increases on average by 1.6 × 10−6 Celsius degree per hour, which corresponds to a Global Warming of 0.014 degree per year. Even if this is a very simple model, with a linear growth, it correspond to the right order of magnitude commonly found. 306 | Alexis Derumigny and Jean-David Fermanian Table 5: Statistics for the OLS estimators of (5) and (6). Std. Error 3.933e+01 2.066e-04 2.526e-02 1.327e-07 p-value <2e-16 <2e-16 <2e-16 1.54e-09 0.2 0.1 0.0 Conditional Kendall’s tau −0.3 −0.2 −0.1 0.2 0.1 0.0 −0.1 −0.3 −0.2 Conditional Kendall’s tau t-value 1265.1 106.8 469.902 6.041 0.3 Estimate 4.976e+04 2.205e-02 1.187e+01 8.014e-07 0.3 a0, power a1, power a0, temp a1, temp Jan Feb Mar Apr May June Jul Aug Sep Oct Nov Dec Jan Day of the year Jan Feb Mar Apr May June Jul Aug Sep Oct Nov Dec Jan Day of the year Figure 5: Conditional Kendall’s tau between the detrended electricity consumption ε̂1,t and the detrended temperature ε̂2,t , given the day of the year and estimated using h CV = 5 days. Figure 6: Conditional Kendall’s tau between the detrended electricity consumption ε̂1,t and the detrended temperature ε̂2,t , given the day of the year and estimated using h* = 12 days. Our goal is to estimate whether the dependence between electricity consumption and temperature is varying as a function of the day of the year (month, season...). The lack of stationarity on the original series had an influence on the conditional Kendall’s tau. Indeed, a part of positive dependence between the original variables is due to the fact that they both increase on average over time. We consider this as a spurious effect caused by the non-stationarity. For this reason, we have studied the (conditional) dependence between the estimated residuals ε̂1,t and ε̂2,t . Concerning the bandwidth h choice, we followed the insights of our simulation in Section 4. Globally, there exist two possibilities: choosing the bandwidth according to the usual rule-of-thumb h* = 1.5 × σ̂(Z) × n−1/5 , or using our cross-validation criterion, which yields h CV . Note that the computation time of this crossvalidation function is of order O(n2 ), by Equation (4). With our sample size n = 329 756, this criterion becomes computationally unfeasible in a reasonable time. To cope with this difficulty, we use a Monte-Carlo approximation CV N, h˜ (h) := N 2  1 X ˜ g k (Xi l , Xj l ) − τ̂−(i l ,j l ), 1,2|Z=(Zi +Zj )/2 1 d(Zi l , Zj l ) ≤ h l l N (7) l=1 where, for every l = 1, . . . , N, we sample independently i l uniformly in [1, n] and j l |i l uniformly on the set ˜ }. In practice, we choose d(a, b) as the number of days between the two dates a {j ∈ [1, n] : d(Z i l , Z j ) ≤ h and b. For instance, the distance between January 1st and December 30th is 2 days. Similarly, (Z i l + Z j l )/2 corresponds to the mean day of the year between the days Z i l and Z j l , and is computed using the package circular [2]. The estimated conditional Kendall’s tau with the bandwidth h CV or h* are displayed in Figures 5 and 6. We observe that conditional Kendall’s tau is negative in winter, meaning that lower temperatures are associated On kernel-based estimation of conditional Kendall’s tau | 307 24 with higher electricity demands. This can be explained by the energy consumption for heating purpose. On the contrary, in summer, higher temperatures are associated with higher energy demand, because of the energy consumption induced by cooling devices. It is interesting to note that the average conditional Kendall’s tau in winter (−0.23) is slightly smaller in absolute value than in summer (0.30). 20 0.2 0.1 15 −0.1 −0.2 10 Hour of the day 0.0 5 −0.3 −0.4 0 −0.5 Jan Feb Mar Apr May June Jul Aug Sep Oct Nov Dec Jan Day of the year Figure 7: Conditional Kendall’s tau between electricity consumption and temperature given the day of the year (h*,1 = 12 days) and the time of the day (in hours, h*,2 = 1 hour). To complete this analysis, we decided to include a second variable, which is the hour of the day. The choice of a bivariate bandwidth is not straightforward. To simplify, we decide to use a diagonal bandwidth given by h*,1 = 1.5 × σ̂(Z1 ) × n−1/5 = 12 days and h*,2 = 1.5 × σ̂(Z2 ) × n−1/5 = 1 hour. The results are displayed on Figure 7. On the x-axis, we globally find the same trend: negative dependence in winter and positive dependence in summer, which is coherent. Moreover, in winter, the conditional Kendall’s tau is more important (around −0.5) during nights (20:00-6:00) than in the daytime. This may be explained by the fact that heating in households has a more important contribution to the total consumption than during daytime, when many people live outside their homes. Note that, during summers, the levels of Kendall’s tau given date and daytime are most often smaller than Kendall’s tau given date only. This may appear as counterintuitive. But, as noticed in [9], the average of the former quantity (over daytimes) is not equal to the latter quantity in general. In our particular case, we can argue that, during summers, the levels of dependence between temperature and energy consumption is rather weak once we control for daytime. This is the same phenomenon with usual factor models, where two variables may be independent given a third one, but they may be strongly dependent (unconditionnally). Acknowledgments This work is supported by the Labex Ecodec under the grant ANR-11-LABEX-0047 from the French Agence Nationale de la Recherche. 308 | Alexis Derumigny and Jean-David Fermanian A Proofs For convenience, we recall Berk’s (1970) inequality (see Theorem A in Serfling [37, p.201]). Note that, if m = 1, this reduces to Bernstein’s inequality. Lemma 11. Let m, n > 0, X1 , . . . , Xn i.i.d. random vectors with values in a measurable space X and g : Xm → [a, b] be a symmetric real bounded function. Set θ := E[g(X1 , . . . , Xm )] and σ2 := Var[g(X1 , . . . , Xm )]. Then, for any t > 0 and n ≥ m,   !−1   X n [n/m]t2   IP g(Xi1 , . . . , Xi m ) − θ ≥ t ≤ exp − , m 2σ2 + (2/3)(b − θ)t c where P c denotes summation over all subgroups of m distinct integers (i1 , . . . , i m ) of {1, . . . n}. A.1 Notations Let us define a few notations that will be used throughout the proofs. For every 1 ≤ i, j ≤ n and z ∈ Rp , let us define    S i,j (z) := n−2 K h (Zi − z)K h (Zj − z) 1 Xi < Xj − IP X1 < X2 Z1 = Z2 = z , (8)     gz (Xi , Zi ), (Xj , Zj ) := K h (Zi − z)K h (Zj − z) 1 Xi < Xj − IP Xi < Xj Zi = Zj = z      , (9) − E K h (Zi − z)K h (Zj − z) 1 Xi < Xj − IP Xi < Xj Zi = Zj = z     g̃ i,j = gz (Xi , Zi ) , (Xj , Zj ) + gz (Xj , Zj ) , (Xi , Zi ) /2, (10) g i := E[g̃ i,j |Xi , Zi ], (11) ξz (Xi , Zi , Xj , Zj ) := ξ i,j := g̃ i,j − g i − g j , `z : (x1 , z1 , x2 , z2 ) 7→ (12) 2p h ξz (x1 , z1 ) , (x2 , z2 ) for a given h > 0, 4C2K (13)  Note that ξ i,j is a degenerate (symmetrical) U-statistics because E[ξ i,j |Xi , Zi ] = E[ξ i,j |Xj , Zj ] = 0, when i ≠ j. In the proofs, we will study the difference τ̂1,2|Z=z − τ1,2|Z=z using two quantities that can be bounded P separately: ˆf 2 (z) and S i,j (z). 1≤i,j≤n Z τ̂1,2|Z=z − τ1,2|Z=z = 4   w i,n (z)w j,n (z)1 Xi < Xj − 4 IP X1 < X2 Z1 = Z2 = z X 1≤i,j≤n =   X  4 K h (Zi − z)K h (Zj − z) 1 Xi < Xj − IP X1 < X2 Z1 = Z2 = z n2 ˆf 2 (z) Z = 1≤i,j≤n 4 S i,j (z), ˆf 2 (z) Z 1≤i,j≤n X (14) This sum can be decomposed in the following way X X  S i,j (z) = S i,j (z) − E[S i,j (z)] + n(n − 1)E[S1,2 (z)] − ∆ n (z). 1≤i,j≤n (15) 1≤i≠j≤n  Pn P 2 2 where the “diagonal term” ∆ n (z) := − ni=1 S i,i (z) = IP X1 < X2 Z1 = Z2 = z i=1 K h (Zi −z)/n . The stochastic component above can itself be rewritten as X  1 X  1 X S i,j (z) − E[S i,j (z)] = 2 gz (Xi , Zi ) , (Xj , Zj ) = 2 g̃ i,j (16) n n 1≤i≠j≤n 1≤i≠j≤n 1≤i≠j≤n On kernel-based estimation of conditional Kendall’s tau = | 309 n 1 X 2(n − 1) X ξ + gi . i,j n2 n2 1≤i≠j≤n (17) i=1 A.2 Proof of Proposition 1 Since there are no ties a.s., 1 + τ̂(1) =4 1,2|Z=z n X n X     w i,n (z)w j,n (z) 1 X i,1 < X j,1 − 1 X i,1 < X j,1 , X i,2 > X j,2 i=1 j=1 =4 n X n X  w i,n (z)w j,n (z)1 X i,1 < X j,1 + τ̂(3) − 1. 1,2|Z=z i=1 j=1 But 1= n X n X w i,n (z)w j,n (z) = i=1 j=1 =2 n X n X     w i,n (z)w j,n (z) 1 X i,1 ≤ X j,1 + 1 X i,1 > X j,1 i=1 j=1 n X n X n X  w2i,n (z), w i,n (z)w j,n (z)1 X i,1 < X j,1 + i=1 j=1 i=1 = 2(1 − s n ) + τ̂(3) − 1, and then τ̂(1) = τ̂(3) − 2s n . Moreover, implying 1 + τ̂(1) 1,2|Z=z 1,2|Z=z 1,2|Z=z 1,2|Z=z τ̂(2) = 1,2|Z=z n X n X    w i,n (z)w j,n (z) 1 X i,1 > X j,1 , X i,2 > X j,2 + 1 X i,1 < X j,1 , X i,2 < X j,2 i=1 j=1    − 1 X i,1 > X j,1 , X i,2 < X j,2 − 1 X i,1 < X j,1 , X i,2 > X j,2 =2 n X n X     w i,n (z)w j,n (z) 1 X i,1 > X j,1 , X i,2 > X j,2 − 1 X i,1 > X j,1 , X i,2 < X j,2 i=1 j=1 = (1) (3)  1 (3)  τ̂1,2|Z=z + τ̂1,2|Z=z 1 (1) τ̂1,2|Z=z + 1 + τ̂1,2|Z=z − 1 = = τ̂(1) + s n = τ̂(3) − sn .  1,2|Z=z 1,2|Z=z 2 2 2 A.3 Proof of Proposition 2 Lemma 12. Under Assumptions 3.1, 3.2 and 3.3, we have for any t > 0,     C hα nh p t2 R . IP ˆfZ (z) − fZ (z) ≥ K,α + t ≤ 2 exp − α! 2fZ,max K 2 + (2/3)C K t This Lemma is proved below. If, for some ϵ > 0, we have C K,α h α /α! + t ≤ fZ,min − ϵ, then ˆf (z) ≥ ϵ > 0 with a  R probability larger than 1 − 2 exp − nh p t2 /(2fZ,max K 2 + (2/3)C K t) . So, we should choose the largest t as possible, which yields Proposition 2. It remains to prove Lemma 12. Use the usual decomposition between a stochastic component and a bias:   ˆfZ (z) − fZ (z) = ˆfZ (z) − E[ˆfZ (z)] + E[ˆfZ (z)] − fZ (z) . We first bound the bias from above. Z    ˆ K(u) fZ z + hu − fZ (z) du. E[fZ (z)] − fZ (z) = Rp 310 | Alexis Derumigny and Jean-David Fermanian  Set ϕz,u (t) := fZ z + thu for t ∈ [0, 1]. This function has at least the same regularity as fZ , so it is αdifferentiable (by Assumption 3.2). By a Taylor-Lagrange expansion, we get  X Z α−1    1 (α) 1 (i) ϕz,u (0) + ϕz,u K(u) fZ z + hu − fZ (z) du = (tz,u ) du, K(u) i! α! i=1 Rp Rp R for some real number tz,u ∈ (0, 1). By Assumption 3.1(c) and for every i < α, Rp K(u)ϕ(i) z,u (0) du = 0. Therefore, Z 1 (α) ˆ E[fZ (z)] − fZ (z) = (tz,u )du K(u) ϕz,u α! p R Z p X  C ∂ α fZ 1 z + tz,u hu du ≤ K,α h α , K(u) h α u i1 . . . u i α = α! ∂z i1 . . . ∂z i α α! i1 ,...,i α =1 Rp Z where the last inequality results from Assumption 3.2. Second, the stochastic component may be written as ˆfZ (z) − E[ˆfZ (z)] = n−1 n X n n h i X X  K h (Zi − z) − E n−1 K h (Zi − z) = n−1 g(Zi ) − E[g(Zi )] , i=1 i=1 i=1 where g(Zi ) := K h (Zi − z). Apply Lemma 11 with m = 1 and the latter g(Zi ). Here, we have b = −a = h−p C K (by     R Assumption 3.1(a)), θ = E g(Z1 ) ≥ 0 (by Assumption 3.1(d)), and Var g(Z1 ) ≤ h−p fZ,max K 2 (combining Assumptions 3.1(b) and 3.3), so that we get n   1X K h (Zi − z) − E K h (Zi − z) ≥ t n IP ! ≤ 2 exp  i=1 − 2h−p fZ,max R  nt2 . K 2 + (2/3)h−p C K t A.4 Proof of Proposition 3 We show the result for k = 1. The two other cases can be proven in the same way. Using the decomposition (14), for any positive numbers x and λ(z), we have       X 1 1 + λ(z) 4(1 + λ(z)) > 2 S (z) > x + IP × IP τ̂1,2|Z=z − τ1,2|Z=z > x ≤ IP i,j ˆf 2 (z) fZ (z) fZ2 (z) Z 1≤i,j≤n     X 1 1 λ(z) 4(1 + λ(z)) ≤ IP − 2 > 2 + IP × S (z) > x . i,j ˆf 2 (z) fZ (z) fZ (z) fZ2 (z) 1≤i,j≤n Z  3 For any t s.t. C K,α h α /α! + t < fZ,min /2, set λ(z) = 16fz2 (z) C K,α h α /α! + t /fZ,min . This yields IP  τ̂1,2|Z=z − τ1,2|Z=z  1 16  C K,α h α > x ≤ IP − > 3 +t α! ˆf 2 (z) fZ2 (z) fZ,min Z  X  fz2 (z)x + IP S i,j (z) > . 4(1 + λ(z))   1 1≤i,j≤n By setting x= R   16fZ2 (z)  C K,α h α 4  CXZ,α h α 3fz (z) K 2 0 + + t 1 + + t , 3 α! 2nh p α! fz2 (z) fZ,min and applying the next two lemmas 13 and 14, we get the result.  On kernel-based estimation of conditional Kendall’s tau | 311 Lemma 13. Under Assumptions 3.1-3.3 and if C K,α h α /α! + t < fZ,min /2 for some t > 0, IP  1 ˆf 2 (z) Z −    1 16  C K,α h α nh p t2 R > + t ≤ 2 exp − , 3 α! 2fZ,max K 2 + (2/3)C K t fZ2 (z) fZ,min and ˆfZ (z) is strictly positive on these events. Proof : Applying the mean value inequality to the function x 7→ 1/x2 , we get the inequality 1/ˆfZ2 (z)−1/fZ2 (z) ≤  2 ˆfZ (z) − fZ (z) /fZ* 3 , where fZ* lies between ˆfZ (z) and fZ (z). Denote by E the event E := |ˆfZ (z) − fZ (z)| ≤ C K,α h α /α! + t . By Lemma 12, we obtain  IP(E) ≥ 1 − 2 exp − 2fZ,max R  nh p t2 . K 2 + (2/3)C K t (18) Therefore, on this event E, ˆfZ (z) − fZ (z) ≤ fZ,min /2. Moreover, we have fZ,min ≤ fZ (z) using Assumption 3.3 and then fZ,min /2 ≤ fZ* . Combining the previous inequalities, we finally get 1 ˆf 2 (z) Z −  1 16 ˆ 16  C K,α h α f (z) − f (z) + t , ≤ ≤ Z Z 3 3 α! fZ2 (z) fZ,min fZ,min on E. But since IP  1 ˆf 2 (z) Z −  16  C K,α h α 1 > 3 +t 2 α! fZ (z) fZ,min  ≤ IP(Ec ), we deduce the result.  Lemma 14. Under Assumptions 3.1-3.4, if C K̃,2 h2 < fz (z), we have for any t > 0 IP  X 1≤i,j≤n + R    CXZ,α h α 3fz (z) K 2 (n − 1)h2p t2 R + t ≤ 2 exp − 2 + S i,j (z) > α! 2nh p 4fZ,max ( K 2 )2 + (8/3)C2K t 2 exp  −  nh p (fz (z) − C K̃,2 h2 )2 . R 8fZ,max K̃ 2 + 4C K̃ (fz (z) − C K̃,2 h2 )/3 P Proof : We will use the decomposition of 1≤i,j≤n S i,j (z) given in Equation (15) and bound separately each of its three components with high probability. R We first bound the negligible diagonal term ∆ n . Note that K̃(·) := K 2 (·)/ K 2 is a two-order kernel, so that ˜fz (z) := Pn K̃ h (Zi − z)/n can be used as an estimator of fZ (z), where K̃ h (·) := h−p K̃(·/h). Therefore, applying i=1 Lemma 12 to ˜f , we have for ε > 0 such that C K̃,2 h2 /2 + ε = fz (z)/2, ! R n  R K 2  C h2  K2 X fZ (z) K 2 K̃,2 K̃ h (Zi − z) − ≥ +ε nh p nh p 2 n2 h p i=1   C K̃,2 h2 ˜ ≤ IP fZ (z) − fZ (z) ≥ +ε 2   nh p ε2 . ≤ 2 exp − R 2fZ,max K̃ 2 + (2/3)C K̃ ε R  3fz (z) K 2 IP ∆ n ≥ ≤ IP 2nh p  R Second, let us deal with the bias term. Simple calculations provide, if i ≠ j,      −2 E[S i,j (z)] = n E K h (Zi − z)K h (Zj − z) 1 Xi < Xj − IP Xi < Xj Zi = Zj = z (19) 312 | Alexis Derumigny and Jean-David Fermanian = n−2 Z    K h (z1 − z)K h (z2 − z) 1 x1 < x2 − IP Xi < Xj Zi = Zj = z R2p+2 = n−2 Z × fX,Z (x1 , z1 ) fX,Z (x2 , z2 ) dx1 dz1 dx2 dz2    K(u)K(v) 1 x1 < x2 − IP Xi < Xj Zi = Zj = z R2p+2       × fX,Z x1 , z + hu fX,Z x2 , z + hv − fX,Z (x1 , z) fX,Z (x2 , z) dx1 du dx2 dv, because, for every z, Z    1 x1 < x2 − IP X1 < X2 Z1 = Z2 = z fX,Z (x1 , z)fX,Z (x2 , z) dx1 dx2 . 0= R4   Apply the Taylor-Lagrange formula to the function ϕx1 ,x2 ,u,v (t) := fX,Z x1 , z + thu fX,Z x2 , z + thv which is differentiable by Assumption 3.4. This yields Z    E[S i,j (z)] = n−2 K(u)K(v) 1 x1 < x2 − IP Xi < Xj Zi = Zj = z  1 1 (k) ϕx1 ,x2 ,u,v (0) + ϕx(α) (t ) dx1 du dx2 dv x ,x ,u,v k! α! 1 ,x2 ,u,v 1 2 k=1 Z  (α) K(u)K(v)   = 1 x < x − IP X < X Z = Z = z ϕx1 ,x2 ,u,v (tx1 ,x2 ,u,v )dx1 du dx2 dv. 1 2 i j i j n2 α! × X α−1 Since ϕ(α) x1 ,x2 ,u,v (t) is equal to ! p α  ∂ α−k f   X X ∂ k fX,Z  α X,Z x1 , z + thu x2 , z + thv , h α u i1 . . . u i k v i k+1 . . . v i α k ∂z i1 . . . ∂z i k ∂z i k+1 . . . ∂z i α k=0 i1 ,...,i α =1 using Assumption 3.4, we get E[S1,2 (z)] ≤ CXZ,α h α /(n2 α!). (20) Third, the stochastic component will be bounded from above. Indeed, X  1 X gz (Xi , Zi ) , (Xj , Zj ) , (S i,j (z) − E[S i,j (z)]) = 2 n 1≤i≠j≤n 1≤i≠j≤n with the function gz defined in (9). We can now apply Lemma 11 to the sum of the g̃ i,j , which are symmetrized   versions of gz . With this notation, θ = E g̃ i,j = 0. Moreover, Z   h i  2 ≤ K 2h (z1 − z)K 2h (z2 − z) 1 x1 < x2 − IP Xi < Xj Zi = Zj = z Var gz (Xi , Zi ), (Xj , Zj ) × fX,Z (x1 , z1 )fX,Z (x2 , z2 ) dx1 dx2 dz1 dz2 2 2 K (t1 )K (t2 ) fX,Z (x1 , z − ht1 )fX,Z (x2 , z − ht2 ) dx1 dx2 dt1 dt2 h2p Z  2 2 ≤ h−2p fZ,max K2 , ≤ Z where in the last line we used Assumptions 3.1(b) and 3.3. The same upper bound applies for g̃ i,j (invoke Cauchy-Schwarz inequality). Here, we choose b = −a = 2C2K h−2p . Applying Lemma 11, for every t > 0, we obtain  X    X  2 S i,j (z) − E[S i,j (z)] ≥ t ≤ IP IP g̃ i,j > t n(n − 1) 1≤i≠j≤n 1≤i<j≤n   [n/2]t2 R ≤ 2 exp − −2p 2 . (21) 2h fZ,max ( K 2 )2 + (4/3)C2K h−2p t The latter inequality, (19) and (20) yield the result.  On kernel-based estimation of conditional Kendall’s tau | 313 A.5 Proof of Proposition 4 We will prove the following lemma, that straightforwardly implies the result. Lemma 15. Under the assumptions and conditions of Proposition 4, we have R  X  CXZ,α h α 3fz (z) K 2 IP + S i,j (z) > +t α! 2nh p 1≤i,j≤n ≤ + nh p (fz (z) − C K̃,2 h2 )2 R 8fZ,max K̃ 2 + 4C K̃ (fz (z) − C K̃,2 h2 )/3   nh p t2 R R R . 2 exp 3 32 K 2 ( |K |)2 fZ,max + 8C K |K |fZ,max t/3 C2 exp  − α2 nh p t R 8fZ,max ( K 2 )  + 2 exp  −  P Proof : As in the proof of Lemma 14, we will use the decomposition of 1≤i,j≤n S i,j (z) given in Equation (15) and bound separately each of its three components with high probability. We keep the same bounds for the diagonal term ∆ n from Equation (19) and for the bias term in Equation (20). The difference from Lemma 14 will come from the treatment of the stochastic term that is detailed below. Now, we consider the function `z defined in Equation (13). Note that k`z k∞ ≤ 1. By usual changes of variables, we get Z `2z (x1 , z1 , x2 , z2 ) fX,Z (x1 , z1 )fX,Z (x2 , z2 ) dx1 dx2 dz1 dz2 R 2 R R 2 ( K 2 fz,max )2 3p K f z,max ( | K | f z,max ) ≤ 3h2p + 6h ≤ σ2 , with 2 2 2 2 (4C K ) (4C K ) σ := h p C σ , C σ := Z K 2 fz,max /(2C2K ), (22) R R R because 6h p K 2 fz,max ( |K |fz,max )2 ≤ ( K 2 fz,max )2 and because of Assumptions 3.1(b) and 3.3. With the notations of [26], this implies D = 1, m = 1 and L is arbitrarily small. Therefore, Theorem 2 in [26] yields     α x 1 X , (23) IP `z (Xi , Zi , Xj , Zj ) > x ≤ C2 exp − 2 2n σ i≠j for some universal constants C2 and α2 when x ≤ nσ3 . By setting t/2 = 4C2K x/(nh2p ) and applying Lemma 11, this provides   X  n 1 1 X ≤ IP 2 ξ ij ≥ t/2 + IP IP g i ≥ t/4 n n 1≤i≠j≤n 1≤i≠j≤n i=1     α2 nth p nh p t2 R R R R ≤ C2 exp − , + 2 exp 3 8fZ,max ( K 2 ) 32 K 2 ( |K |)2 fZ,max + 8/3C K |K |fZ,max t  X  S i,j (z) − E[S i,j (z)] ≥ t   R 3 when t ≤ 2h p ( K 2 )3 fZ,max /C4K . Combining this inequality, (19) and (20) with the decomposition (15) conclude the proof.  A.6 Proof of Proposition 6 For k τ1,2|Z=z = 1, we follow the path of the proof of Proposition 4 (of Section A.5). Since τ̂1,2|Z=z − P = 4 1≤i,j≤n S i,j (z)/ˆfZ2 (z) (by Equation 14), we prove the result if we bound from above 1/ˆfZ2 (z) and 314 | Alexis Derumigny and Jean-David Fermanian 1≤i,j≤n S i,j (z) uniformly w.r.t. z ∈ Z. To be specific, for any positive constant µ −2 then 1/ˆfZ2 (z) ≤ fz,min (1 − µ)−2 . We deduce P < 1, if |ˆfZ (z)−fZ (z)| ≤ µfz,min ,      4 sup IP sup τ̂1,2|Z=z − τ1,2|Z=z > x ≤ IP kˆfZ − fZ k∞ > µfz,min + IP 2 f (1 − µ)2 z∈Z z∈Z Z,min X  S i,j (z) > x . 1≤i,j≤n First invoke the uniform exponential inequality, as stated in [35], Proposition 9: for every ε < R b K K 2 fZ,max /C K ,      C hα IP kˆfZ − fZ k∞ > ε + XZ,α ≤ IP kˆfZ − E[ˆfZ ]k∞ > ε ≤ L K exp − C f ,K nh p ε2 , (24) α! for n sufficiently large. Then, apply Lemma 16, by setting (x, ε) so that R C  α 3fz,max K 2 C hα 4 XZ,α h + = µfz,min .  x= 2 + t and ε + XZ,α p 2 α! 2nh α! fz,min (1 − µ) Lemma 16. Under the assumptions and conditions of Proposition 6, we have ! R   X CXZ,α h α 3fz,max K 2 α2 nth p R + t + ≤ C D exp − IP sup S i,j (z) > 2 α! 2nh p 8fZ,max ( K 2 ) z∈Z 1≤i,j≤n       C f , K̃ nh p (fz,max − C̃XZ,2 h2 )2 A2 nh p t2 C−4 A2 nh p t + 2 exp − + L K̃ exp − + 2 exp − 2 2 R 2 3 K R . 4 16C2K A1 16 A1 K fz,max ( |K |)2 Proof : We will use the same arguments as in the proofs of Lemmas 14 and 15. We still invoke the decomposiR P tion (15). First let us find a uniform bound for the “diagonal term” ∆ n (z) = ni=1 S i,i (z) = K 2 ˜fz (z)/(nh p ). As R in (24), for every ε < b K̃ K̃ 2 fZ,max /C K̃ ,    C̃ h2 IP k˜fZ − fZ k∞ > ε + XZ,2 ≤ L K̃ exp − C f , K̃ nh p ε2 , 2 for n sufficiently large. This implies R 2 n R  R 2  !  K X fZ (z) K 2 K C̃XZ,2 h2 ≥ ε+ ≤ L K̃ exp − C f , K̃ nh p ε2 . IP sup 2 p K̃ h (Zi − z) − p p nh nh 2 n h z∈Z i=1 Choose ε s.t. C̃XZ,2 h2 /2 + ε = fz,max /2 so that we have the bound   Z  IP sup |∆ n (z)| ≥ 3fz,max K 2 /(2nh p ) ≤ L K̃ exp − C f , K̃ nh p ε2 . z∈Z (25) Second, it is easy to see that the bias term is uniformly bounded by sup E[S1,2 (z)] ≤ CXZ,α h α /(n2 α!). z∈Z (26) Third, we bound the two components of the stochastic termogiven by (17). Now apply Theorem 1 in [26], n by recalling (13) and considering the family F := `z , z ∈ Z , for a fixed bandwidth h. The constant σ has the same value as in (22). It is easy to check that the latter class of functions is L2 dense (see [26]). Set ε ∈ (0, 1). Since K is λ K -Lipschitz by Assumption 3.5, every function `z ∈ F can be approximated in L2 by R a function `zj ∈ F, for some j ∈ {1, . . . , m} s.t. |`z − `zi |2 dν ≤ ε2 , for any probability measure ν. Indeed, R |`z − `zi |2 dν ≤ 64λ2K kz − zj k2∞ C2K h−2 that is less than ε2 , if we cover Z by a grid of m points (zj ) in Z s.t.  Qp kz − zj k∞ ≤ εh/(8C K λ K ) := εδ. This can be done with m ≤ ε−p d k=1 (b k − a k )/δ e = ε−p dVδ−p e points. Then, with the notations of [26], L = p and D = V(8C K λ K /h)p . As above, this yields !  α nh p t Z   1 X IP sup 2 ξZ (Xi , Zi , Xj , Zj ) > t ≤ C2 D exp − 2 K2 , (27) 8fZ,max n z∈Z 1≤i≠j≤n On kernel-based estimation of conditional Kendall’s tau | 315 R 3 when t ≤ 2h p ( K 2 )3 fZ,max /C4K . It remains to bound IP(supz∈Z |n−1 Pn i=1 g i | > t/4). Consider the family of functions F := {(x1 , z1 ) ∈ R × Z 7→ hp E[gz (x1 , z1 , X, Z)], z ∈ Z}. 4C2K 2 R R 3 This family of functions is bounded by one and its variance is less than σ2 := h p K 2 fz,max |K | . Therefore, using Assumption 3.5, we can apply Propositions 9 and 10 in [12] that are coming from [11]: for some universal constants A1 and A2 , some constant A g that depends on K and fz,max (see Proposition 1 in [11]) and for every x > 0, !   n   hp X  A2 x2 1/2 IP sup 2 ≤ 2 exp − + 2e−A2 x , E gz (Xi , Zi , X, Z) Xi , Zi > A1 x + A g n σ ln(1/σ) nσ2 z∈Z 4C K i=1 that can be rewritten as   n Ag σ 1 X g i > 4A1 C2K x − 1/2 p ln(σ) IP sup n n h z∈Z ! ≤ 2 exp  − i=1 A2 nh2p x2 σ2  + 2 exp(−A2 nh p x). For any positive t s.t. 4A1 C2K (n−1)A g σ ln(1/σ) < n3/2 h p t/8, note that we can find a real x > th p /(16C2K A1 ). Then, we have !     n A2 nh p t2 C−4 t (n − 1) X A2 nh p t KR R > g . (28) IP sup ≤ 2 exp − + 2 exp − i 3 4 n2 16C2K A1 162 A21 K 2 fz,max ( |K |)2 z∈Z i=1 The proof is completed by combining all the inequalities (25), (26), (27) and (28) with the decompositions (15) and (17).  A.7 Proof of Proposition 7   Note that τ1,2|Z=z = E g k (X1 , X2 ) Z1 = z, Z2 = z for every k = 1, 2, 3, and that our estimators with the weights (2) can be written as τ̂(k) := U n (g k ) / {U n (1) + ϵ n }, where 1,2|Z=z U n (g) := X X K h (z − Zi )K h (z − Zj ) 1 1 =: g(Xi , Xj ) g i,j , n(n − 1) E[K h (z − Z)]2 n(n − 1) 1≤i≠j≤n 1≤i≠j≤n Pn 2 for any measurable bounded function g, with the residual diagonal term ϵ n := i=1 K h (z − Zi )/ { n(n − 2 p −1 1)E[K h (z − Z)] }. By Bochner’s lemma (see Bosq and Lecoutre [5]), ϵ n is O P ((nh ) ), and it will be negligible compared to U n (1). Since the reasoning will be exactly the same for every estimator τ(k) , i.e. for every 1,2|z function g k , k = 1, 2, 3, we omit the sub-index k. Then, the functions g k will be simply denoted by g. The expectation of our U-statistics is     E U n (g) := E g(X1 , X2 )K h (z − Z1 )K h (z − Z2 ) /E[K h (z − Z)]2 Z = g(x1 , x2 )K(t1 )K(t2 )fX,Z (x1 , z + ht1 )fX,Z (x2 , z + ht2 )dx1 dx2 dt1 dt2 /E[K h (z − Z)]2 Z   1 → g(x1 , x2 )fX,Z (x1 , z)fX,Z (x2 , z)dx1 dx2 = E g(X1 , X2 ) Z1 = z, Z2 = z , fZ2 (z) R applying Bochner’s lemma to z 7→ g(x1 , x2 )fX|Z=z (x1 )fX|Z=z (x2 ) dx1 dx2 = τ1,2|Z=z , that is a continuous function by assumption. 316 | Alexis Derumigny and Jean-David Fermanian Set θ n := E[U n (g)], g * (x1 , x2 ) := (g(x1 , x2 ) + g(x2 , x1 ))/2 and g *i,j = (g i,j + g j,i )/2 for every (i, j), i ≠ j. Note that U n (g) = U n (g * ). Since g * is symmetrical, the HÃąjek projection Û n (g * ) of U n (g * ) satisfies P * Û n (g * ) := 2 nj=1 E[g0,j |Xj , Zj ]/n − θ n . Note that E[Û n (g * )] = θ n = τ1,2|Z=z + o P (1). Since Var(Û n (g * ) = * 4Var(E[g0,j |Xj , Zj ])/n = O((nh p )−1 ), then Û n (g * ) = θ n + o P (1) = τ1,2|Z=z + o P (1). Moreover, using the notation g i,j := g*i,j − E[g *i,j |Xj , Zj ] − E[g *i,j |Xi , Zi ] + θ n for 1 ≤ i ≠ j ≤ n, we have P U n (g* ) − Û n (g * ) = 1≤i≠j≤n g i,j /n(n − 1). By usual U-statistics calculations, it can be easily checked that  Var U n (g * ) − Û n (g * ) = 1 n2 (n − 1)2 X X E[g i1 ,j1 g i2 ,j2 ] = O 1≤i1 ≠j1 ≤n 1≤i2 ≠j2 ≤n 1  . n2 h2p Indeed, when all indices (i1 , i2 , j1 , j2 ) are different, or when there is a single identity among them, E[g i1 ,j1 g i2 ,j2 ] is zero. The first nonzero terms arise when there are two identities among the indices, i.e. i1 = i2 and j1 = j2 (or i1 = j2 and j1 = i2 ). In the latter case, we get an upper bound as O((nh p )−2 ) when fZ is continuous at z, by usual changes of variable techniques and Bochner’s Lemma. Then, U n (g* ) = Û n (g * ) + o P (1) = τ1,2|Z=z + o P (1). Note that U n (1) + ϵ n tends to one in probability (Bochner’s lemma). As a consequence, τ̂1,2|Z=z = U n (g* ) / (U n (1) + ϵ n ) tends to τ1,2|Z=z /1 by the continuous mapping theorem.  A.8 Proof of Proposition 8 Let us note that   τ1,2|Z=z = E g k (X1 , X2 ) Z1 = z, Z2 = z = Z g k (x1 , x2 )fX|Z=z (x1 )fX|Z=z (x2 )dx1 dx2 = ϕ k (z) , fZ2 (z) R ˆ k (z)/ˆf 2 (z), where ϕ ˆ k (z) := = ϕ where ϕ k (z) := g k (x1 , x2 )fX,Z (x1 , z)fX,Z (x2 , z)dx1 dx2 . Also write τ̂(k) Z 1,2|Z=z P P n−2 ni,j=1 K h (Zi − z)K h (Zj − z)g k (Xi , Xj ) and ˆfZ (z) := n−1 ni=1 K h (Zi − z). Therefore, we have τ̂(k) − τ1,2|Z=z = 1,2|Z=z ˆ k (z) − ϕ k (z) ˆf (z) − fZ (z)  ϕ − τ1,2|Z=z Z × ˆfZ (z) + fZ (z) . ˆf 2 (z) ˆf 2 (z) Z Z By usual uniform consistency results (see for example Bosq and Lecoutre [5]), supz∈Z ˆfZ (z) − fZ (z) → 0 almost surely, as n → ∞. We deduce that 2 min ˆfZ2 (z) ≥ fZ,min /2, and max |ˆfZ (z) + fZ (z)| ≤ 2 max fZ (z) a.s. z∈Z z∈Z z∈Z ˆ k on Z, to obtain that sup This means it is sufficient to prove the uniform strong consistency of ϕ τ̂(k) − z∈Z 1,2|Z=z tends to zero a.s. τ(k) 1,2|Z=z ˆ k (z)] − ϕ k (z) → 0. Then, it remains to show that Note that, by Bochner’s Lemma, supz∈Z E[ϕ ˆ ˆ supz∈Z ϕ k (z) − E[ϕ k (z)] → 0 almost surely. Let ρ n > 0 be such that we cover Z by the union of l n open balls B(tl , ρ n ), where t1 , . . . , tl n ∈ Rp and l n ∈ N* . Then ˆ k (z) − E[ϕ ˆ k (z)] ≤ sup sup ϕ z∈Z ˆ k (tl ) − E[ϕ ˆ k (tl )] + A n , ϕ l=1,...l n ˆ k (z) − ϕ ˆ k (tl ) − (E[ϕ ˆ k (z)] − E[ϕ ˆ k (tl )]) . For any index l ∈ {1, . . . , l n } and where A n := supl=1,...l n supz∈B(tl ,ρ n ) ϕ any z ∈ B(tl , ρ n ), a first-order expansion yields ˆ k (z) − ϕ ˆ k (tl ) − (E[ϕ ˆ k (z)] − E[ϕ ˆ k (tl )]) ϕ X 1 g k (Xi , Xj )K h (z − Zi )K h (z − Zj ) = n(n − 1) 1≤i≠j≤n On kernel-based estimation of conditional Kendall’s tau | − 317 X 1 g k (Xi , Xj )K h (tl − Zi )K h (tl − Zj ) n(n − 1) 1≤i≠j≤n      − E g k (X1 , X2 )K h (z − Z1 )K h (z − Z2 ) − E g k (Xi , Xj )K h (tl − Zi )K h (tl − Zj )    X  C Lip,K 1 |g k (Xi , Xj )| |z − tl | E |g k (X1 , X2 )| + 2p+1 h n(n − 1) 1≤i≠j≤n   ρn = O 2p+1 = o(1), h ≤ for some constant C Lip,K and by choosing ρ n = o(h2p+1 ). Actually, we can cover Z in such a way that l n = n −p(2p+1) O(h n ). This is always possible because Z is a bounded set in Rp . The previous upper bound is uniform w.r.t. l and z ∈ B(tl , ρ n ), proving A n = o(1) everywhere. Now, for every l ≤ l n , apply Equation (21) for every z = tl . For any t > 0, this yields   h  C nh2p t2  X (l)  i 1 , g (Xi , Zi ), (Xj , Zj ) − E g (l) (X1 , Z1 ), (X2 , Z2 ) IP > t ≤ exp − 0 n C1 + C2 t n(n − 1) i≠j for some positive constants C0 , C1 , C2 , by setting  g (l) (Xi , Zi ), (Xj , Zj ) := g k (Xi , Xj )K h (tl − Zi )K h (tl − Zj ). Therefore, we deduce IP ˆ k (tl ) − E[ϕ ˆ k (tl )] ≥ t ϕ sup l=1,...l n !  C nh2p t2  ≤ C4 h−p(2p+1) exp − 0 n , n C1 + C2 t ˆ k (z) − E[ϕ ˆ k (z)] tends to zero a.s., for some constant C4 . Finally, applying Borel-Cantelli lemma, supz∈Z ϕ proving the result.  A.9 Proof of Proposition 9 By Markov’s inequality, Pn i=1 w2i,n (z) = O P ((nh p )−1 ) for any z, that tends to zero. Then, by Slutsky’s theorem, , k = 1, 2, 3, and of their linearly we get an asymptotic equivalence between the limiting laws of any τ̂(k) 1,2|z transformed versions τ̃1,2|z . Thus, we will prove the asymptotic normality of τ̂(k) for some index k = 1, 2, 3, 1,2|z simply denoted by τ̂1,2|z . Let g * (x1 , x2 ) := (g k (x1 , x2 ) + g k (x2 , x1 ))/2 for some index k = 1, 2, 3 (that will be implicit in the proof). We now study the joint behavior of (τ̂1,2|Z=z0i − τ1,2|Z=z0i )i=1,...,n0 . We will extend Stute [38]’s approach, in the case of multivariate conditioning variable z and studying the joint distribution of U-statistics at several conditioning points. As in the proof of Proposition 7, the estimator with the weights given by (2) can be rewritten as τ̂1,2|Z=z0i := U n,i (g * ) / (U n,i (1) + ϵ n,i ), where U n,i (g) := 1 n(n − 1)E[K h (z0i − Z)]2 n X g(Xj1 , Xj2 )K h (z0i − Zj1 )K h (z0i − Zj2 ), j1 ,j2 =1,j1 ≠j2 for any bounded measurable function g : R4 → R.  Now, we prove the joint asymptotic normality of U n,i (g) i=1,...,n0 . The HÃąjek projection Û n,i (g) of U n,i (g)    P satisfies Û n,i (g) := 2 nj=1 g n,i Xj , Zj /n − θ n , where θ n := E U n,i (g) (see [37, Section 5.3.1]) and   g n,i (x, z) := K h (z0i − z)E g(X, x)K h (z0i − Z) / E[K h (z0i − Z)]2 . 318 | Alexis Derumigny and Jean-David Fermanian Lemma 17. Under the assumptions of Proposition 9, for any measurable bounded function g,    D −→ N(0, M∞ (g)), as n → ∞, (nh p )1/2 Û n,i (g) − E U n,i (g) i=1,...,n0 where, for 1 ≤ i, j ≤ n0 , [M∞ (g)]i,j := 4 R K 2 1{z0i =z0j } Z fZ (z0i ) g x1 , x)g x2 , x)fX|Z=z0i (x)fX|Z=z0i (x1 )fX|Z=z0i (x2 )dx dx1 dx2 . This lemma is proved in A.10. Similarly as in the proof of Lemma 2.2 in Stute [38], for every i = 1, . . . , n0 and   every bounded symmetrical measurable function g, we have (nh p )1/2 Var Û n,i (g) − U n,i (g) = o(1), which implies    D −→ N(0, M∞ (g)), as n → ∞. (nh p )1/2 U n,i (g) − E U n,i (g) i=1,...,n0 Considering two measurable bounded functions g1 and g2 , we have U n,i (c1 g1 + c2 g2 ) = c1 U n,i (g1 ) + c2 U n,i (g2 ) for every numbers c1 , c2 . By the CramÃľr-Wold device, we check that        (nh p )1/2 U n,i (g1 ) − E U n,i (g1 ) , U n,i (g2 ) − E U n,i (g2 ) i=1,...,n0 i=1,...,n0 " #! M∞ (g1 ) M∞ (g1 , g2 ) D −→ N 0, , M∞ (g1 , g2 ) M∞ (g2 ) as n → ∞, where [M∞ (g1 , g2 )]i,j := 4 R K 2 1{z0i =z0j } Z fZ (z0i ) g1 x1 , x)g2 x2 , x)fX|Z=z0i (x)fX|Z=z0i (x1 )fX|Z=z0i (x2 )dx dx1 dx2 . Set τ̃1,2|Z=z0i := U n,i (g * ) / U n,i (1). Note that supi=1,...,n0 |ϵ n,i | = O P (n−1 h−p ). Since (nh pn )1/2 τ̂1,2|Z=z0i −   τ̃1,2|Z=z0i = O P (nh pn )1/2 ϵ n,i is o P (1) by Assumption 3.6(i), it is sufficient to establish the asymptotic law  of (nh pn )1/2 τ̃1,2|Z=z0i − τ1,2|Z=z0i . By a limited expansion of fX,Z w.r.t. its second argument, and under As  sumption 3.4, we easily check that E U n,i (g * ) = τ1,2|Z=z0i + r n,i , where |r n,i | ≤ C0 h αn /fZ2 (z0i ), for some constant C0 that is independent of i. Since E[U n,i (1)] = 1 + o((nh p )−1/2 ) and E[U n,i (g * )] = τ1,2|Z=z0i + o((nh pn )−1/2 ) by Assumption 3.6(i), we get      (nh p )1/2 U n,i (g * ) − τ1,2|Z=z0i , U n,i (1) − 1 i=1,...,n0 i=1,...,n0 " #! M∞ (g * ) M∞ (g * , 1) D −→ N 0, , as n → ∞. M∞ (g * , 1) M∞ (1) Now apply the Delta-method with the function ρ(x, y) := x/y where x and y are real-valued vectors of size n0 and the division has to be understood component-wise. The Jacobian of ρ is given by the n0 × 2n0 matrix h  i −1 −2 −2 J ρ (x, y) = Diag y−1 , 1 , . . . y n0 , Diag − x 1 y 1 , · · · − x n0 y n0 where, for any vector v of size n0 ,Diag(v) is the diagonal matrix whose diagonal elements are the v i , with  D 0 p 1/2 i = 1, . . . , n . We deduce (nh ) τ̃1,2|Z=z0i − τ1,2|Z=z0i −→ N(0, H), as n → ∞, setting i=1,...,n0 " H := J ρ (~τ , e) M∞ (g* ) M∞ (g * , 1) # M∞ (g * , 1) J ρ (~τ , e)T , M∞ (1) On kernel-based estimation of conditional Kendall’s tau | 319   where ~τ = τ1,2|Z=z0i and e is the vector of size n0 whose all components are equal to 1. Thus, we have i=1,...,n h i 0 J ρ (~τ , e) = Id n0 , −Diag(~τ) , denoting by Id n0 the identity matrix of size n0 and by Diag(~τ) the diagonal matrix of size n0 whose diagonal elements are the τ1,2|z0i , for i = 1, . . . , n0 . To be specific, we get H = M∞ (g * ) − Diag(~τ)M∞ (g * , 1) − M∞ (g * , 1)Diag(~τ) + Diag(~τ)M∞ (1)Diag(~τ). For i, j in {1, . . . , n0 } and using the symmetry of the function g* , we obtain Z [M∞ (g * )]i,j = 4 K 2 1{z0i =z0j } E[g* (X1 , X)g * (X2 , X)|Z = Z1 = Z2 = z0i ]/fZ (z0i ), Z [Diag(~τ)M∞ (g * , 1)]i,j = 4τ1,2|Z=z0i K 2 1{z0i =z0j } E[g * (X1 , X)|Z = Z1 = z0i ]/fZ (z0i ) Z = 4 K 2 1{z0i =z0j } τ21,2|Z=z0 /fZ (z0i ) = [M∞ (g * , 1)Diag(~τ)]i,j = [Diag(~τ)M∞ (1)Diag(~τ)]i,j . i As a consequence, we obtain R  4 K 2 1{z0i =z0j }  2 0 * * [H]i,j = ] − τ E[g (X , X)g (X , X) | Z = Z = Z = z 0 .  1 2 1 2 i 1,2|Z=z i fZ (z0i ) A.10 Proof of Lemma 17 Let us first evaluate the variance-covariance matrix M n,n0       E g n,i (Xj , Zj ) = E Û n,i = E U n,i (g) , and that   (nh p )1/2 Û n,i − E[U n,i (g)] i=1,...,n0 = := [Cov(Û n,i , Û n,j )]1≤i,j≤n0 . Note that n  2h p/2 X g n,i (Xj , Zj ) − E[U n,i (g)] i=1,...,n0 , n1/2 j=1   that is a sum of independent vectors. Thus, Cov(Û n,i , Û n,j ) = 4n−1 Cov g n,i X, Z , g n,j X, Z , for every i, j in {1, . . . , n0 }, and   E g n,i (X, Z)g n,j (X, Z)     Z E g(X, x)K h (z0i − Z) E g(X, x)K h (z0j − Z) 0 0 = K h (zi − z)K h (zj − z) fX,Z (x, z)dx dz E[K h (z0i − Z)]2 E[K h (z0j − Z)]2 Z 1 g x1 , x)g x2 , x)K h (z0i − z)K h (z0j − z)K h (z0i − w1 )K h (z0j − w2 ) ∼ h p fZ2 (z0i )fZ2 (z0j ) × fX,Z (x, z)fX,Z (x1 , w1 )fX,Z (x2 , w2 )dx dz dx1 dw1 dx2 dw2 Z z0j − z0i 1 g x , x)g x , x)K(u )K(u )K(u)K( + u)fX,Z (x, z0i − hu) 1 2 1 2 2 0 2 0 h h p fZ (zi )fZ (zj ) ∼ fX,Z (x1 , z0i − hu1 )fX,Z (x2 , z0j − hu2 )dx du dx1 du1 dx2 du2 . × When i ≠ j and for n sufficiently large, the latter term is zero because K is compactly supported (Assumption 3.6(ii)). In this case, we have Cov(Û n,i , Û n,j ) = −4n−1 E[U n,i ]E[U n,j ] ∼ −4n−1 τ1,2|Z=z0i τ1,2|Z=z0j = h  i o (nh p )−1 . Otherwise, i = j and, as E g n,i X1 , Z1 = O(1), we have  Var 2  g n,i (X, Z) ∼ 1 p h fZ4 (z0i ) Z g x1 , x)g x2 , x)K(u1 )K(u2 )K 2 (u)fX,Z (x, z0i − hu) × fX,Z (x1 , z0i − hu1 )fX,Z (x2 , z0i − hu2 ) dx du dx1 du1 dx2 du2 320 | Alexis Derumigny and Jean-David Fermanian K2 ∼ p h fZ (z0i ) R Z g x1 , x)g x2 , x)fX|Z=z0i (x)fX|Z=z0i (x1 )fX|Z=z0i (x2 ) dx dx1 dx2 , by Bochner’s lemma and 3.1. We have proved that, for every i, j ∈ {1, . . . , n0 }, R 4 K 2 1{z0i =z0j } Z p g x1 , x)g x2 , x)fX|Z=z0i (x)fX|Z=z0i (x1 )fX|Z=z0i (x2 ) dx dx1 dx2 , nh [M n,n0 ]i,j → fZ (z0i ) as n → ∞. Therefore, nh p M n,n0 tends to M∞ . We now verify Lyapunov’s condition with third-order moments, so that the usual multivariate central limit theorem would apply. It is then sufficient to show that n h  h p/2 3 X i 3 E g n,i (Xj , Zj ) − E[U n,i (g)] = o(1). 1/2 n (29) j=1 For any j = 1, . . . , n, we have h i 3 E g n,i (Xj , Zj ) − E[U n,i (g)] Z Z  3 1 g(x1 , x)K h (z0i − z1 )K h (z0i − z)fX,Z (x1 , z1 )dx1 dz1 − E U n,i (g) fX,Z (x, z)dx dz. ∼ 2 0 fZ (zi ) By the change of variable z1 = z0i − ht1 and z = z0i − ht, we get Z Z h i 1 3 E g n,i (Xj , Zj ) − E[U n,i (g)] ∼ h−2p g(x1 , x)K(t1 )K(t)fX,Z (x1 , z0i − ht1 )dx1 dt1 fZ2 (z0i )  3 − h p E U n,i (g) fX,Z (x, z0i − ht)dx dt = O(h−2p ), because of Bochner’s lemma and Assumptions 3.1 and 3.4. Therefore, we have obtained n  h p/2 3 X h i 3 E g (X , Z ) − E[U (g)] = O(h3p/2 n−3/2 nh−2p ) = O((nh p )−1/2 ) = o(1), n,i j j n,i n1/2 j=1 applying Assumption 3.6(i). Therefore, we have checked Lyapunov’s condition and the result follows.  References [1] [2] [3] Acar, E. F., C. Genest, and J. Nešlehová (2012). Beyond simplified pair-copula constructions. J. Multivariate Anal. 110, 74–90. 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Fermanian (2019). A classification point-of-view about conditional Kendall’s tau. Comput. Statist. Data Anal. 135, 70–94. [10] Dony, J. and D. M. Mason (2008). Uniform in bandwidth consistency of conditional U-statistics. Bernoulli 14(4), 1108–1133. [11] Einmahl, U. and D. M. Mason (2005). Uniform in bandwidth consistency of kernel-type function estimators. Ann. Statist. 33(3), 1380–1403. On kernel-based estimation of conditional Kendall’s tau | 321 [12] Fermanian, J.-D. and O. Lopez (2018). Single-index copulas. J. Multivariate Anal. 165, 27–55. [13] Fermanian, J.-D. and M. H. Wegkamp (2012). Time-dependent copulas. J. Multivariate Anal. 110, 19–29. [14] Filzmoser, P., H. Fritz, and K. Kalcher (2018). pcaPP: Robust PCA by Projection Pursuit. R package version 1.9-73. Available on CRAN. [15] Gijbels, I., N. Veraverbeke, and M. Omelka (2011). Conditional copulas, association measures and their applications. Comput. Statist. Data Anal. 55(5), 1919–1932. [16] Giné, E. and A. Guillou (2002). Rates of strong uniform consistency for multivariate kernel density estimators. Ann. Inst. Henri Poincaré Probab. Stat. 38(6), 907–921. [17] Hobæk Haff, I., K. Aas, and A. Frigessi (2010). On the simplified pair-copula construction – Simply useful or too simplistic? J. Multivariate Anal. 101(5), 1296–1310. [18] Hollander, M. and D. A. Wolfe (1973). Nonparametric Statistical Methods. John Wiley & Sons, New York. [19] Hsieh, J.-J. and W.-C. Huang (2015). Nonparametric estimation and test of conditional Kendall’s tau under semi-competing risks data and truncated data. J. Appl. Stat. 42(7), 1602–1616. [20] Joe, H. (1997). Multivariate Models and Dependence Concepts. CRC Press, Boca Raton FL. [21] Kim, Y.-J. (2015). Estimation of conditional KendallâĂŹs tau for bivariate interval censored data. Commun. Stat. Appl. Methods 22(6), 599–604. [22] Kruskal, W. H. (1958). Ordinal measures of association. J. Amer. Statist. Assoc. 53(284), 814–861. [23] Lakhal, L., L.-P. Rivest, and B. Abdous (2008). Estimating survival and association in a semicompeting risks model. Biometrics 64(1), 180–188. [24] Lehmann, E. L. (1975). Nonparametrics: Statistical Methods Based on Ranks. Holden-Day, San Francisco. [25] Liu, A., Y. Hou, and L. Peng (2015). Interval estimation for a measure of tail dependence. Insurance Math. Econom. 64, 294–305. [26] Major, P. (2006). An estimate on the supremum of a nice class of stochastic integrals and U-statistics. Probab. Theory Related Fields 134(3), 489–537. [27] Manatunga, A. K. and D. Oakes (1996). A measure of association for bivariate frailty distributions. J. Multivariate Anal. 56(1), 60–74. [28] Martin, E. C. and R. A. Betensky (2005). Testing quasi-independence of failure and truncation times via conditional Kendall’s tau. J. Amer. Statist. Assoc. 100(470), 484–492. [29] Moral-Carcedo, J. and J. Pérez-García (2019). Time of day effects of temperature and daylight on short term electricity load. Energy 174, 169–183. [30] Nelsen, R. B. (2006). An Introduction to Copulas. Second edition. Springer, New York. [31] Oakes, D. (1989). Bivariate survival models induced by frailties. J. Amer. Statist. Assoc. 84(406), 487–493. [32] Pardo, A., V. Meneu, and E. Valor (2002). Temperature and seasonality influences on Spanish electricity load. Energy Econ. 24(1), 55–70. [33] Patton, A. (2006a). Estimation of multivariate models for time series of possibly different lengths. J. Appl. Econometrics 21(2), 147–173. [34] Patton, A. (2006b). Modelling asymmetric exchange rate dependence. Internat. Econom. Rev. 47(2), 527–556. [35] Rinaldo, A. and L. Wasserman (2010). Generalized density clustering. Ann. Statist. 38(5), 2678–2722. [36] Sabeti, A., M. Wei, and R. V. Craiu (2014). Additive models for conditional copulas. Stat 3(1), 300–312. [37] Serfling, R. J. (1980). Approximation Theorems of Mathematical Statistics. John Wiley & Sons, New York. [38] Stute, W. (1991). Conditional U-statistics. Ann. Probab. 19(2), 812–825. [39] Tsai, W.-Y. (1990). Testing the assumption of independence of truncation time and failure time. Biometrika 77(1), 169–177. [40] Veraverbeke, N., M. Omelka, and I. Gijbels (2011). Estimation of a conditional copula and association measures. Scand. J. Stat. 38(4), 766–780.
https://openalex.org/W2075512617
http://www.scielo.cl/pdf/iusetp/v16n2/art14.pdf, https://www.redalyc.org/pdf/197/19715603014.pdf
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PRISIÓN PREVENTIVA, TERREMOTO Y SAQUEOS: COMENTARIO A LAS SENTENCIAS DE LA CORTE SUPREMA
Ius et Praxis
2,010
cc-by
10,641
Revista Ius et Praxis, Año 16, Nº 2, 2010, pp. 393 - 414 ISSN 0717 - 2877 Universidad de Talca - Facultad de Ciencias Jurídicas y Sociales “Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema” Humberto Alarcón Corsi Prisión preventiva, terremoto y saqueos: comentario a las sentencias de la Corte Suprema* Humberto Alarcón Corsi** I. Contexto de las sentencias comentadas Momentos después del terremoto y maremoto del 27 de febrero de 2010, ocurrido en la zona centro sur del país, se produjeron sucesos consistentes en ataques masivos a establecimientos de comercio, los cuales fueron calificados de saqueos1. Dichos hechos ocurrieron especialmente en los principales centros urbanos de la Provincia de Concepción, capital de la Región del Bío-Bío, los que produjeron preocupación y temor en la ciudadanía2. La autoridad de la época3, dados los sucesos descritos, decretó de conformidad con lo dispuesto en el artículo 40 Nº 2 de la Constitución Política de la República (en adelante CPR), el estado excepcional de emergencia constitucional, con la finalidad de: 1) Mantener, y garantizar el orden público en las regiones más afectadas por el terremoto y maremoto; 2) Permitir que la ayuda estatal llegase a las víctimas, * Colaboración recibida el 20 de octubre y aprobada el 29 de octubre de 2010. ** Abogado, Universidad de Talca; Mg. Derecho Penal. Profesor de Derecho Penal, Universidad de Talca; Defensor Local Jefe de Concepción. Correo electrónico: halarcon@utalca.cl. Dicha expresión no existe, al menos como una categoría típica en el texto de nuestro Código Penal, ni en nuestra legislación. Sin embargo, fue utilizada masivamente por toda la comunidad a partir del 27 de febrero de 2010. Así puede verse en los titulares de los periódicos de aquellos días, a modo ejemplar: véase portada de los diarios: “La Tercera” del 1 de marzo de 2010. En: http://papeldigital.info/lt/index. html?2010030101 [visitado el: 17/10/2010] y cuerpo de reportajes del diario “El Sur” de Concepción, de fecha 21 de marzo de 2010. En: http://www.elsur.cl/diarioelsur/20100321/16/papeldigital.html [visitado 17/10/2010]. A diferencia de lo que ocurre en las ciencias jurídicas, en otras ciencias sociales, la conceptualización de los saqueos ha tenido un mayor desarrollo, así Green, Stuar, “Looting, Law, and Lawlessness”, 2006, p. 7, En: http://law.bepress.com/cgi/viewcontent.cgi?article=6879&context=expr esso [visitado el 21/09/2010], conceptualiza los saqueos, “como entrar sin autorización a una casa o negocio el cual no posee sistemas de seguridad en virtud de la vulnerabilidad producida por un desastre natural o desórdenes colectivos, obteniendo así el control, y removiendo o dañando la propiedad de otros sujetos” Indica, que el origen histórico de dicho concepto se vincula con la guerra. 1 Para una cabal comprensión de la situación, puede consultarse en la Web cualquier periódico de circulación nacional o regional. 2 3 Con fecha 28 de febrero de 2010, la ex Presidenta de la República, Sra. Michelle Bachelet, decretó el estado de excepción constitucional de emergencia. Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 393 Humberto Alarcón Corsi Jurisprudencia y 3) Finalmente, entre otras, permitir la iniciación de las labores de reposición y/o reconstrucción de los servicios básicos que habían sido dañados por el evento natural ya referido. Días más tarde, la policía bajo la dirección del Ministerio Público realizó operativos policiales que condujeron a la detención de un número importante de ciudadanos (los llamados saqueadores). La gran mayoría de ellos, o casi su totalidad, eran quienes poseían, guardaban o tenían a cualquier título, especies muebles que provenían de dichos actos; es decir, autores del delito de receptación, tipificado y sancionado en el artículo 456 bis A del Código Penal (en adelante CP). Todas estas personas fueron formalizadas por este delito, y en su minoría por el delito de robo con fuerza en las cosas que se encuentran en lugar no habitado, tipificado y sancionado en el artículo 442 del CP. En casi la totalidad de los casos4, se decretó la prisión preventiva de los imputados formalizados, pues los magistrados que conocieron de dichos causas, consideraron que la libertad de estas personas constituía un “peligro para la seguridad de la sociedad”. Sin duda, que hasta aquí no hemos dicho nada nuevo, pues dichas acciones –las detenciones y posteriores privaciones de libertad– podrían ser consideradas como una consecuencia esperada, y por algunos necesaria, ante los sucesos que hemos narrado; pero sin duda, ello sólo puede ser pacífico, en tanto y en cuanto, dicho discurso sea analizado desde una sola mirada: “La gravedad de los hechos ocurridos en una catástrofe natural”. Más aún, puede ser la consecuencia de la actual configuración de ciertos agentes sociales capaces de generar visiones y/o puntos de vista en el actual esquema social, como son los medios de comunicación. Sin embargo, dicho análisis pasa a ser cuestionable, cuando se comienza a revisar cada caso, conforme con la regulación legal de la prisión preventiva y con la naturaleza misma de dicha institución. En este sentido, el presente comentario analiza dos resoluciones de la Excelentísima Corte Suprema, referentes a delitos de receptación ocurridos horas después del terremoto y maremoto del 27 de febrero. Se revisará la procedencia y finalidad de la prisión preventiva en un estado de excepción constitucional, para terminar concluyendo que la imposición de esta medida cautelar, aun en un Según información del Sistema Informático de Apoyo a la Gestión de Defensa Penal Pública (SIGDP), al 17 de junio de 2010, en la Región del Bío-Bío, hubo 324 personas en prisión preventiva por hechos vinculados a los sucesos post 27 de febrero de 2010. De esta cifra, 166 personas habían sido formalizadas por el delito de receptación; otras 14, por el delito de hurto simple; 66 por el delito de robo con fuerza de cosas que se encuentran en un lugar habitado o destinado a la habitación, y 78 personas formalizadas y sometidas a prisión preventiva por el delito de robo con fuerza en las cosas que se encuentran en un lugar no habitado. Esta información fue proporcionada por el encargado de la Oficina de Información, Reclamación y Sugerencias (OIRS) de la Defensoría Regional del Bío-Bío, Sr. Pablo Carrasco Pérez, mediante correo electrónico de fecha 22 de septiembre de 2010. Como se ve, no existió ninguna ponderación para decretar la prisión u otra medida cautelar, en uno u otro delito, tal como se insistirá más adelante. 4 394 Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema estado excepcional de garantías, como el vigente a la época de los hechos por los cuales se impuso, no cumplió más que con fines puramente simbólicos. II. Consideraciones y fundamentaciones de las Sentencias de la Excelentísima Corte Suprema, Rol Nº 2218-2010 y Rol Nº 1975-2010 a) Dada la similitud de los hechos y las fundamentaciones de las resoluciones, se describirán en forma conjunta las sentencias que serán objeto del presente comentario. Así, en ambos casos se trata de imputados que fueron formalizados por delitos de receptación5, esencialmente por guardar en su domicilio una serie de alimentos no perecibles en un caso; y en el otro una lavadora. Ambos imputados gozaban de irreprochable conducta anterior, no teniendo ni siquiera antecedentes policiales previos, es decir, se trataba de su primer contacto con el sistema criminal. Las resoluciones que decretaron la prisión preventiva tuvieron por acreditado el presupuesto material, es decir, se acreditó la existencia del delito y la participación, pese a que en uno de los casos al menos, ni siquiera en los hechos formalizados se indicaba a quién pertenecía el artefacto electrodoméstico que se imputada haber tenido en su poder, simplemente, se indicaba que provenía de bodegas comerciales de la ciudad, sin saber a cuál de todas las casas comerciales que tienen bodegas en dicho lugar pertenecía ese objeto. Se consideró, además, que la libertad de los imputados era peligrosa para la seguridad de la sociedad. Dicho peligro habría estado dado por lo siguiente: 1) El Ministerio Público invocó las agravantes contenidas en: a) El artículo 12 Nº 10 del Código Penal, y b) la agravante contenida en el inciso 7º del artículo 5º, de la Ley Nº 16.2826; 2) El estado de excepción que estaba vigente en la ciudad; 3) El carácter y ocurrencia del hecho punible y su impacto en la mantención En la causa RUC 1010006270-K, los hechos que constan en el acta de formalización son: “El día 16 de marzo de 2010, siendo la 11:20 horas de la mañana aproximadamente, el imputado M.A.M.Z tenía en su poder al interior de su domicilio ubicado en …, comuna de Concepción, distintas especies de propiedad del supermercado Alvi, a saber, 3 cajas de cereal Nestum, 8 paquetes de corbatas marca Aconcagua, un paquete de espirales marca Carozzi, 8 cajas de café marca Nescafé contenedoras de 100 sobres cada una, dos caja de café marca Gold contenedoras de 100 sobres cada una y 30 cajas de Té Club etiqueta roja. Dichas especies habían sido robadas desde el supermercado Alvi, ubicado en Avenida Los Carrera Nº 555 de la comuna de Concepción el día 28 de febrero de 2010 producto de los saqueos que afectaron a distintos locales de Concepción en forma posterior al terremoto de fecha 27 de febrero de 2010; el imputado sabía o no podía menos que saber el origen ilícito de dichas especies”. En la causa RUC 010005682-3, los hechos son: “El día 7 de marzo de 2010, alrededor de las 00:30 horas de la madrugada, el imputado Carlos Rubén J. S., mantenía en su poder una lavadora marca Cónsul, la cual había sido sustraída desde el interior de las bodegas de tiendas comerciales ubicadas en el sector Palomares de la comuna de Concepción. El imputado conocía, o no podía menos que conocer el origen ilícito de las especies”. 5 6 El artículo 5º inciso 7º, dispone: En los delitos contra las personas o la propiedad será considerado agravante el hecho de haber sido cometido el delito en la zona afectada. Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 395 Humberto Alarcón Corsi Jurisprudencia del orden público, alterado ostensiblemente por los desmanes, robos y hurtos por saqueadores. Frente a dichas resoluciones, los defensores penales públicos de los imputados, presentaron ante la Ilustrísima Corte de Apelaciones de esa misma ciudad la acción constitucional de amparo, fundándola, esencialmente en: 1) La falta del presupuesto material de la medida cautelar decretada y 2) La falta de proporcionalidad de la misma medida. b) La Ilustrísima Corte de Apelaciones de Concepción7 rechazó las acciones constitucionales de amparo, indicando esencialmente y escuetamente, tanto en la resolución de fecha 12 de marzo de 2010, como la del 22 del mismo mes y año, que la resoluciones del Juzgado de Garantía de Concepción, que habían decretado la prisión preventiva en contra de los recurridos, fueron expedidas conforme a derecho, observado el cumplimiento de los requisitos del artículo 140 del Código Procesal Penal (en adelante CPP). Es decir, la Ilustrísima Corte de Apelaciones no se pronunció mayormente sobre la falta de presupuesto material, ni sobre la falta de proporcionalidad de la medida cautelar. c) La defensa de los amparados apeló las resoluciones antes indicadas. Así, estos hechos fueron de conocimiento de la Excelentísima Corte Suprema, la cual, en ambos casos, confirmó lo resuelto por la Ilustrísima Corte de Apelaciones de Concepción, sin mayor fundamentación, con la única salvedad de que, en uno de los casos –sentencia Rol 2218-210– fue confirmada, por mayoría, con un voto en contra, el cual estuvo por acoger la acción constitucional de amparo, en virtud del carácter de ultima ratio de la medida cautelar. Conviene aclarar que las resoluciones que se analizarán tratan de casos en que: 1) El delito imputado no es de aquellos cuya gravedad amerita, en todo caso y en abstracto, la exclusión de beneficios alternativos al cumplimiento de la pena en forma privativa de libertad, 2) Se trata de imputados con irreprochable conducta anterior, lo que implica que en el peor de los casos, si éstos llegasen a ser condenados, no cumplirían sus penas en forma efectiva, 3) En uno de los casos, al menos, se trata de hechos que aisladamente considerados, pueden ser calificados como insignificantes o de bagatela8 y 4) Se trata de resoluciones, Nos referimos a las resoluciones de la Ilustrísima Corte de Apelaciones de 22 de marzo de 2010, Rol 6-2010. En: http://corte.poderjudicial.cl/SITCORTEPORWEB/?opc_menu=7 [visitado el 21/09/2010]; y resolución de la Iltma. Corte de Apelaciones de Concepción, que rechazó acción constitucional de amparo, de fecha 12 de marzo de 2010, Rol 1-2010. 7 Al respecto, Silva Sánchez, Jesús María, “Delincuencia patrimonial leve: una observación del estado de la cuestión”, Revista de Estudios Penales y Criminológicos Nº 25, Universidad de Santiago de Compostela, 2005, pp. 333-334, para quien: “Los delitos patrimoniales leves muestran características específicas en el conjunto de la criminalidad. Por un lado, aisladamente considerados, muestran una lesividad muy limitada –se consideran, en general, hechos de bagatela–, de modo que la imposición de sanciones penales convencionales podría parecer escasamente justificada desde la perspectiva del 8 396 Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema que no cumplen la exigencia de fundamentación contenida en los artículos 36 y 143 del Código Procesal Penal. III. Respecto a la medida cautelar de prisión preventiva 1. Consideraciones generales La doctrina procesal penal tradicional atribuye a la prisión preventiva una misión puramente cautelar o provisional, lo que se encuentra dado esencialmente, por cuanto a través de ella se pretende el aseguramiento de la realización de los actos del procedimiento, lo que implica el juzgamiento efectivo del acusado y la ejecución de la sentencia del presunto responsable cuando sea el caso9, lo que podría verse frustrado, por cuanto el imputado podría darse a la fuga, lo que imposibilitaría la realización del juicios y la imposición de la principio de proporcionalidad. Por otro lado, sin embargo, también es cierto que afectan a un derecho individual que resulta esencial en la autocompresión de nuestra sociedad (la propiedad privada). En tercer lugar, expresan una forma de comportamiento típica de la sociedad de masas, esto es, conforman a su vez un fenómeno masivo. Ello determina que den lugar a daños materiales globales muy elevados, que incidan de modo directo en la sensación social de inseguridad y que, a la vez, contribuyan de modo decisivo a la sobrecarga de la administración de justicia penal pese a la elevada cifra oscura existente también en este ámbito”. Duce Julio, Mauricio; Riego R., Cristián, Proceso Penal, Editorial Jurídica de Chile, Santiago, 2007, p. 250, para quienes la prisión preventiva, conforme la regulación del artículo 4° del Código Procesal Penal, que establece el principio de inocencia, “podría resultar justificable que para poder llevar adelante el proceso, y para asegurar el cumplimiento de la decisión que se tome en la sentencia, adoptar medidas de resguardo que signifiquen formas de coerción intensas sobre el imputado”, con lo que reconocen el carácter cautelar de la prisión preventiva como medida cautelar personal. Carocca Pérez, Álex, Manual El Nuevo Sistema Procesal Penal, Editorial LexisNexis, Santiago, 2005, p. 156, para quien las medidas cautelares, entre ellas la prisión preventiva, sólo tienen como finalidad la realización de los fines de procedimiento, y por ello su temporabilidad, es decir, duran mientras éstos subsistan. En una opinión similar, pero con una variante importante se encuentran: Horvitz Lennon, María Inés; López Masle, Julián, Derecho Procesal Penal Chileno, Tomo I, Editorial Jurídica de Chile, Santiago, 2002, p. 344, para quienes si bien las medidas cautelares personales, entre las cuales está la prisión preventiva, están llamadas a “asegurar la persona del imputado en el curso del procedimiento penal” –naturaleza cautelar propiamente tal– reconocen estos autores que existen las denominadas “medidas de coerción procesal” que “exceden la naturaleza cautelar que supone la tutela de fines procesales”, citando a modo de ejemplo la prisión preventiva cuando es impuesta como medida de peligrosidad social, para tal efecto, critican duramente la causal de peligro para la seguridad de la sociedad, como una justificación de naturaleza cautelar para imponer una privación de libertad. En el derecho comparado, Roxin, Claus, Derecho Procesal Penal, Traducción de Córdoba, Gabriela; Pastor, Daniel, Revisada por Mayer, Julio, Editores del Puerto, Buenos Aires, 2000, p. 257. Para quien la prisión preventiva en el proceso penal es la privación de la libertad del imputado con el fin de asegurar el proceso de conocimiento o la ejecución de la pena. Ella sirve a tres objetivos: 1. Pretende asegurar la presencia del imputado en el procedimiento penal (§112, II, Nºs. 1 y 2). 2. Pretende garantizar una investigación de los hechos, en debida forma, por los órganos de la persecución penal (§ 112, II, Nº 3). 3. Pretende asegurar la ejecución penal (§ 457). 9 Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 397 Humberto Alarcón Corsi Jurisprudencia condena; y/o la destrucción de las pruebas de cargo, lo que imposibilitaría a la acusación probar la culpabilidad del acusado, con lo cual también se frustraría la imposición de la pena. En nuestra legislación, la prisión preventiva se encuentra regulada a nivel constitucional, en el artículo 19 Nº 7 letra e) y en el artículo 5º inciso 2º, de la CPR, que introduce a la legislación interna los tratados internacionales sobre derechos fundamentales. Por otro lado, el propio CP, regula dentro de su Libro I, Título V, las medidas cautelares personales, y en el párrafo 4º la prisión preventiva, regulación que en términos generales exige que ésta sea decretada por resolución judicial fundada (artículo 143 del CPP), en una audiencia pública, una vez que el Ministerio Público o el querellante, en su caso, puedan acreditar, con antecedentes fundados, la existencia del delito. Además, se les exige que esos mismos antecedentes permitan presumir fundadamente la participación del imputado en dicho hecho típico y antijurídico (artículo 140 letras a) y b) del CPP). Además de dicho presupuesto, al que comúnmente se le suele llamar material10, se exige según lo entiende la doctrina y la jurisprudencia, el llamado presupuesto cautelar. En este sentido, no es baladí que el legislador, al momento de comenzar la regulación de esta medida, resalte dicho presupuesto, al indicar en el artículo 139 del CPP, que: “La prisión preventiva procederá sólo cuando las demás medidas cautelares personales fueren estimadas por el juez como insuficientes para asegurar las finalidades del procedimiento, la seguridad del ofendido o de la sociedad”. Así, el artículo 140 del CPP en su letra c), distingue cuatro causales alternativas, que configuran la necesidad de cautela, y que justifican la prisión preventiva de una persona que se presume inocente. Estas causales son señaladas por el legislador mediante cláusulas genéricas que, a su vez, en algunos casos añaden cláusulas específicas pensadas para casos especiales como: reiteración o habitualidad en conductas delictivas. Estas causales son: 1) Peligro para la seguridad del ofendido, 2) Peligro para el éxito de diligencias precisas y determinadas de la investigación, 3) Peligro para la seguridad de la sociedad, y 4) Peligro de fuga11. Así entonces, la necesidad de cautela en nuestra 10 Entre otros, Duce; Riego, Proceso, cit., nota n. 9, p. 251. Con la dictación de la Ley Nº 20.253 de 11/03/2008, se incorpora en forma explícita al artículo 140 del CPP, como causal de justificación cautelar: “el peligro de fuga”, como una causal alternativa del “peligro para la seguridad de la sociedad”. Como se verá más adelante, la primera causal, era considerada por la doctrina procesal penal nacional como equivalente a la segunda, o en otros términos, los esfuerzos interpretativos consideraban que la única interpretación posible, conforme al texto constitucional y los tratados internacionales sobre derechos fundamentales incorporados al derecho interno, conforme el artículo 5º inciso 2º de la CPR, era considerar que la letra c) del artículo 140 del CPP, contenía en la cláusula genérica: “peligro para la seguridad de la sociedad”, una causal de riesgo de fuga del imputado, y con ello frustrar los fines del proceso. 11 398 Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema legislación viene dada por exigencias que se agrupan, al decir de la doctrina12, en un “(…) mosaico y variopinto de presupuestos de difícil reconducción a un denominador común (…)”, caracterizado por el “reino de la incertidumbre y del arbitrio judicial, que puede llegar a ser «arbitrariedad» apenas limitada por unos presupuestos en los que predomina la apreciación subjetiva del juez que debe tomar la decisión”. Se debe agregar que, además de los presupuestos indicados, la prisión preventiva tiene como límites en cuanto a su procedencia, ciertos principios, los cuales se encuentran explicitados en el CPP, y ellos son: La subsidiariedad, es decir, esta medida sólo puede operar cuando las restantes medidas cautelares personales son insuficientes para lograr los fines procesales y del sistema penal, principio consagrado en los artículos 112 y 139 inciso 2º del CPP. Además de ello, la prisión preventiva deberá respetar el principio de proporcionalidad, lo cual implica que ella no puede ser más gravosa que la sanción probable; y/o que los costos que implica para el sistema la libertad del imputado, son mayores que el costo que implica su afectación de libertad. La doctrina ve la consagración de dicho principio en los artículos 122, 124; y, 141 del CPP. Respecto de las causales relativas a la necesidad de cautela, aquella que mayor problema plantea en su interpretación es la cláusula genérica denominada por nuestra legislación: “Peligro para la seguridad de la sociedad”. Dicha problemática se acrecienta, luego de las reformas que se han ido introduciendo al CPP, a poco tiempo de su entrada en vigencia. Dentro de estas modificaciones, se encuentra la Ley Nº 20.253 conocida como “agenda corta antidelincuencia”, que introdujo diversas modificaciones en materias tales como: Facultades policiales, Flagrancia, Reincidencia, y muy especialmente en la regulación de la prisión preventiva, en donde las modificaciones más sustanciales y polémicas dicen relación con el efecto del recurso de apelación interpuesto por el Ministerio Público en determinados delitos, y la inclusión del peligro de fuga como una causal alternativa del peligro para la seguridad de la sociedad. Lo anterior, acrecienta las dificultades para dilucidar el contenido de la cláusula “peligro para la seguridad de la sociedad”, pues al hacer el legislador la distinción entre ésta y el peligro de fuga, podría llevar a pensar que esta polémica cláusula implica necesariamente ser considerada de un modo diferente a la segunda13 12 Muñoz Conde, Francisco, “Cuestiones teóricas y problemas prácticos de la prisión provisional”, en Prisión provisional, detención preventiva y derechos fundamentales, Ediciones de la Universidad de Castilla - La Mancha (Estudios; 41), Cuenca - España, 1997, p. 223. 13 Lama Díaz, Rossy, “Agenda Corta Antidelincuencia. Modificaciones al Código Procesal Penal”, en Gaceta Jurídica Nº 238, 2008, p. 17, para quien “su inclusión como elemento adicional plantea dos cuestiones, la primera de ellas es que se permite decretar la prisión preventiva por la sola existencia de esta circunstancia; y como elemento adicional ésta deberá tener una aplicación restringida, toda vez que nos se establecieron los elementos que lo determinan, como las demás causales; por lo tanto, se deberá aplicar en forma subsidiaria y fundarla según las circunstancias que cada caso lo ameri- Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 399 Humberto Alarcón Corsi Jurisprudencia y, por ende, considerar a la primera como un mecanismo dirigido a combatir a los imputados reincidentes, es decir, se estará utilizando la “prisión preventiva” como un medio de control social14. Para efectos del análisis de los casos en comento, creemos necesario hacer una somera descripción del estado de la cuestión, en específico, en lo que comúnmente se ha exigido por presupuesto material, proporcionalidad y peligro para la seguridad de la sociedad, que son aquellos requisitos exigidos por la ley, doctrina y jurisprudencia, como necesarios para decretar esta medida cautelar y que, en la especie, entendemos no han sido respetados por las razones que se indicarán. 2. Presupuesto material15 Dichos requisitos se encuentran establecidos en el artículo 140 del CPP16. Se ha entendido por nuestra doctrina, que para poder decretar la prisión preventiva, en un proceso seguido en contra de una persona que se presume inocente, se requiere que el juez necesariamente haga una ponderación de los antecedentes que presenta el Ministerio Público o el querellante en la audiencia respectiva, y que los mismos lleven al juzgador, mediante un juicio de probabilidad acerca de la participación del imputado y la existencia del delito, a concluir que existe un alto grado de probabilidad de que: 1) El caso será llevado a juicio, o no se le dará termino a través de mecanismos alternativos a él, a excepción de un procedimiento abreviado y 2) Que en ese juicio existirá, conforme a esos antecedentes y los que razonablemente aparezcan durante el curso de la investigación, una gran probabilidad de dictarse una sentencia condenatoria en contra del imputado. te”. Sin embargo, no concordamos con dicha interpretación que da la autora, toda vez que, como se indicará, nuestra doctrina en su mayoría siempre entendió que una interpretación racionalmente posible de la causal de peligro para la seguridad de la sociedad, debía ser el considerar el peligro de fuga del imputado, pues entenderlo de otro modo era incompatible con el texto constitucional. En este contexto, creemos que el intérprete dentro de las tantas opciones que tenga debe conducir su labor por aquella que se ajuste a la Constitución, en ese orden de cosas, puede señalarse que lo que el legislador quiere es reforzar este peligro de fuga, que impediría el cumplimiento de los fines de proceso y del sistema penal. 14 Al respecto, pueden consultarse: Horvitz; López, Derecho, cit. nota n. 9. Duce; Riego, Proceso, cit. nota n. 9. Para un análisis detallado sobre el mismo, puede consultarse Duce; Riego, Proceso, cit. nota n. 9, pp. 251 y ss., Horvitz; López, Derecho, cit. nota n. 9, p. 400 y siguientes; y, la obra más actual, que incluye las últimas modificaciones legales: Maturana Miquel, Cristián; Montero López, Raúl, Derecho Procesal Penal, Tomo I, Editorial AbeledoPerrot LegalPublishing, Santiago, 2010, pp. 491 y ss. 15 16 El artículo 140 del CPP, dispone en sus letras a y b, lo siguiente: a) Que existen antecedentes que justificaren la existencia del delito que se investigare; b) Que existen antecedentes que permitieren presumir fundadamente que el imputado ha tenido participación en el delito como autor, cómplice o encubridor. 400 Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema 3. Peligro para la seguridad de la sociedad Si bien, no pretendemos en este comentario hacer un análisis profundo de la causal ni desentrañar el contenido de la misma, sí podemos indicar que nuestra doctrina procesal ha hecho importantes esfuerzos por interpretar dicha cláusula. Al respecto, se debe tener presente que, en una materia como ésta, por ser limitativa de derechos y por así disponerlo el artículo 5º inciso 2º del CPP, la interpretación de la misma debe ser restrictiva, proscribiéndose la analogía. El legislador ha entregado algunos criterios respecto de cuándo la libertad del imputado es peligrosa para la seguridad de la sociedad. Así el artículo 140 letra c) del CPP, dispone que: (…) Para estimar si la libertad del imputado resulta o no peligrosa para la seguridad de la sociedad, el tribunal deberá considerar especialmente alguna de las siguientes circunstancias: La gravedad de la pena asignada al delito; el número de delitos que se le imputare y el carácter de los mismos; la existencia de procesos pendientes, y el hecho de haber actuado en grupo o pandilla. Se entenderá, especialmente, que la libertad del imputado constituye un peligro para la seguridad de la sociedad, cuando los delitos imputados tengan asignada pena de crimen en la ley que los consagra; cuando el imputado hubiere sido condenado con anterioridad por delito al que la ley señale igual o mayor pena, sea que la hubiere cumplido efectivamente o no; cuando se encontrare sujeto a alguna medida cautelar personal, en libertad condicional o gozando de alguno de los beneficios alternativos a la ejecución de las penas privativas o restrictivas de libertad contemplados en la ley (…)”. La doctrina procesal penal nacional que ha interpretado esta causal, lo ha hecho en forma previa a la modificación de la Ley Nº 20.253. Sin embargo, conviene traer a colación sus argumentos, pues igualmente orientarán la interpretación de un asunto que no es de fácil despacho. Si bien Marín González17 parte por reconocer la problemática que esta causal conlleva, indica que el legislador en el artículo140 del CPP proporciona ciertos elementos que permiten reconducir la interpretación de dicha norma a los fines cautelares que la doctrina señala debe cumplir esta institución, “lo que busca el legislador al explicitar en este inciso –el tercero– los motivos que especialmente debe tener presente el juez al considerar si la libertad del imputado es peligrosa para la seguridad de la sociedad, no es otro que poner de manifiesto el peligro de que en definitiva el imputado no comparezca al juicio y, en su día, a la aplicación de la eventual pena”. 17 Marín González, Juan Carlos, “Las medidas cautelares personales en el nuevo Código Procesal Penal Chileno”, Revista de Estudios de la Justicia Nº 1, 2002. En: http://web.derecho.uchile.cl/cej/ recej/recej1/ archivos/Medidas_Cautelares_personales%20(5).pdf [visitado el 21/09/2010]. Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 401 Humberto Alarcón Corsi Jurisprudencia Por su parte, Horvitz y López18 plantean que, si bien existen interesantes esfuerzos en ver en la causal en comento, un símil del peligro de fuga –citan en su obra él ya aludido artículo de Marín19– dicha argumentación no les convence, dada la fuerza cultural que en nuestro sistema tiene esta causal cautelar. Por ello, para estos autores, la causal no es más que un “peligro de reincidencia”, lo que puede observarse cuando el legislador alude a consideraciones como: la existencia de procesos pendientes, el hecho de encontrarse sujeto a alguna medida cautelar personal, en libertad condicional o gozando de algunos de los beneficios alternativos a la ejecución de las penas privativas o restrictivas de libertad, la existencia de condenas anteriores cuyo cumplimiento se encontrare pendiente, entre otros. En definitiva, en concepto de estos autores, a través de dicha cláusula se estarán legitimando fines de prevención especial negativos, o mecanismos de control social, cuya ilegitimidad es patente y, por lo mismo, comprometería el incumplimiento de las obligaciones del Estado de Chile contraídas en los documentos internacionales que han sido suscritos sobre la materia20. Finalmente, para Duce y Riego21, la ambigüedad que ha existido sobre lo que implica el peligro para la seguridad de la sociedad, es algo que se traspasó de la antigua legislación22 al CPP. Así, para estos autores, los criterios informativos que el artículo 140 letra c) señala, no serían más que criterios destinados a ser ponderados por el arbitrio judicial. De este modo, el peligro para la seguridad de la sociedad incluiría, según Duce y Riego, el peligro de fuga, la reiteración delictiva y la alarma pública o legitimidad del sistema. Lo primero y segundo, lo deducen de las consideraciones que la ley indica en el artículo 140 del CPP, 18 Horvitz; López, Derecho, cit. nota n. 9, pp. 415- 416. Así indican que: “El peligro para la seguridad de la sociedad es, sin lugar a dudas, la justificación más problemática para la prisión preventiva, porque resulta evidente que, en este caso, deja de ser una medida cautelar para convertirse en un instrumento de control social, lo que claramente pone en crisis su legitimidad”. Horvitz; López, Derecho, cit. nota n. 9, pp. 415- 416, “El mérito de este argumento es indudable, en cuanto pretende solucionar, por vía interpretativa, una seria inconsistencia de nuestro ordenamiento jurídico que, entendido de otro modo, autoriza la privación de libertad sobre la base de criterios de defensa social que nos parecen inaceptables. Sin embargo, se trata de un esfuerzo interpretativo que no resulta convincente, porque no logra desvirtuar toda la fuerza que, en nuestra cultura jurídica, tiene la noción de ’peligro para la seguridad de la sociedad‘, como equivalente de ’peligro de reincidencia‘. 19 El artículo 9.3 del Pacto Internacional de los Derechos Civiles y Políticos, por su parte, sólo permite subordinar la libertad a “garantías que aseguren la comparecencia del acusado en el acto del juicio, o en cualquier otro momento de las diligencias procesales y, en su caso, para la ejecución del fallo”. Por su parte, la Convención Americana de Derechos Humanos, en su artículo 7.5 sólo autoriza a condicionar la libertad del imputado “a garantías que aseguren su comparecencia en el juicio”. 20 21 Duce; Riego, Proceso, cit. nota n. 9, pp. 260 y ss. Nos referimos a la regulación que existía en el antiguo 363 del Código de Procedimiento Penal de 1906, y que sufrió modificaciones mediante las Leyes Nºs. 19.503 de 1997 y 19.661 de 2000. 22 402 Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema y para el tercer supuesto de peligro para la seguridad de la sociedad, lo extraen que una negación de la misma puede provocar una grave afectación de la legitimidad del sistema, lo que podría originar una alarma social o deteriorar la seguridad que el mismo sistema debe brindar a la población. Ciertamente, que estos postulados son de compleja justificación, y muy cuestionables desde el punto de vista constitucional, en un Estado respetuoso de los derechos humanos y de la dignidad humana, pero con una visión bastante realista del modo como esta medida cautelar es utilizada en la práctica. En consecuencia, y tal como lo indicábamos en un comienzo, nos encontramos ante causales bastante indeterminadas, lo que, en palabras de Muñoz Conde23, deja abierta la puerta a lo incierto, transformando el arbitrio del juzgador en algo arbitrario, legitimándose mediante esta cláusula verdaderos mecanismos de control social. Pero no debemos perder de vista que, en la práctica, más allá del marco teórico y conceptual que hemos desarrollado, la aplicación de la prisión preventiva es utilizada político criminalmente en la lucha contra un determinado grupo de imputados: 1) Los reincidentes, 2) Los delitos contra la propiedad, esencialmente el robo en cualquiera de sus formas y 3) La violencia intrafamiliar, en casos de supuesta reiteración. Esto es cuestionable, ciertamente, en tanto implica considerar que la prisión preventiva deja de ser una medida cautelar que tenga por objeto el cumplimiento de los fines del proceso, lo cual sería más bien una función de la pena y, por otro lado, al asignarle a la prisión preventiva fines preventivos especiales, se vulneraría el principio de inocencia, pues se estaría imponiendo una pena, no obstante, no ha existido juicio alguno en contra del imputado, infringiéndose con ello garantías constitucionales. Pero, reiteramos, que dichos fundamentos sin ser explícitamente señalados, son reiteradamente ocupados en el día a día, y es lo que se indica como fundamentos apócrifos de la prisión preventiva. Ratifica dicha situación, que el año 2006 fueron sometidos a prisión preventiva en nuestro país 14.348 imputados, tres años más tarde, esta cifra aumentó a 19.979 personas24. Estas críticas son actualmente objeto de análisis, haciéndose esfuerzos por superar las inconsistencias que presentaría la fundamentación cautelar de la prisión preventiva. En este sentido, autores como Ragués25 consideran que la 23 Cit. nota n. 12. 24 MEMORIA ANUAL DE LA DEFENSORÍA PENAL PÚBLICA DE CHILE, 2009, p. 61. Véase en: Ragués I Valles, Ramón, “Derecho Penal Sustantivo y Derecho Penal: Hacia una visión integrada”, Anuario de Derecho Penal, Perú, 2004, pp. 129-163, y “Prisión Provisional y Prevención de Delitos ¿Legítima protección de bienes jurídicos o derecho penal del enemigo?”, en Cancio Melia, Manuel; Gómez-Jara Diez, Carlos (Coords.), Derecho Penal del Enemigo. El discurso penal de la exclusión, Editorial B de F, Buenos Aires-Argentina, 2006, pp. 713 - 734. 25 Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 403 Humberto Alarcón Corsi Jurisprudencia tradicional separación que ha existido entre el Derecho Penal y Procesal Penal, ha provocado que distintas instituciones como la prueba, la prescripción y la prisión preventiva sean analizadas exclusivamente desde un prisma procesal. En ese contexto, considera que “el proceso penal no es un fin en sí mismo susceptible de legitimación, sino sólo el cauce previsto para que pueda imponerse la pena y ésta despliegue sus efectos preventivos. En otra palabras: la frustración en un caso concreto del fin del proceso no es algo negativo per se, sino sólo en la medida en que dicha frustración impide que la pena pueda desplegar sus efectos preventivos y contribuir al fin último de pacificación social que pretende la globalidad del sistema”26. En ese contexto, postula que la prisión preventiva evita que puedan frustrarse los fines de la pena, contribuyendo con ello a la función pacificadora del Derecho Penal, siempre que la misma –prisión preventiva- cumpla los presupuestos de: proporcionalidad, subsidiariedad y probabilidad27. Así, concluye que la prisión preventiva sólo será legítima como medio en la prevención de delitos, en aquellos casos en los que, si el imputado permaneciera en libertad, existiría un riesgo grave y concreto de la alteración de la paz social o de lesión o puesta en peligro grave de los bienes jurídicos más importantes, sin que para conjurar dicho peligro, exista ningún medio menos lesivo que la privación de libertad del imputado. 4. Proporcionalidad Como se indicó anteriormente, este principio se encuentra contemplado en los artículos 122, 139 inciso 2º, y en el artículo 141 del Código Procesal Penal. La doctrina procesal penal indica que el principio de proporcionalidad, en las medidas cautelares personales que se adopten en el curso de un proceso penal, han de estar en relación con la finalidad del procedimiento que se persigue cautelar y con la gravedad del hecho que se investiga28. Ahora bien, la proporcionalidad en la prisión preventiva guarda directa relación con otros principios limitadores de esta medida, como es su instrumentalidad (idoneidad como proporcionalidad en sentido amplio), es decir, ellas son impuestas para que el proceso logre sus fines (artículo 122 inciso 2º). Así se indica que una interpretación en contrario, implicaría poner los medios por sobre los fines29. 26 Ragués, “Prisión”, cit. nota n. 25, p. 716. Ragués, “Derecho”, cit. nota n. 25, este autor plantea que: para legitimar la prisión preventiva como un instrumento que posibilite el cumplimiento de los fines de la pena, no frustrando los mismos, o afectándolos negativamente, los antecedentes que fundamentan la existencia del hecho y la participación del imputado, deben llevar a una alta probabilidad de que en un juicio el imputado será condenado, a fin de evitar encarcelamientos injustificados. 27 28 Horvitz; López, Derecho, cit. nota n. 9, p. 353. 29 Duce; Riego, Proceso, cit. nota n. 9, p. 266. 404 Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema Por otro lado, también se vincula a este principio con la subsidiariedad de las medidas cautelares, es decir, sólo se justifica una privación de libertad en el proceso, si no existen otras medidas menos gravosas que permitan cumplir con las finalidades del proceso (necesariedad como componente de la proporcionalidad), lo que se consagra en el artículo 139 inciso 2º del CPP. Finalmente, también se le vincula con el principio de la temporalidad de las mismas, lo que implica que la prisión preventiva sólo durará mientras subsistan los presupuestos que la hacían procedente, tal como se indica en el artículo 152 del CPP (proporcionalidad en sentido estricto). Determinada la idoneidad, necesidad y ponderación de las circunstancias que concurran en la especie, podemos realizar el juicio de proporcionalidad en sentido estricto de la prisión preventiva. Así, ésta será proporcional cuando “el sacrificio de los intereses individuales que comporta la injerencia, guarda una relación razonable o proporcionada con la importancia del interés estatal que se trata de salvaguardar30”. En consecuencia, “si el sacrificio resulta excesivo, la medida deberá considerarse inadmisible, aunque satisfaga el resto de presupuestos y requisitos derivados del principio de proporcionalidad”31. IV. Consideraciones sobre las sentencias en comento a) Tanto en la resolución de la Ilustrísima Corte de Apelaciones de Concepción, que conoció las acciones constitucionales de amparo en contra de las resoluciones de los Juzgados de Garantía de Concepción, como las resoluciones de la Excelentísima Corte Suprema, que conocieron de las apelaciones de las acciones de amparo, se aprecia una ausencia de fundamentación. Lo anterior, creemos que es una deficiencia de las resoluciones que comentamos, pues se trata de resoluciones que recaen en asuntos sobre derechos y garantías fundamentales. Así, por lo demás, el artículo 36 del CPP establece el deber de fundamentar toda resolución judicial, norma que se ve reafirmada por lo que dispone el artículo 143 del mismo Código, que es aplicable en específico a la prisión preventiva. Podría observarse que la resolución del Juzgado de Garantía que decretó la medida cautelar, fue debidamente motivada. Sin embargo, somos de opinión que, dada la trascendencia de los mismos –se trataba de casos ocurridos en una situación de emergencia constitucional, producida por un desastre natural–, la exigencia para resolver y mantener la privación de libertad por razones de interés público o como se indica: “peligro para la seguridad de la sociedad”, debe ser suficientemente fundada, lo que no ocurrió en la especie. González-Cuéllar Serrano, Nicolás, Proporcionalidad y Derechos Fundamentales en el Derecho Penal, Editorial COLEX, Madrid, España, 1990, p. 225. 30 31 González-Cuéllar, Proporcionalidad, cit. nota n. 30, p. 225. Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 405 Humberto Alarcón Corsi Jurisprudencia Esta será la única forma de evitar la arbitrariedad y posibilitar al mismo tiempo el control32. Así, Ragués33es de la opinión que una prisión preventiva que pudiera ser considerada legítima por su contribución directa al aseguramiento de la paz social, exigiría mucho más que la constatación de un riesgo abstracto de perturbación del orden, siendo necesario que dicho riesgo fuera apreciado por el juez de forma motivada en el momento de adoptar la medida sobre la base de antecedentes inequívocos. En la especie, podemos apreciar que los fallos se limitan a reproducir las resoluciones recurridas mediante la cláusula “vistos se confirma”, y en el caso de las resoluciones de Cortes de Apelaciones, éstas se limitan a la reproducción de lo argumentado por los recurrentes y las resoluciones recurridas, para en dos breves considerandos, desechar las acciones constitucionales. Todo lo anterior, no es nada más contrario a lo que se espera de las actuaciones de los órganos jurisdiccionales en un Estado Democrático de Derecho, conforme a los artículos 1º, 4º y 5º inciso 2º de la CPR34. De este modo, las resoluciones de los Tribunales de Garantía, que privaron de libertad a personas sin antecedentes penales y por delitos de baja penalidad, haciendo alusión en su fundamentación a la calamidad pública producida por el terremoto, y los posteriores ataques a la propiedad privada, denominados saqueos, sin hacer referencia a cómo la libertad del imputado afectaría el orden público, o cómo la privación de libertad contribuiría al restablecimiento del mismo, ya sea en razón del peligro de reiteración criminal o, simplemente, por razones del peligro que la libertad del imputado puede generar graves reacciones de la comunidad y, con ello, la deslegitimación del sistema criminal. Por ello, la simple utilización o alusión de frases sacramentales, resultan insuficientes para justificar una privación de libertad. En sentido, es un lugar común el planteamiento de que reunidos los supuestos señalados en el artículo 140 del CPP relativos a “peligro para la seguridad de la sociedad”, se debe casi automáticamente decretar la prisión preventiva. Nada de ello puede ser más contrario al tenor de la ley y la Constitución, en tanto y en cuanto es el juez quien debe ponderar dichas circunstancias, éstas y los antecedentes del caso concreto determinarán según su razonar si la prisión preventiva es o no aplicable. Así nuestra Excelentísima Corte Suprema, lo ha 32 González-Cuéllar, Proporcionalidad, cit. nota n. 30, pp. 141 y ss. 33 Ragués, “Prisión”, cit. nota n. 25, p. 726. En este sentido el Tribunal Europeo de Derechos Humanos en el caso “Letelier”, sentencia del año 1991, señaló que la prisión preventiva puede estar legitimada por ciertos motivos de orden público, pero dichos motivos deben estar suficientemente motivados, y así también, el tribunal exige, como es obvio, que para acordar la prisión por este motivo existan datos capaces de acreditar la existencia del tal riesgo. Citado por Ragués, “Derecho”, cit. nota n. 25, p. 157. 34 406 Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema reiterado en números fallos35. Ello implica que la resolución que decrete estas medidas debe ser fundada, y no puede simplemente repetir estas causales, pues aquello incumple los artículos 36 y 143 del CPP. En la especie, como decíamos, y por haberse decretado esta medida en una situación excepcional y por fundamentos cuestionables, como es la alarma social, originada por la calamidad pública producida por el terremoto del 27 de febrero de 2010, la fundamentación debió ser mucho más detallada, y no simplemente hacer alusiones genéricas, pues es aquello, precisamente, lo que la doctrina denuncia como el paso de la razonabilidad judicial a lo irrazonable36. b) Como se indicó, las citadas resoluciones omiten fundamentar lo resuelto y, por lo mismo, reproducen las resoluciones recurridas de amparo, lo que resulta criticable bajo todo punto de vista. Ahora bien, si se consideran como fundamentos aquellos esgrimidos por los respectivos jueces de garantía recurridos, nos percatamos que como es tradicional, estas resoluciones se centran básicamente en fundar la prisión preventiva, haciendo referencia casi en su totalidad a la necesidad de cautela. Ello, como se dijo en el punto anterior, mediante la utilización de supuestos generales y abstractos indicados en el artículo 140 del CPP, y además en estos casos, en la situación de excepción. Esto, nos lleva a concluir que los requisitos materiales, como existencia del ilícito y participación, como es costumbre37 no son analizados con la rigurosidad que la materia amerita, lo cual es inconsistente con la afectación de derechos y garantías, que la resolución que se dicta importa. De este modo, resulta curioso como en uno de los casos en análisis, los hechos formalizados consistirían en que el imputado tendría en su poder una lavadora que provendría de unas bodegas comerciales del sector Palomares de Concepción, no indicándose en la comunicación fáctica a quién, previamente, pertenecía dicho artefacto, ni menos se invoca si la receptación provendría de otros delitos contra la propiedad, o de otra receptación, conforme el tipo del artículo 456 bis A del CP. Se indica simplemente que dicha especie habría sido “sustraída”. Es decir, la propia formalización de cargos no contendría todos los supuestos fácticos que el tipo exige. Esto tiene relevancia, pues de acuerdo 35 Sentencias de la Excelentísima Corte Suprema: 1) Aquella que acoge recursos de apelación en contra de la resolución de la Ilustrísima Corte de Apelaciones de San Miguel, que rechazó la acción de amparo constitucional, 13 de enero de 2009, rol 192-2009, 2) Aquella que acoge recursos de apelación en contra de la resolución de la Ilustrísima Corte de Apelaciones de San Miguel, que rechazó la acción de amparo constitucional, 15 de julio de 2009, rol 4823-2009 y 3) Aquella que acoge recursos de apelación, en contra de la resolución de la Ilustrísima Corte de Apelaciones de Santiago, que rechazó la acción de amparo constitucional, 20 de julio de 2009, rol 4922-2009. 36 Muñoz, “Cuestiones”, cit. nota n. 9. 37 Al respecto, Ragués, “Derecho”, cit. nota n. 25. Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 407 Humberto Alarcón Corsi Jurisprudencia con lo dispuesto en el artículo 259 del CPP, la acusación debe referirse a los mismos hechos que los contenidos en la formalización. Ahora bien, creemos que dicha situación, y que se refiere a la descripción de la conducta que debe encuadrarse en el tipo del artículo 456 bis A del CP, incide en los presupuestos de las letras a y b del artículo 140 del CPP, pues el tipo penal exige que las especies hubieren sido hurtadas, o robadas, o producto de otra receptación, ello como mínimo para establecer que la conducta típica imputada es constitutiva del delito imputado u otro. En la especie, la formalización no cumple las exigencias del tipo penal de receptación y, en consecuencia, no se podría haber tenido por acreditado el presupuesto material, toda vez que ni siquiera la imputación cumplía las exigencias del tipo por el que se formalizó investigación. Lo denunciado, en ningún caso puede ser considerado irrelevante, puesto que los mismos hechos que fueron comunicados a los amparados deberán posteriormente ser objeto de acusación, y luego sentencia, acorde lo indica el artículo 341 del CPP. La falta de dicha congruencia, acarrea la nulidad del juicio oral y la sentencia de acuerdo con el artículo 374 letra e) del CPP. Por otro lado, cabe tener presente que la Ilustrísima Corte de Concepción, conociendo recursos de nulidad en causas en juicios simplificados por delitos de receptación, entiende que: si los hechos probados se limitan a indicar que las especies han sido sustraídas, dichos hechos no son constitutivos del delito de receptación del artículo 456 bis A del CP38. Dicha situación, ni siquiera aparece enunciada en ninguno de los fallos en análisis. Aunque no compartimos del todo que la prisión preventiva pueda ser esgrimida para fines preventivos generales, la doctrina entiende que “asumiendo tal función, puede conseguirse una importante restricción de su empleo, exigiendo que para su aplicación no baste con la mera constatación de la concurrencia de meras sospechas o indicios de criminalidad, sino la necesidad de que consten en lo instruido elementos indiciarios que, por su número e importancia, permitan afirmar con un escaso margen de error que, en el caso de hacerse valer en el acto del juicio por la acusación, permitirán considerar probada la culpabilidad del imputado39”. De este modo, a las resoluciones en análisis, y por las especiales circunstancias del caso, les era exigible una mayor motivación del presupuesto material, dado que lo que se intentaba comunicar mediante ellas, era que la privación de libertad de los imputados era algo necesario, debido a la alarma 38 Sentencia de la Iltma. Corte de Apelaciones de Concepción, acoge recurso de nulidad en contra de la sentencia del Tribunal de Garantía de Cañete, presentado por la defensa, 25 de mayo 2010, Rol 155-2010. 39 Ragués, “Derecho”, cit. nota n. 25, p. 159. 408 Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema social originada por los saqueos en los cuales, supuestamente, ellos habían participado, guardando las especies provenientes de los mismos. Por tal motivo, y si se estima que la prisión preventiva puede operar con fines preventivos generales (negativos o positivos), lo cual como decíamos es discutible40, debe exigirse una motivación suficiente del presupuesto material. Entender lo contrario, implica y provoca un uso masivo del encarcelamiento preventivo con lo cual se vulneraría la garantía jurisdiccional de la pena. Como se dijo, nada de esto ocurrió en la especie, ni con el presupuesto material, ni con la necesidad cautelar de peligro para la seguridad de la sociedad. Lo anterior, creemos que lamentablemente ocurrió con la utilización masiva que se hizo de esta medida cautelar en los hechos vinculados al 27 de febrero. Así, más de 300 personas fueron detenidas y encarceladas preventivamente en la Región del Bío-Bío41, todas ellas, o en su mayoría, con el único fundamento de privarlas de su libertad por la “alarma social” que su libertad, supuestamente, contribuía a aumentar, y con presupuestos materiales muy precarios. Sin embargo, esta práctica parece no ser sólo aplicable en tiempos de excepción, pues según cifras de la Defensoría Penal Pública, existe un creciente número de personas de son privadas de libertad y luego absueltas. Así, según su Memoria Anual 200942, un 22,1% de los imputados absueltos fueron privados de libertad. Seguramente en muchos de esos casos, las resoluciones que privaron de libertad a los imputados no tuvieron un adecuado fundamento del presupuesto material43. c) Si bien la prisión preventiva es una medida cautelar, no podemos negarnos a la realidad que implica que es un instrumento, a través del cual el sistema penal cumple su función más importante, como es la aplicación y ejecución de la pena y sus efectos44. Por ello, no podemos dejar de analizar la prisión preventiva como un instrumento que garantiza que la pena despliegue todas Asencio Mellado, José María, La Prisión Provisional. Tesis Doctoral de la Universidad de Alicante, España, 1987, p. 27. En: http://rua.ua.es/dspace/handle/10045/3483 [visitado el 29/09/2010]. 40 41 Cifra entregada por OIRS Defensoría Regional del Bío-Bío, cit. n. 4. 42 Cit. nota n. 24. Un caso paradigmático para el sistema de justicia nacional, lo constituye en esta materia el llamado “Caso del Violador de Nuñoa”, quien fuera detenido y sometido a prisión preventiva por la Ilustrísima Corte de Apelaciones de San Miguel, pese a que el Octavo Juzgado de Garantía de Santiago decretara su libertad, por cuanto los antecedentes del proceso no eran suficientes para acreditar su participación. Días más tarde, el propio Ministerio Público aceptaría la revocación de la medida, puesto que la prueba científica (ADN) ratificaba su inocencia. 43 44 Sobre la materia, como se ha indicado, ver Ragués, en los artículos ya citados: “Prisión” y “Derecho”, cit. nota n. 25. Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 409 Humberto Alarcón Corsi Jurisprudencia sus consecuencias, ello no obstante, estar convencidos del carácter cautelar y procesal de la medida. Ahora bien, queda meridianamente claro que en los casos en comento, la naturaleza cautelar de la prisión preventiva no fue su sustento. Por lo mismo, podríamos buscar su fundamentación, vinculándola con los fines de la pena, conforme a una de las opciones que hemos revisado anteriormente. Sin embargo, creemos que ninguno de los aquellos fines –de la pena– podría haber permitido que la prisión preventiva hubiere sido aplicada. Así, creemos que aunque cabe descartar de antemano que ella hubiere sido aplicada para fines preventivos especiales positivos, puesto que como indica Ragués45, parece poco probable que se pueda considerar necesario privar de libertad a un sujeto para evitar frustrar la eficacia de la pena, por un retraso en la resocialización (por la demora de la práctica del juicio); en el evento que ello no fuera así, como se indicaba más arriba, se trataba de imputados sin antecedentes penales, con actividad laboral actual al momento de los hechos y con arraigo social. En ese contexto, la prisión preventiva no puede ser el instrumento que permita que el sistema penal cumpla sus funciones resocializadoras, ante la falta de agilidad en la aplicación de la pena derivada de la demora en la realización del juicio. Tampoco podríamos señalar que la prisión preventiva, en este caso, sirve de instrumento para evitar una probable afectación de bienes jurídicos, pues, dadas la características de los hechos y de los amparados, no existía riesgo de reiteración. En este sentido, la doctrina46 manifiesta que la prisión preventiva sólo podría justificar estos fines cuando, además de existir un riesgo de reincidencia, exista un peligro de afectación para bienes jurídicos de tal entidad, que hagan que el costo de privar a una persona de su libertad sea inferior a la lesión o ataque de bienes de tal envergadura, como puedan ser la vida, la integridad de la persona o su seguridad la libertad sexual, entre otros. O en el caso de bienes jurídicos supraindividuales, cuando a través de dicha afectación se afecte de modo indirecto tales bienes –vida, salud, libertad sexual, seguridad y libertad individual– como son los atentados contra el medio ambiente o la salud pública. Por el contrario, una justificación en esa línea, es decir, que hubiera existido tal peligro de reiteración de conductas atentatorias contra la propiedad o que fomenten tales conductas –receptación, por ejemplo–, debe igualmente ser rechazada, por cuanto colisiona con la necesariedad de la prisión preventiva, como componente de la proporcionalidad en sentido amplio, pues, sí existían otras medidas menos restrictivas de derecho que posibilitaban dichos fines, y que iban desde aplicar alguna de las 45 Ragués, “Prisión”, cit. nota n. 25, p. 723. 46 Ragués, “Prisión”, cit. nota n. 25, p. 724. 410 Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema que contiene el catálogo del artículo 155 del CPP, hasta la responsabilidad de los agentes del Estado en haber decretado en tiempo oportuno el estado de excepción constitucional, y haberlo hecho efectivo en toda su magnitud, es decir, mediante una prevención previa, a través de la presencia en terreno de los efectivos militares y policiales. Dicha ausencia, impide legitimar una medida como ésta. Finalmente, si la prisión preventiva hubiera sido en esos casos considerada como instrumento para evitar, no sólo la frustración de la pena, sino que además para negar toda finalidad preventiva general de la misma, dicha fundamentación tampoco creemos que en el caso en concreto pueda legitimar su aplicación en las situaciones de los fallos que hemos venido comentando. Así, la prisión preventiva, en estos casos, no podía ser un instrumento para fines preventivos generales positivos ni negativos, pues resulta imposible determinar en qué medida dichas privaciones de libertad –que se produjeron a semanas de la catástrofe natural del 27 de febrero– podrían haber incidido en la intimidación de potenciales delincuentes (prevención general negativa), o en la confianza de los ciudadanos en la fidelidad al derecho (prevención general positiva). A mayor abundamiento, debemos considerar que, comportamientos como los enjuiciados, es decir, acopio de especies luego de una catástrofe natural, o evento revolucionario, son conductas que a pesar de la aplicación del sistema penal –la pena– son reiterativas en el tiempo. Así, en nuestra historia, ya en la revolución de 1891 y en el terremoto de Valparaíso de 190647 se registraron hechos como los ocurridos luego del 27 de febrero de este año, pese a que tanto en la guerra civil como luego en el puerto, los autores de aquellos hechos fueron sancionados severamente, no obstante, esas sanciones y estas conductas se repiten en el tiempo. Ello no es más que una consecuencia de factores socio-estructurales, psicológicos y del actuar colectivo en situaciones de catástrofe, en donde las personas actúan pensando en el “aquí”, tiempo presente, olvidando lo pasado y lo futuro, dando rienda suelta a sus impulsos48, y en donde se “despiertan y 47 Brevemente sobre sucesos como los ocurridos en forma posterior al 27 de febrero, pueden verse En: http://latercera.com/contenido/1453_230311_9.shtml [visitado el 17/10/2010]. Aquí se relata la participación del Almirante Luis Gómez Carreño, como el encargado de restaurar el orden en la ciudad de Valparaíso luego del terremoto de 1906, suceso que provocó saqueos y disturbios en la ciudad. Al respecto, cuenta la historia que algunos autores de tales actos fueron fusilados en el lugar por orden de la autoridad de la Armada. Sobre el particular, ver Green, “Looting”, cit. nota n. 1. Allí se hace un análisis histórico de las situaciones que configuran lo que se califica como saqueo, y se ejemplifica con lo sucedido luego del huracán Katrina, donde luego de la catástrofe las personas dieron rienda suelta a su desesperación, haciéndose fácil presa de los medios de comunicación que informaban y juzgaban lo ocurrido, calificándolos de buenos y malos saqueadores. Los primeros, aquellos que acumulaban y recogían especies para su alimentación (generalmente de raza blanca), y los segundos, los que acopiaban y sacaban de 48 Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 411 Humberto Alarcón Corsi Jurisprudencia posicionan necesidades a resolverse individual o colectivamente, a raíz de la ineficiencia de las autoridades”49 En consecuencia, y dado que sucesos como los ocurridos el 27 de febrero de 2010, son eventos que gatillan conductas en las personas que difícilmente pueden ser reconducidas a un respeto siempre irrestricto a las normas, dados los factores que hemos indicado, podemos concluir que la prisión preventiva, incluso para efectos preventivos generales no cumple finalidad alguna, pues no existirá intimidación penal que pueda garantizar, que en 25 años más, de repetirse en Chile un evento como éste –lo que es altamente probable, dada nuestra estadística histórica en la materia–, no vuelvan a ocurrir eventos como los que hemos comentado. En consecuencia, en estos casos la prisión preventiva está motivada por fines claramente simbólicos, es decir, se trató de una intervención penal no suficientemente legítima, que no se acomoda al fin político criminal que funda la pena y, por lo mismo, el sistema penal50. La argumentación dada por las resoluciones objeto de comentario, es decir, que la libertad de los imputados constituía un peligro para la sociedad, son motivos que no satisfacen un juicio de proporcionalidad. e) Finalmente, consideramos que en ambos casos la prisión preventiva no sólo resultaba desproporcionada, por no ser idónea ni necesaria, sino que también por ser desproporcionada con la sanción probable. En la especie, en ambos casos se trata de situaciones en que los imputados cumplirán sus penas en libertad, gozando de los beneficios de la Ley Nº 18.216 sobre formas alternativas al cumplimiento de penas privativas de libertad. Es más, en ambos casos, sus causas han terminado con penas cuyo cumplimiento no es privativo de libertad. Así, en uno de los casos, causa RUC 1010006270-K, la pena fue de 41 días de prisión en su grado medio, más la pena pecuniaria de 2 unidades tributarias mensuales. Dicha sentencia fue recurrida por la defensa del imputado, fallo que se encuentra pendiente a esta fecha, y que será objeto de nuevo comentario. En conclusión, las resoluciones que se comentan no cumplieron las exigencias de una adecuada fundamentación, ni legitimación de la medida de privación de derechos que estaban decretando, exigencias que en una situación todo (generalmente de raza afroamericana). En uno y en otro caso, este autor indica que se trata de situaciones límite en donde las personas no actúan pensando en lo que sucederá ni en los sucedido, sino cómo y qué me puede ayudar a subsistir, lo que puede ser alimento, o también especies que pueda luego reducir o cambiar. Matus Acuña, Alejandra, “Nuestro Huracán Katrina”, Diario Electrónico El Mostrador, 1 de marzo de 2010. En: http://www.elmostrador.cl/opinion/2010/03/01/nuestro-huracan-katrina/ [visitado el 17/10/2010]. 49 50 Díez Ripollés, José Luis, “El Derecho Penal Simbólico y los Efectos de la Pena”, en Crítica y Justificación del Derecho Penal en el cambio de siglo, Ediciones Universidad Castilla - La Mancha (Estudios; 91), Cuenca 2003, pp. 147-172. 412 Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 Prisión preventiva, terremoto y saqueos: Comentario a las sentencias de la Corte Suprema de excepción son aún más exigibles, toda vez que la Constitución mantiene el control del apego a la juridicidad en manos de los órganos judiciales. Por ello, como indicaron al poco tiempo de sucedido el terremoto y maremoto, Hernández y Couso51: “las medidas excepcionales adoptadas en ese marco siguen sometidas al derecho, uno que en nuestros días no se entiende sin referencia a los derechos humanos (…) y que consecuentemente sólo legitima el ejercicio de la fuerza estricta y racionalmente necesaria para la mantención del orden, sin espacio para alardes ejemplificadores”, como al parecer, fue lo que sucedió en la especie. 51 Hernández, Héctor; Couso, Jaime, “Derecho y los Tiempos de Excepción”, Diario la Tercera, Ideas y Debates, 4 de marzo de 2010, Santiago de Chile, p. 4. Revista Ius et Praxis, Año 16, Nº 2 2010, pp. 393 - 414 413
https://openalex.org/W1975854049
https://europepmc.org/articles/pmc2900240?pdf=render
English
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The relationship between mosquito abundance and rice field density in the Republic of Korea
International journal of health geographics
2,010
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Abstract Background: Japanese encephalitis virus (JEV), the causative agent of Japanese encephalitis (JE), is endemic to the Republic of Korea (ROK) where unvaccinated United States (U.S.) military Service members, civilians and family members are stationed. The primary vector of the JEV in the ROK is Culex tritaeniorhynchus. The ecological relationship between Culex spp. and rice fields has been studied extensively; rice fields have been shown to increase the prevalence of Cx. tritaeniorhynchus. This research was conducted to determine if the quantification of rice field land cover surrounding U.S. military installations in the ROK should be used as a parameter in a larger risk model that predicts the abundance of Cx. tritaeniorhynchus populations. Mosquito data from the U.S. Forces Korea (USFK) mosquito surveillance program were used in this project. The average number of female Cx. tritaeniorhynchus collected per trap night for the months of August and September, 2002-2008, was calculated. Rice fields were manually digitized inside 1.5 km buffer zones surrounding U.S. military installations on high-resolution satellite images, and the proportion of rice fields was calculated for each buffer zone. Results: Mosquito data collected from seventeen sample sites were analyzed for an association with the proportion of rice field land cover. Results demonstrated that the linear relationship between the proportion of rice fields and mosquito abundance was statistically significant (R2 = 0.62, r = .79, F = 22.72, p < 0.001). Conclusions: The analysis presented shows a statistically significant linear relationship between the two parameters, proportion of rice field land cover and log10 of the average number of Cx. tritaeniorhynchus collected per trap night. The findings confirm that agricultural land cover should be included in future studies to develop JE risk prediction models for non-indigenous personnel living at military installations in the ROK. its primary vector Culex tritaeniorhynchus is plentiful in many Asian countries. It has been shown that the number of JEV vector mosquitoes collected in an area is highly correlated with the number of JE patients in that area [3]. While a reliable JE vaccination exists, this disease still affects many Southeast Asian countries [4,5]. Recent out- breaks in the last five years (2005 through 2010) have occurred in the indigenous population and unvaccinated expatriates and travellers in India, Nepal, Taiwan, Malay- sia, China, and Vietnam [6-12]. Recent maps showing the geographical distribution of JE have been published in several different papers [2,12,13]. © 2010 Richards et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract The JE distribution map in Figure 1 is based on the U.S. Centers for Disease Con- trol and Prevention (CDC) 2009 version of the map cur- rently distributed to international travellers [13]. Research The relationship between mosquito abundance and rice field density in the Republic of Korea Erin E Richards*1, Penny Masuoka1, David Brett-Major1,2, Matthew Smith3, Terry A Klein4, Heung Chul Kim5, Assaf Anyamba3 and John Grieco1 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Background Japanese encephalitis virus has been identified by the U.S. National Center for Medical Intelligence as operationally important to the U.S. military. Similarly, the pathogen is important to unvaccinated personnel from other militar- ies around the globe, expatriates, and travelers [1]. JE is a potentially debilitating and deadly flavivirus that is endemic in rural areas in east, south, and southwest Asia. Successful vaccination programs have diminished the number of illnesses in many countries, causing many to consider the disease to be rare and exotic [2]. However, the JEV is maintained in populations of wading birds and * Correspondence: erin.e.richards@us.army.mil 1 Department of Preventive Medicine and Biometrics, Uniformed Services University, Bethesda, Maryland, USA Full list of author information is available at the end of the article Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Page 2 of 10 Figure 1 Geographical distribution of Japanese encephalitis. Geographical distribution of Japanese Encephalitis as published in CDC Health In- formation for International Travel 2010 [13]. Guam and Saipan (not shown on this map) have also had cases of Japanese Encephalitis. Figure 1 Geographical distribution of Japanese encephalitis. Geographical distribution of Japanese Encephalitis as published in CDC Health In- formation for International Travel 2010 [13]. Guam and Saipan (not shown on this map) have also had cases of Japanese Encephalitis. Culex tritaeniorhynchus is exophagic, prefers zoonotic and domestic hosts, and tends to feed interspecifically [18]. Primary vertebrate reservoirs for JEV are large water birds of the family Ardeidae, while wild and domestic pigs are amplifying hosts [17,19]. Cx. tritaeniorhynchus is highly susceptible to viral infection; studies suggest that over 30% become infected after feeding on a viremic pig [20]. Mosquito populations are dependent on environ- mental and seasonal factors for their propagation. In the ROK, seasonal occurrence of Cx. tritaeniorhynchus are reported between mid-June and early October, with adult peak populations from late July through early September [21-26]. JEV infections within vector populations peak in late July and early August, with human disease rates peaking in late August and September [15,27]. Culex tri- taeniorhynchus breed in open sunlit temporary and per- manent water habitats with vegetation, and have an average flight range of 1.5 km [4,28]. The relative abun- dance of Cx. Methods Study Area The study area comprised seventeen U.S. military instal- lations in the ROK and their immediate surrounding areas. Military installations included in this study are a convenience sample based on availability of high resolu- tion images and mosquito data provided by the USFK mosquito surveillance program. Installations included in this study are Camp Humphreys, Camp Carroll, Gwangju Air Base, Warrior Base, Camp Red Cloud, Camp Stanley, Camp Jackson, Camp Essoyons, Camp Long, Camp Eagle, Camp Casey, Camp Castle, Camp Nimble, Camp Hovey, Osan Air Base, and Gunsan Air Base (Figure 2). Past studies on relative seasonal abundance and geo- graphical distribution of Cx. tritaeniorhynchus in the ROK have contributed to the success and development of a JE disease surveillance systems for local populations [34]. These surveillance systems have been based on monitoring vector populations and seroprevalence in swine from selected slaughterhouses; while such surveil- lance systems have been effective, they have a negative impact on the limited human resources and man-power available to public health. For this reason, the Uniformed Services University, the Armed Forces Health Surveil- lance Center, Global Emerging Infections Surveillance and Response System (AFHSC-GEIS), the National Aero- nautics and Space Administration (NASA) Goddard Space Flight Center (GSFC), and the 65th Medical Bri- gade-Korea, began working together to develop a JEV risk model in the ROK that incorporates remote sensing, land cover, elevation, and historical climate data. y g Reorganization of the U.S. military in the ROK has led to the realignment of existing military installations and closure of others. Camp Humphreys, which has been under construction since late 2007, is one of the largest installations and has been augmented in order to accom- modate an additional 20,000 relocated military, civilian, and family members. Wetland rice fields adjacent to Camp Humphreys were purchased for installation expan- sion, with fill dirt used to elevate the low-lying rice pad- dies for development, thus changing the local landscape. A portion of the secured rice paddies are programmed to lay fallow, thereby contributing to a possible increase in Cx. tritaeniorhynchus populations during the wet Mon- soons (June-September). Two images of Camp Hum- phreys were used in this project; one image is a 2006 QuickBird image and the other is a 2008 IKONOS image of the same location. The rice field density statistics used in analysis for Camp Humphreys is based on the 2006 image only. Background tritaeniorhynchus is closely related to local rice agricultural practices, where wetland rice fields and similar irrigation systems provide an optimal habitat for While JE clinical manifestations occur only in a small number that become infected, the case fatality rate can be as high as 40% for those demonstrating symptoms. Per- manent neurologic sequelae are observed in 40 to 50% of those who survive severe disease, resulting in minor to severe complications and early death [14,15]. Further- more, JE is often misdiagnosed and lacks effective treat- ment beyond supportive care [16,17]. U.S. military personnel have been stationed in the ROK since World War II. Currently, programmed extended tour lengths have greatly increased the number of accom- panying family, placing family members and young unvaccinated children at risk of infection. While an estab- lished Korean pediatric JEV vaccination program has greatly reduced the number of cases occurring in the Korean population, JEV continues to be of military public health concern in the ROK because U.S. personnel are not vaccinated for JE. Because of this disparity, human disease rates in the indigenous population are unreliable for estimating transmission and disease risks to U.S. mili- tary, civilian, and family members stationed there. Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Page 3 of 10 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 larval development [18]. The ecological relationship between mosquitoes and rice fields has been studied extensively [29-31]; results show that these man-made breeding sites result in a greater prevalence of Cx. tritae- niorhynchus than natural breeding sites [32,33]. rate risk model based on remotely sensed land and cli- mate data will allow for more efficient detection of increased JE risk to U.S. military populations in the ROK. Additionally, the risk model would diminish reliance on man-power intensive surveillance systems, and may pro- vide rationale for the implementation of mandatory JEV vaccination to USFK military, civilian, and family mem- bers assigned to the ROK. Remote sensing and Geographical Information Systems (GIS) are increasingly used in disease epidemiology to map vector and disease distributions so that vector con- trol efforts and disease intervention strategies are admin- istered efficiently and effectively [29]. Past research has demonstrated that remote sensing and GIS capabilities can be used successfully to identify breeding habitats of Cx. Background tritaeniorhynchus in Japan, the ROK, India, and Aus- tralia [18]. Methods Study Area The 2008 image shows the amount of rice fields lost as a result of installation construction. The two images were used in an exploratory fashion to help describe how changes in local land cover effect the abun- dance of Cx. tritaeniorhynchus. The goal of this project was to determine if quantifica- tion of wetland rice field land cover via remote sensing and GIS techniques could feasibly be used as a parameter in a larger risk model to predict the abundance of Cx. tri- taeniorhynchus at U.S. military installations in the ROK. While past studies have shown a correlation between Cx. tritaeniorhynchus collected at cow and pig sheds and sur- rounding rice field acreage [35,36], this study examines the number of Cx. tritaeniorhynchus collected on pri- marily urban military bases and compares the number of mosquitoes collected to the amount of rice field sur- rounding those bases. Quantifying the relationship between the amount of rice fields surrounding U.S. mili- tary installations in the ROK and the abundance of Cx. tritaeniorhynchus captured at these sites will enhance the U.S. military's capability to predict the risk of JEV trans- mission to military, civilians, and family members assigned to the ROK. This proposed risk model would be used in conjunction with a predictive model for seasonal JEV transmission using real-time data and would serve as a disease risk monitoring system for U.S. military and civilians living in the ROK. The development of an accu- Mosquito Data Retrospective mosquito data were provided by the USFK, which conducts routine mosquito surveillance on U.S. military installations to monitor all mosquito species. Mosquitoes were collected weekly using un-baited New Jersey (NJ) light traps in accordance with USFK preven- tive medicine protocol from May through October, 2002 to 2008. One to eight traps were established at each mili- Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Page 4 of 10 Figure 2 Study area. The following military installations within South Korea are shown: Camp Humphreys, Camp Carroll, Gwangju Air Base (Kwangju) Warrior Base, Camp Red Cloud, Camp Stanley, Camp Jackson, Camp Essoyons, Camp Long, Camp Eagle, Camp Casey, Camp Castle, Camp Nimble, Camp Hovey, Osan Air Base, and Gunsan Air Base (Kunsan). Land cover obtained from MODIS Land Cover Group http://www-modis.bu.edu/landcover Figure 2 Study area. The following military installations within South Korea are shown: Camp Humphreys, Camp Carroll, Gwangju Air Base (Kwangju), Warrior Base, Camp Red Cloud, Camp Stanley, Camp Jackson, Camp Essoyons, Camp Long, Camp Eagle, Camp Casey, Camp Castle, Camp Nimble, Camp Hovey, Osan Air Base, and Gunsan Air Base (Kunsan). Land cover obtained from MODIS Land Cover Group http://www-modis.bu.edu/landcover. Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Page 5 of 10 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 tary installation. Collections were sent to the Entomology Section, 5th Medical Detachment, for identification where data on adult female mosquitoes (i.e. species, trap night, month, and year) were prepared. A summary of the total number of mosquitoes (males plus females) collected at each location from 2002 to 2008 is listed in Table 1. Although NJ light traps are relatively inefficient for col- lecting mosquitoes when compared to newer technolo- gies, they are easy to operate and data can be compared with collections made over more than 20 years of surveil- lance in the ROK. comparison studies have demonstrated that land classifi- cation outcomes are analogous for both image types [37]. Within each of the ten QuickBird images and one IKO- NOS image, military installations were located using lati- tude and longitude coordinates. Processing of image data involved two steps: digitizing and area computation. Mosquito Data Rice fields were identified using photointerpretation and manual digitization via ArcGIS® 9.3 software (Envi- ronmental Systems Research Institute, Redlands, CA, USA, http://www.esri.com). The border of each military installation was digitized using publically available instal- lation maps as aids. Buffers were used to designate the study inclusion area. The buffer area surrounding each military installation was based on the average flight range of Cx. tritaeniorhynchus [4], and was set at 1.5 km from the digitized military installation border. Rice fields within the buffer area of each military installation were then manually digitized as polygons. Manual digitization was chosen because the majority of images available for this project were acquired during the winter months when rice fields were bare and spectrally similar to other land cover, making automated classification difficult. Rice field land cover was digitized as large polygons consisting of many individual rice fields. Other non-rice features such as irrigation ditches and small roads may have been included in the rice field land cover. To minimize varia- tion, all digitization was completed by one researcher in a consistent manner. The final mosquito count at each military installation used in the main analysis of this study is an average from August to September from 2002 to 2008. August and Sep- tember were selected for analysis to capture the peak Cx. tritaeniorhynchus breeding cycle [21]. To reduce the effects of sampling variation between years and installa- tions, data were standardized as the number of female mosquitoes collected per trap night per month [mosqui- toes per trap night = total female mosquitoes collected/ (number of traps * number of nights)]. The final mos- quito capture rate for each military installation was calcu- lated by adding the number of mosquitoes per trap night for months August and September from 2002 to 2008, then dividing by the number of nights mosquito sampling was conducted during that time period. *Data are not adjusted for number of trap nights. The numbers in this table include both male and female mosquitoes and those trapped at Gunsan, which was later dropped from the study. High Resolution Satellite Data A regression model was developed from the data to predict mosquito abundance at Camp Humphreys after environmental changes in 2007 altered the amount of rice fields surrounding the installation. Rice field density in the 2008 Camp Humphreys image was applied to the regression model to determine a predicted mosquito count and then compared to the observed 2008 number of mosquitoes per trap night. This test was used to explore the model's ability to predict the abundance of female Cx. tritaeniorhynchus collected at an installation. High Resolution Satellite Data One IKONOS and ten QuickBird high resolution images, encompassing visible and near infrared data, taken between 2004 and 2008 were used for land cover classifi- cation. QuickBird is a commercial earth observation sat- ellite operated by DigitalGlobe http:// www.digitalglobe.com that records multispectral imagery at 2.6 meter resolution at nadir. IKONOS is a similar commercial earth observation satellite operated by Geo- Eye http://www.geoeye.com that provides multispectral images at four meter resolution. Although the QuickBird images have a higher resolution than the IKONOS image, To obtain area measurements in kilometers, the digi- tized military installations buffer area and rice field shape files were reprojected from a Geographic Coordinate Sys- tem (GCS) to a Universal Transverse Mercator (UTM) map projection. The buffer area at each military installa- tion was calculated and reported in square kilometers. The digitized rice field polygons within the buffer area of each military installation was calculated and reported in km2. To account for variation in installation size and thus buffer area size, rice field densities were calculated as the proportion of rice fields within the buffer area at each Table 1: Number of Culex tritaeniorhynchus mosquitoes collected in the ROK from 2002 to 2008 by month* MAY JUN JUL AUG SEP OCT Total 2002 1 28 3724 27515 17995 524 49787 2003 0 7 315 1790 2282 38 4432 2004 0 12 650 32957 9446 1487 44552 2005 0 2 294 4264 2502 136 7198 2006 0 6 40 580 1046 6 1678 2007 1 12 986 2976 845 122 4942 2008 0 5 584 2421 1584 33 4627 *Data are not adjusted for number of trap nights. The numbers in this table include both male and female mosquitoes and those trapped at Gunsan, which was later dropped from the study. Table 1: Number of Culex tritaeniorhynchus mosquitoes collected in the ROK from 2002 to 2008 by m *Data are not adjusted for number of trap nights. The numbers in this table include both male and female mosquitoes and those trapped at Gunsan, which was later dropped from the study. Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Page 6 of 10 installation (rice fields proportion = rice field area/mili- tary installation buffer area). An example of digitized rice field data is presented in Figure 3. Discussion Thi This research addresses the issues of mosquito abun- dance and spatial patterns of agricultural land use. Emphasis has been put on determining the relationship between average Cx. tritaeniorhynchus collected per trap night and density of rice fields surrounding U.S. military installations in the ROK; as well as assessing the value of that relationship for inclusion in a larger disease risk model. The future application of rice field density as a parameter in models used to predict JEV disease risks can be based on the strength of linear association, as it is pre- sented here. A priori statistical power analysis stated that a sample of sixteen sites carried 80% power to detect the propor- tion of variability between mosquito abundance and rice field density in the model with a coefficient of determina- tion (R2) of 0.65. For our purposes, an R2 of 0.65 was desired. The correlation coefficient (r) was also used in this analysis to elucidate the relationship between mos- quito abundance and the rice field density seen in the data. Results revealed that 62% of the variation in the log10 of Cx. tritaeniorhynchus collected per trap night on base was accounted for by the density of rice fields in the area surrounding the military base. The remaining 38% can be explained by inherent variability or other variables, such as species breeding cycle, proximity to blood source, or regional climatic conditions [17,19-21,31]. Our data reaf- firms past JE and Cx. tritaeniorhynchus research and sug- gests that rice fields account for a large portion of the mosquito's abundance but that populations cannot be predicted by rice fields alone [29-31,35,36]. Rice Field Analysis The Mosquito Magnet is the most effective trap for collecting Cx. tritaenio- rhynchus; capturing up to 650 times as many mosquitoes as the NJ light trap [23]. Primarily because trapping methods were substantially different at Gunsan than those at all other installations in the study sample, Gun- san Air Base was excluded from the final analysis. all other years (Table 1). An observational retrospective study of mosquito prevalence at U.S. military installations in the ROK found that Cx. tritaeniorhynchus was the most common mosquito species collected in 2002 [38]. In 2002, due to a high number of mosquitoes collected at Gunsan Air Base, the overall average of Cx. tritaenio- rhynchus populations in the ROK increased by 27.2%, while populations of other mosquito species remained relatively constant during the same time period [38]. The increased number of Cx. tritaeniorhynchus caught at Gunsan Air Base in 2002 and 2004 could be due to the use of more efficient collection methods during these two years. At Gunsan, NJ light traps were baited with dry ice during collections in 2002 and the Mosquito Magnet® was used for collections in 2004 [38]. The Mosquito Magnet is the most effective trap for collecting Cx. tritaenio- rhynchus; capturing up to 650 times as many mosquitoes as the NJ light trap [23]. Primarily because trapping methods were substantially different at Gunsan than those at all other installations in the study sample, Gun- san Air Base was excluded from the final analysis. In an exploratory analysis the regression model was used to predict the abundance of Cx. tritaeniorhynchus at Camp Humphreys in 2008. Despite major changes to the Camp Humphreys area, the proportion of rice fields sur- rounding the installation increased by only 1%. The num- ber of predicted mosquitoes per trap night was 18.2 for the 2008 Camp Humphreys image; the number of observed mosquitoes per trap night was 22.2. Rice Field Analysis Simple linear regression analysis, using the SPSS® statisti- cal program (SPSS Inc., Chicago, IL, USA) was conducted on the data using two continuous variables, rice field den- sity and log10 of the average number of Cx. tritaenio- rhynchus per trap night from 2002-2008. The rice field density statistic representing the proportion of rice fields surrounding Camp Humphreys was based on the 2006 image only. Mosquito prevalence trend analysis showed extreme variation over time. Years 2002 and 2004 had abnormally high counts of Cx. tritaeniorhynchus when compared to Figure 3 Digitized rice field data example. The above is an image of a military installation located in the ROK taken in October. The base is shown with a solid grey cover; the extent of the buffer zone area is depicted with a dark blue line; rice fields are shown with a solid yellow cover. The buffer zone area extends 1.5 km from the military installation perimeter. Figure 3 Digitized rice field data example. The above is an image of a military installation located in the ROK taken in October. The base is shown with a solid grey cover; the extent of the buffer zone area is depicted with a dark blue line; rice fields are shown with a solid yellow cover. The buffer zone area extends 1.5 km from the military installation perimeter. Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Page 7 of 10 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 increase of female Cx. tritaeniorhynchus per trap night can be expected. all other years (Table 1). An observational retrospective study of mosquito prevalence at U.S. military installations in the ROK found that Cx. tritaeniorhynchus was the most common mosquito species collected in 2002 [38]. In 2002, due to a high number of mosquitoes collected at Gunsan Air Base, the overall average of Cx. tritaenio- rhynchus populations in the ROK increased by 27.2%, while populations of other mosquito species remained relatively constant during the same time period [38]. The increased number of Cx. tritaeniorhynchus caught at Gunsan Air Base in 2002 and 2004 could be due to the use of more efficient collection methods during these two years. At Gunsan, NJ light traps were baited with dry ice during collections in 2002 and the Mosquito Magnet® was used for collections in 2004 [38]. Results Average mosquito counts per trap night and the corre- sponding rice field density statistics are presented for each installation in Table 2. The area surrounding half of the installations in this study were comprised of less than 10% rice fields. This is in sharp contrast to installations that were surrounded by the most rice fields; coverage ranged between 30-56% of the land surrounding five installations. Mosquito data were log10 transformed prior to regression analysis. Analysis conducted using log10 transformed mosquito data from 2002-2008 demon- strated a statistically significant linear relationship between rice field density and mosquito abundance (R2 = 0.62, r = .79, F = 22.72, p < 0.001). A scatter plot of the data with the regression line is presented in Figure 4. A statistically significant linear association was demon- strated between rice field density and mosquito popula- tion. Given the strong relationship demonstrated between rice field density and mosquito populations, this variable should be considered when modelling Cx. tritae- niorhynchus propagation or JEV transmission risks. Specific limitations to this study with regard to image data include the inability to automatically extract rice fields due to the lack of ground vegetation in many of the images used. Due to cloud cover and other limiting fac- tors, the remotely sensed imagery used in analysis were not all acquired during the rice growing season, making automated land cover extraction software unable to accu- rately identify rice fields. While rice fields were extracted manually, the potential for misclassification of land cover remained. Field shape, image interpretation, and area photographs guided rice field identification. This study was also limited by the lack of images at each installation for each year or month within the study period. Thus, the authors were unable to explore variation in the correla- The resulting linear model [y = 2.71 × -0.28; where y equals the log10 of the average mosquitoes per trap night, and × equals the proportion of rice field land cover] was used to predict the abundance of post-construction Cx. tritaeniorhynchus at Camp Humphreys using the 2008 image. The data reveals that for every 10% increase of rice field land cover surrounding an installation, an 86% Richards et al. Results International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Page 8 of 10 Table 2: Rice field density and average number of mosquitoes collected per trap night, by installation** Installation Proportion of Rice Fields in Buffer Area Monthly Average Number Female Mosquitoes per Trap Night 2002-2008 (Aug-Sept) Camp Jackson 0.00 0.62 Camp Casey 0.01 0.83 Camp Hovey 0.02 0.74 Camp Essoyons 0.02 0.73 Camp Nimble 0.02 0.44 Camp Mobile 0.02 1.23 Camp Red Cloud 0.03 0.82 Camp Castle 0.05 0.86 Camp Stanley 0.11 0.57 Camp Long 0.13 0.36 Camp Carroll 0.18 2.36 Camp Eagle 0.21 0.23 Gwangju Air Base 0.30 14.40 Warrior Base 0.38 14.81 Osan Air Base 0.44 3.64 Gunsan AB 0.53 222.42 Camp Humphreys 0.56 22.20 **Gunsan was dropped from subsequent analysis. 2: Rice field density and average number of mosquitoes collected per trap night, by installation** **Gunsan was dropped from subsequent analysis. This limitation restricts analysis and does not allow the geographical variability among installations to be explored. tion between rice field density and Cx. tritaeniorhynchus throughout time. This study, and potentially all studies conducted on military bases in the ROK, will be limited by the number of installations and number of installa- tions within the USFK mosquito surveillance program. Despite limitations, this study has a number of strengths. It utilized USFK mosquito surveillance data collected consistently for over 8 years in the ROK. This data continues to be collected and can be similarly used in the future. It also uses high resolution remotely sensed imagery to determine rice field land cover. Using remotely sensed data to map rice field land cover is less time consuming than conventional ground survey meth- ods used in the past to calculate agricultural land use. Figure 4 Fitted curve of model. The above is a scatter plot of the data and the resulting regression line (y = 2.71 × -0.28). Each dot represents data from one installation. mosquito per trap night proportion of rice fields log10 of the average m mosquito per trap night proportion of rice fields log10 of the average m Abbreviations AFHSC A d 9. Japanese encephalitis - Taiwan [http://www.promedmail.org]. Accession Number 20060909.2565 AFHSC: Armed Forces Health Surveillance Center; CDC: Centers for Disease Control and Prevention; GCS: Geographic Coordinate System; GEIS: Depart- ment of Defense Global Emerging Infections Surveillance and Response Sys- tem; GIS: Geographical Information Systems; GSFC: Goddard Space Flight Center; JE: Japanese encephalitis; JEV: Japanese encephalitis virus; NASA: National Aeronautics and Space Administration; NJ: New Jersey; ROK: Republic of Korea; USFK: United States Forces Korea; UTM: Universal Transverse Mercator. 10. Japanese encephalitis - Malaysia (Kelantan) [http:// www.promedmail.org]. Accession Number 20060130.0301 11. Japanese encephalitis & other - India (02): (AP) [http:// www.promedmail.org]. Accession Number 20100422.1309 12. van den Hurk AF, Ritchie SA, Mackenzie JS: Ecology and geographical expansion of Japanese encephalitis virus. Annual Review of Entomology 2009, 54:17-35. expansion of Japanese encephalitis virus. Annual Review of Entomology 2009, 54:17-35. Competing interests Th h d l h 13. Brunette GW, Kozarsky PE, Magill AJ, Shlim DR, Whatley AD: CDC Health Information for International Travel 2010 (The Yellow Book) 2010 edition. CDC; 2009. p g The authors declare that they have no competing interests. The authors declare that they have no competing interests. Authors' contributions l d h 14. Thongcharoen P: Japanese encephalitis virus encephalitis: an overview. Southeast Asian Journal of Tropical Medicine and Public Health 1989, 20:559-573. 14. Thongcharoen P: Japanese encephalitis virus encephalitis: an overview. Southeast Asian Journal of Tropical Medicine and Public Health 1989, 20:559-573. ER implemented the mapping project, analysis of the data, drafting of the manuscript, and contributed to the study design. PM conceived the study design, acquired land cover data and contributed to the coordination of the study, implementation of the mapping project, and revision of the manuscript. DB contributed to the study design and revision of the manuscript. MS partici- pated in the creation of the mapping project and revision of the manuscript. AA contributed to the coordination of the study and advised on study design. HCK assisted with mosquito data collection, provided advice on mosquito data analysis and provided coordination with USFK. TAK collected mosquito data, provided advice on mosquito data analysis, provided coordination with USFK, and assisted with manuscript revision. JG provided project resources, advised on study design and analysis, and assisted in final editing. All authors have read and approved the final manuscript. 15. Vaughn DW, Hoke CH Jr: The epidemiology of Japanese encephalitis: prospects for prevention. Epidemiologic Reviews 1992, 14:197-221. 16. Kitchen LW, Vaughn DW: Role of U.S. military research programs in the development of U.S.-licensed vaccines for naturally occurring infectious diseases. Vaccine 2007, 25:7017-7030. 17. Sabin AB: Insect borne virus diseases of military importance. Military Medicine 1955, 116:245-251. 18. Keiser J, Maltese MF, Erlanger TE, Bos R, Tanner M, Singer BH, Utzinger J: Effect of irrigated rice agriculture on Japanese encephalitis, including challenges and opportunities for integrated vector management. Acta Tropica 2005, 95:40-57. 19. Buescher EL, Scherer WF: Ecologic studies of Japanese encephalitis virus in Japan. IX. Epidemiologic correlations and conclusions. American Journal of Tropical Medicine and Hygiene 1959, 8:719-722. Acknowledgements h k This work was supported through the partnership between the Uniformed Services University, the AFHSC-GEIS, NASA GSFC, and the 65th Medical Brigade, Korea. We thank Dr. Cara Olsen and Dr. Rodger Gibson from the Uniformed Ser- vices University, who contributed to the analysis, methods and interpretation of this project. We thank the Commander and Soldiers of the 5th Medical Detachment, 168th Medical Battalion, 65th Medical Brigade, who performed the collection and identification of mosquitoes used in this study. We are grateful to the National Geospatial-Intelligence Agency (NGA) who provided imagery for this project. 20. Maeda O, Takenokuma K, Karoji Y, Kuroda A, Sasaki O, Karaki T, Ishii T: Epidemiological studies on Japanese encephalitis in Kyoto City area, Japan. Japanese Journal of Medical Science & Biology 1978, 31:317-324. 21. Lee KW, Gupta RK, Wildie JA: The Collection of Adult Larval Mosquitoes in U.S. Army Compounds in the Republic of Korea During 1979~1983. The Korean Journal of Parasitology 1984, 22:102-108. 22. Joo CY, Wada Y: Seasonal Prevalence of the Vector Mosquitoes of Japanese Encephalitis Virus in Kyungpook Province, Korea. Korean Journal of Parasitology 1985, 23:139-150. Conclusions Using the data presented here, an overall statistically sig- nificant linear relationship between rice field density and Cx. tritaeniorhynchus abundance was found. Use of the regression model to predict mosquito abundance was inconsistent. Future studies to develop JE risk prediction models for non-indigenous personnel living at military installations in the ROK should include agriculture land use and irrigation patterns as variables. There are a number of implications in this study for future research in JE risk prediction and Cx. tritaenio- rhynchus population modelling in the vicinity of U.S. mil- itary installations in the ROK. First, automated risk Figure 4 Fitted curve of model. The above is a scatter plot of the data and the resulting regression line (y = 2.71 × -0.28). Each dot represents data from one installation. Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 Page 9 of 10 Page 9 of 10 3. Solomon T, Dung NM, Kneen R, Gainsborough M, Vaughn DW, Khanh VT: Japanese encephalitis. Journal of Neurology, Neurosurgery & Psychiatry 2000, 68:405-415. models must utilize land cover maps derived from remotely sensed imagery acquired during the rice grow- ing season. The use of images acquired with fallow rice fields could hinder the accuracy of automated rice field mapping, and could inhibit model efficiency. Second, if possible, imagery should be acquired for each month or year during the study period to facilitate the analysis of rice field density and Cx. tritaeniorhynchus within and among installations, and account for annual fluctuation in average mosquito per trap night. 4. Bista MB, Shrestha JM: Epidemiological situation of Japanese encephalitis in Nepal. Journal of Nepal Medical Association 2005, 44:51-56. 5. Kanojia PC: Ecological study on mosquito vectors of Japanese encephalitis virus in Bellary district, Karnataka. Indian Journal of Medical Research 2007, 126:152-157. 6. Japanese encephalitis - Belgium ex China: RFI [http:// www.promedmail.org]. Accession Number 20050413.1070 7. Japanese encephalitis - Viet Nam [http://www.promedmail.org]. Accession Number 20050626.1795 8. Japanese encephalitis - Nepal [http://www.promedmail.org]. Accession Number 20060831.2475 2. Solomon T: Control of Japanese encephalitis-within our grasp? New England Journal of Medicine 2006, 355:869-871. Received: 5 April 2010 Accepted: 23 June 2010 Published: 23 June 2010 This article is available from: http://www.ij-healthgeographics.com/content/9/1/32 © 2010 Richards et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use International Journal of Health Geographics 2010, 9:32 26. Kim HC, Lee KW, Robert LL, Sardelis MR, Chase FE: Seasonal prevalence of mosquitoes collected from light traps in Korea (1991- 1992). Korean Journal of Entomology 1995, 25:225-234. 27. Scherer WF, Buescher EL: Ecologic studies of Japanese encephalitis virus in Japan. I. Introduction. American Journal of Tropical Medicine and Hygiene 1959, 8:644-650. 1. Japanese encephalitis [http://www.who.int/vaccine_research/diseases/ vector/en/index2.html] vector/en/index2.html] Author Details 23. Burkett DA, Lee WJ, Lee KW, Kim CH, Lee HI, Lee JS, Shin EH, Wirtz RA, Cho HW, Claborn DM, Coleman RE, Kim WY, Klein TA: Late season commercial mosquito trap and host seeking activity evaluation against mosquitoes in a malarious area of the Republic of Korea. Korean Journal of Parasitology 2002, 40:45-50. 1Department of Preventive Medicine and Biometrics, Uniformed Services University, Bethesda, Maryland, USA, 2Military Tropical Medicine Course, Navy Medicine Manpower Personnel Training and Education Command, Uniformed Services University, Bethesda, Maryland, USA, 3Biospheric Sciences Branch, Goddard Space Flight Center, National Aeronautics and Space Administration, Greenbelt, Maryland, USA, 4Force Health Protection and Preventive Medicine, 65th Medical Brigade/MEDDAC-Korea, Seoul, Republic of Korea and 55th Medical Detachment, 168th Medical Battalion, 65th Medical Brigade, Seoul, Republic of Korea 24. Kim HC, Lee KW, Jones JW, Korch GW: Seasonal prevalence of mosquitoes collected from light trap in Korea (1993-1994). Korean Journal of Entomology 1997, 27:21-28. 25. Kim HC, Lee KW, Klein TA, Strickman DA: Seasonal prevalence of mosquitoes collected from light traps in Korea (1995-1996). Korean Journal of Entomology 1999, 29:181-187. Received: 5 April 2010 Accepted: 23 June 2010 Published: 23 June 2010 This article is available from: http://www.ij-healthgeographics.com/content/9/1/32 © 2010 Richards et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted u International Journal of Health Geographics 2010, 9:32 References Page 10 of 10 Richards et al. International Journal of Health Geographics 2010, 9:32 http://www.ij-healthgeographics.com/content/9/1/32 28. Henrich TJ, Hutchaleelaha S, Jiwariyavej V, Barbazan P, Nitatpattana N, Yoksan S, Gonzalez JP: Geographic dynamics of viral encephalitis in Thailand. Microbes and Infection 2003, 5:603-611. 29. Beck LR, Lobitz BM, Wood BL: Remote Sensing and Human Health: New Sensors and New Opportunities. Emerging Infectious Diseases 2000, 6:217-226. 30. Wood BL, Beck LR, Washino RK, Hibbard KA, Salute JS: Estimating high mosquito-producing rice fields using spectral and spacial data. International Journal of Remote Sensing 1992, 13:2813-2826. International Journal of Remote Sensing 1992, 13:2813-2826. 31. Wood BL, Beck LR, Washino RK, Palchick SM, Sebesta PD: Spectral and spatial characterization of rice field mosquito habitat. International Journal of Remote Sensing 1991, 12:621-626. 32. Suzuki T: Bibliography on Culex tritaeniorhynchus in Japan 1945-1966. Book Bibliography on Culex tritaeniorhynchus in Japan 1945-1966 (Editor ed.^eds.). City 1967. 33. Lacey L, Lacey C: The medical importance of rice-land mosquitoes and their control using alternatives to chemical insecticides. Journal of the American Mosquito Control Association 1990, 2:1-93. 34. Self LS, Shin HK, Kim KW, Lee CY, Chow CY, Hong HK: Ecological Studies on Culex tritaeniorhynchus as a Vector of Japanese Encephalitis. Bulletin of the WHO 1973, 49:41-47. 35. Matsuzaki S: Population dynamics of Culex tritaeniorhynchus in relation to the epidemics of Japanese encephalitis in Kochi Prefecture, Japan. Japanese Journal of Sanitary Zoology 1990, 41:247-255. 36. Ree HI, Lee SK: Studies on mosquito population dynamics in Chollabug- do, Korea (1985-1990) II. Factors influencing population sizes of Culex tritaeniorhynchus and Anopheles sinensis. Korean Journal of Entomology 1993, 23:185-194. 37. Wang L, Sousa W, Gong P, Biging G: Comparison of IKONOS and QuickBird images for mapping mangrove species on the Caribbean coast of Panama. Remote Sensing of Environment 2004, 91:432-440. 38. Kim HC, Chong S, Collier BW, Lee HC, Klein TA: Seasonal Prevalence of Mosquitoes Collected from Light Traps in the Republic of Korea, 2004. Entomological Research 2007:180-189. doi: 10.1186/1476-072X-9-32 Cite this article as: Richards et al., The relationship between mosquito abun- dance and rice field density in the Republic of Korea International Journal of Health Geographics 2010, 9:32
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Abstract. Global crude steel production is expected to continue to increase in the coming decades to meet the demands of the growing world population. Currently, the dominant steelmaking technology worldwide is the conventional highly CO2-intensive Blast Furnace–Basic Oxygen Furnace production route (also known as the Linz–Donawitz process) using iron ore as raw material and coke as a reducing agent. As a result, large quantities of special gases that are rich in carbon monoxide (CO) are by- 5 products of the various stages of the steelmaking process. Given the challenges associated with satellite-based estimates of carbon dioxide (CO2) emissions at the scale of emitting installations due to significant background levels, co-emitted CO may serve as a valuable indicator of the carbon footprint of steel plants. We show that regional CO release from steel production sites can be monitored from space using 5 years of measurements (2018-2022) from the TROPOspheric monitoring instrument (TROPOMI) on board the Sentinel-5 Precursor satellite benefiting 10 from its relatively high spatial resolution and daily global coverage. We analyse all German steel plants with blast furnaces and basic oxygen furnaces and obtain associated CO emissions in the range of 50-400 kt yr−1 per site. A comparison with the respective CO2 emissions on the level of emitting installations available from emissions trading data of the European Union Emissions Trading System yields a linear relationship with a sector-specific CO/CO2 emission ratio for the analysed (2018-2022) from the TROPOspheric monitoring instrument (TROPOMI) on board the Sentinel-5 Precursor satellite benefiting 10 from its relatively high spatial resolution and daily global coverage. We analyse all German steel plants with blast furnaces and basic oxygen furnaces and obtain associated CO emissions in the range of 50-400 kt yr−1 per site. A comparison with the respective CO2 emissions on the level of emitting installations available from emissions trading data of the European Union Emissions Trading System yields a linear relationship with a sector-specific CO/CO2 emission ratio for the analysed steelworks of 3.24%[2.73 −3.89; 1σ] suggesting the feasibility of using CO as a proxy for CO2 emissions from comparable 15 steel production sites. https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. Towards a sector-specific CO/CO2 emission ratio: Satellite-based observation of CO release from steel production in Germany Oliver Schneising, Michael Buchwitz, Maximilian Reuter, Michael Weimer, Heinrich Bovensmann, John P. Burrows, and Hartmut Bösch Institute of Environmental Physics (IUP), University of Bremen FB1, Bremen, Germany Correspondence: O. Schneising (oliver.schneising@iup.physik.uni-bremen.de) Major sources of CO emissions include transportation, residential heating and cooking, biomass burning, industrial pro- cesses, and natural sources like wildfires. In the broader category of industrial emissions, CO is generated as a byproduct of incomplete combustion or chemical reactions. An important example is the steel producing industry with CO emissions mainly due to the formation and release of CO-rich gases in the widely used Linz–Donawitz process of integrated steel plants: 40 1) Sinter gas produced in a pre-treatment process step agglomerating iron ore fines into a porous, consistent high quality burden suitable for direct use in the blast furnace, 2) blast furnace gas arising during iron ore reduction with carbon (primarily in the form of coke), and 3) converter gas resulting from conversion of molten pig iron to steel by oxidation of carbon impurities to harden the metal (Ishioka et al., 1992; Kim et al., 2016). These CO-rich by-product gases can be incinerated within the steel mainly due to the formation and release of CO-rich gases in the widely used Linz–Donawitz process of integrated steel plants: 40 1) Sinter gas produced in a pre-treatment process step agglomerating iron ore fines into a porous, consistent high quality burden suitable for direct use in the blast furnace, 2) blast furnace gas arising during iron ore reduction with carbon (primarily in the form of coke), and 3) converter gas resulting from conversion of molten pig iron to steel by oxidation of carbon impurities to harden the metal (Ishioka et al., 1992; Kim et al., 2016). These CO-rich by-product gases can be incinerated within the steel production route for heat supply (Backes et al., 2021) or reused in the steelmaking process to replace some of the solid carbon 45 fuels to reduce CO2 emissions substantially (He and Wang, 2017; Kildahl et al., 2023). Understanding the CO loss processes throughout the entire steelmaking workflow and their link to CO2 emissions is crucial for addressing the twin challenge of en- vironmental pollution and climate change mitigation until the planned transformation to green steel is completed and the Blast Furnace–Basic Oxygen Furnace route has been replaced by the Direct Reduction–Electric Arc Furnace route using pure hy- drogen (H2) obtained from renewable sources as the reducing agent avoiding direct emissions of non-condensable greenhouse 50 gases almost entirely (Graupner et al., 2023). 1 Introduction Carbon monoxide (CO) has a dual role as both an air pollutant and a crucial component of atmospheric chemistry. Its reactiv- ity with the hydroxyl radical (OH) and other atmospheric constituents has a significant effect on the oxidising capacity of the atmosphere, which subsequently influences the abundances of greenhouse gases, such as methane, and the formation of sec- 0 ondary pollutants, including tropospheric ozone (Holloway et al., 2000). It is therefore essential to gain accurate knowledge of the sources of CO to ensure efficient air quality control, pollution management, and an improved understanding of atmospheric composition and its impact on climate change. The atmospheric lifetime of CO is approximately 1-2 months, so that it is well suited for tracing the transport of pollutants and can be used as a proxy for co-emitted CO2 (Wu et al., 2022; MacDonald et al., 20 1 1 https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. 2023), which is harder to observe from space than CO because CO2 is well-mixed in the atmosphere resulting in small signals 25 relative to large background levels. Satellite missions with global coverage significantly improve our ability to analyse atmospheric CO. Instruments using measurements of shortwave infrared (SWIR) radiances to retrieve CO column abundances in the atmosphere are sensitive to the planetary boundary layer and operate during daytime when there is sufficient sunlight to illuminate the Earth’s surface. 2023), which is harder to observe from space than CO because CO2 is well-mixed in the atmosphere resulting in small signals 25 relative to large background levels. Satellite missions with global coverage significantly improve our ability to analyse atmospheric CO. Instruments using measurements of shortwave infrared (SWIR) radiances to retrieve CO column abundances in the atmosphere are sensitive to the planetary boundary layer and operate during daytime when there is sufficient sunlight to illuminate the Earth’s surface. Prominent instruments measuring in this spectral range include the Measurement of Pollution in the Troposphere (MOPITT) 30 instrument (Drummond et al., 2010) on board NASA’s Terra satellite, the SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY) (Burrows et al., 1995; Bovensmann et al., 1999) on board ESA’s ENVISAT, and the Thermal And Near infrared Sensor for carbon Observations Fourier Transform Spectrometer 2 (TANSO-FTS-2) on board GOSAT-2 (Suto et al., 2021). The application areas for satellite data were further extended with the TROPOspheric Moni- Prominent instruments measuring in this spectral range include the Measurement of Pollution in the Troposphere (MOPITT) 30 instrument (Drummond et al., 2010) on board NASA’s Terra satellite, the SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY) (Burrows et al., 1995; Bovensmann et al., 1999) on board ESA’s ENVISAT, and the Thermal And Near infrared Sensor for carbon Observations Fourier Transform Spectrometer 2 (TANSO-FTS-2) on board GOSAT-2 (Suto et al., 2021). The application areas for satellite data were further extended with the TROPOspheric Moni- toring Instrument (TROPOMI) (Veefkind et al 2012) which is considered a milestone for the determination of atmospheric 35 toring Instrument (TROPOMI) (Veefkind et al., 2012), which is considered a milestone for the determination of atmospheric 35 composition, including CO, from space by combining high spatio-temporal sampling and data quality. There are only a few studies on sector-specific CO emissions from steel production that were obtained by remote sensing. Atmospheric CO enhancements from steel production in Asia and Europe have been qualitatively analysed with TROPOMI data before (Schneising et al., 2019, 2023). Tian et al. (2022) quantify CO emission rates for industrial parks in Asia using TROPOMI data without attributing them to a specific sector. There are also some other analyses that deal with urban emissions 65 (Park et al., 2021; Wu et al., 2022), but these are usually a mixture of emissions from different sectors, e.g. transport, heating, and industry-related. Wu et al. (2022) derive CO/CO2 ratios for cities, including two in China that are explicitly highlighted as industry- and energy-oriented with metal production sites such as aluminium or steel plants. In this manuscript, we use TROPOMI observations and their unique features to systematically quantify the CO emissions of all German steelworks applying the Linz–Donawitz process and to determine the corresponding sector-specific CO/CO2 70 emission ratio, which is as a first step towards the potential use of co-emitted CO as a proxy for CO2 emissions from the steel industry. The locations of the analysed production sites are shown in Figure 1. of all German steelworks applying the Linz–Donawitz process and to determine the corresponding sector-specific CO/CO2 70 emission ratio, which is as a first step towards the potential use of co-emitted CO as a proxy for CO2 emissions from the steel industry. The locations of the analysed production sites are shown in Figure 1. Given that the steel industry is highly energy-intensive and one of the leading industrial contributors to global anthropogenic CO2 emissions, with a share of around 7%, the rapid and systematic decarbonisation of steel production is essential to meet climate targets (International Energy Agency, 2020). With around 40 million tonnes of crude steel production, Germany is the largest steel producer in Europe and will likely exceed its sectoral CO2 budget for a 1.5◦C warming scenario in the 2030s at 55 the latest (Harpprecht et al., 2022). In both Germany and worldwide, the predominant method accounting for around 70% of steel production is through primary production utilising the Blast Furnace–Basic Oxygen Furnace production route. There are several studies analysing the environmental impact of steel production sites using a bottom-up life cycle assessment (Suer et al., 2022, and references therein), but most of them focus on CO2 emissions and do not quantify co-emitted CO There are several studies analysing the environmental impact of steel production sites using a bottom-up life cycle assessment (Suer et al., 2022, and references therein), but most of them focus on CO2 emissions and do not quantify co-emitted CO 2 2 Figure 1. Locations of the analysed German steel production sites. https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. Figure 1. Locations of the analysed German steel production sites. Figure 1. Locations of the analysed German steel production sites. explicitly. One exception is the study by Burchart-Korol (2013), in which all inputs and outputs of the sub-processes involved 60 in steelmaking are explicitly broken down for an integrated steel plant in Poland and summarised in a corresponding inventory. There are only a few studies on sector-specific CO emissions from steel production that were obtained by remote sensing. Atmospheric CO enhancements from steel production in Asia and Europe have been qualitatively analysed with TROPOMI data before (Schneising et al., 2019, 2023). Tian et al. (2022) quantify CO emission rates for industrial parks in Asia using explicitly. One exception is the study by Burchart-Korol (2013), in which all inputs and outputs of the sub-processes involved 60 in steelmaking are explicitly broken down for an integrated steel plant in Poland and summarised in a corresponding inventory. 2 Data and methods Sentinel-5 Precursor, launched in October 2017, operates in a sun-synchronous orbit with an Sentinel-5 Precursor, launched in October 2017, operates in a sun-synchronous orbit with an equator crossing time of 13:30 Sentinel-5 Precursor, launched in October 2017, operates in a sun-synchronous orbit with an equator crossing time of 13:30 local time. TROPOMI is a spaceborne nadir-viewing imaging spectrometer designed to measure solar radiation reflected by the 75 Earth in a push-broom configuration. With a swath width of 2600 km, it provides a rare combination of relatively high spatial resolution and daily global coverage. The nadir measurements in the shortwave infrared (SWIR) offer a horizontal resolution of 5.5×7 km2 at nadir (7×7 km2 before 6 August 2019) and are sensitive to all altitude levels, including the planetary boundary layer, making them well-suited for studying emissions from sources on the ground such as steelworks. local time. TROPOMI is a spaceborne nadir-viewing imaging spectrometer designed to measure solar radiation reflected by the 75 Earth in a push-broom configuration. With a swath width of 2600 km, it provides a rare combination of relatively high spatial resolution and daily global coverage. The nadir measurements in the shortwave infrared (SWIR) offer a horizontal resolution of 5.5×7 km2 at nadir (7×7 km2 before 6 August 2019) and are sensitive to all altitude levels, including the planetary boundary layer, making them well-suited for studying emissions from sources on the ground such as steelworks. 3 https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. Figure 2. Example daily data for Duisburg to demonstrate the emission estimation process. The coordinate system has been rotated to the wind direction. The background region is highlighted in cyan, the plume region in orange, and the hot spot region in magenta. The dimensions and position of these regions remain constant for all days analysed within the rotated coordinate system. The hot spot region is only used to establish selection criteria that ensure sufficient data coverage (see main text for details) and is not used directly in the emission estimation process itself. The cross sections utilised for calculating the daily flux are indicated in red. Figure 2. Example daily data for Duisburg to demonstrate the emission estimation process. The coordinate system has been rotated to the wind direction. The background region is highlighted in cyan, the plume region in orange, and the hot spot region in magenta. 2 Data and methods The dimensions and position of these regions remain constant for all days analysed within the rotated coordinate system. The hot spot region is only used to establish selection criteria that ensure sufficient data coverage (see main text for details) and is not used directly in the emission estimation process itself. The cross sections utilised for calculating the daily flux are indicated in red. In this research, we use the latest version of the Weighting Function Modified DOAS (WFM-DOAS) algorithm, specifically 80 optimised for the simultaneous retrieval of methane and carbon monoxide from TROPOMI (Schneising et al., 2019, 2023). The involved column-averaged dry air mole fractions of carbon monoxide, denoted as XCO, retrieved with the scientific TROPOMI/WFMD algorithm v1.8, are characterised by a random error (precision) of 5.1 ppb and a spatio-temporal systematic error (relative accuracy) of 2.6 ppb after quality filtering (Schneising et al., 2023). In this research, we use the latest version of the Weighting Function Modified DOAS (WFM-DOAS) algorithm, specifically 80 optimised for the simultaneous retrieval of methane and carbon monoxide from TROPOMI (Schneising et al., 2019, 2023). The involved column-averaged dry air mole fractions of carbon monoxide, denoted as XCO, retrieved with the scientific TROPOMI/WFMD algorithm v1.8, are characterised by a random error (precision) of 5.1 ppb and a spatio-temporal systematic error (relative accuracy) of 2.6 ppb after quality filtering (Schneising et al., 2023). 80 The estimation of emissions presented here relies on the daily observations provided by TROPOMI and a Gaussian integral 85 method, also referred to as the cross-sectional flux method. To automatically process quality-filtered daily XCO retrievals for a specific source region, the estimation method of Schneising et al. (2020b) is applied, which is briefly recapitulated in the following. Initially, the data given as latitude and longitude are transformed to a coordinate system rotated to the wind direction, in which the prime meridian and the equator are aligned with the centre of the analysed region and the zonal direction The estimation of emissions presented here relies on the daily observations provided by TROPOMI and a Gaussian integral 85 method, also referred to as the cross-sectional flux method. To automatically process quality-filtered daily XCO retrievals for a specific source region, the estimation method of Schneising et al. (2020b) is applied, which is briefly recapitulated in the following. 2 Data and methods Initially, the data given as latitude and longitude are transformed to a coordinate system rotated to the wind direction, in which the prime meridian and the equator are aligned with the centre of the analysed region and the zonal direction The estimation of emissions presented here relies on the daily observations provided by TROPOMI and a Gaussian integral 85 method, also referred to as the cross-sectional flux method. To automatically process quality-filtered daily XCO retrievals for a specific source region, the estimation method of Schneising et al. (2020b) is applied, which is briefly recapitulated in the following. Initially, the data given as latitude and longitude are transformed to a coordinate system rotated to the wind direction, in which the prime meridian and the equator are aligned with the centre of the analysed region and the zonal direction corresponds to the mean boundary layer wind direction (within the region of interest and within a time window of two hours 90 before the satellite overpass) obtained from the European Centre for Medium-Range Weather Forecasts (ECMWF) ERA5 reanalysis product (Hersbach et al., 2018). Subsequently, the transformed daily data is gridded on a 0.05◦× 0.05◦grid, which is comparable to the horizontal nadir resolution of TROPOMI, and a mean background upwind of the source is subtracted. An example highlighting the position of the background and plume region is shown in Figure 2. corresponds to the mean boundary layer wind direction (within the region of interest and within a time window of two hours 90 before the satellite overpass) obtained from the European Centre for Medium-Range Weather Forecasts (ECMWF) ERA5 reanalysis product (Hersbach et al., 2018). Subsequently, the transformed daily data is gridded on a 0.05◦× 0.05◦grid, which is comparable to the horizontal nadir resolution of TROPOMI, and a mean background upwind of the source is subtracted. An example highlighting the position of the background and plume region is shown in Figure 2. Let E represent the total column enhancement (in units of mass per area) and v the average wind speed within the boundary 95 layer. To assess the emission, we use the divergence theorem and compute the flux of the vector field Ev through cross Let E represent the total column enhancement (in units of mass per area) and v the average wind speed within the boundary 95 layer. The molar mass of carbon monoxide, MCO, is 28.01g mol−1, the Avogadro constant, NA, is 6.022·1023 molec mol−1 the O2 column (in units of molecules per area) depends on the actual mean surface pressure, and the dry air mole fraction of oxygen, XO2, is 0.209. These values are used to convert between the enhancement in XCO and the total column enhancement 105 E. Additionally, ACO is the value of the lowest layer of the averaging kernel (which is approximately 0.95 for all analysed Here, ∆l represents the size of a grid cell and i corresponds to the meridional summation along the respective cross section given by k. The molar mass of carbon monoxide, MCO, is 28.01g mol−1, the Avogadro constant, NA, is 6.022·1023 molec mol−1 the O2 column (in units of molecules per area) depends on the actual mean surface pressure, and the dry air mole fraction of oxygen, XO2, is 0.209. These values are used to convert between the enhancement in XCO and the total column enhancement 105 E. Additionally, ACO is the value of the lowest layer of the averaging kernel (which is approximately 0.95 for all analysed source regions) characterising the boundary layer sensitivity of the retrieval method. oxygen, XO2, is 0.209. These values are used to convert between the enhancement in XCO and the total column enhancement 105 E. Additionally, ACO is the value of the lowest layer of the averaging kernel (which is approximately 0.95 for all analysed source regions) characterising the boundary layer sensitivity of the retrieval method. Taking the average of all cross-sectional fluxes Φk results in the daily flux estimate, denoted as Φ, with the corresponding uncertainty depending on the variability of the enhancements derived for the different cross sections, the variability of the Taking the average of all cross-sectional fluxes Φk results in the daily flux estimate, denoted as Φ, with the corresponding uncertainty depending on the variability of the enhancements derived for the different cross sections, the variability of the absolute wind speed over the region, the wind history, and on the variability of the O2 column, which is determined by surface 110 pressure (Schneising et al., 2020b). In this daily averaging procedure, only those Φk are considered where at least 60% of the maximum possible grid cells along the cross-section are validly filled with data. https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. sections (red lines in Figure 2) perpendicular to wind direction, which is assumed to match the plume axis after rotation of the coordinate system. Consequently, the fluxes through boundaries other than the cross sections under consideration are zero, as the unit normals of the zonal boundaries are perpendicular to wind direction and there is no flux through any upwind meridional boundary. Thus, the emission rate is equal to the flux through the kth cross section for all k and given by 100 100 Φk = Z V (∇· Ev)dV = I ∂V =S Ev · dS = X i Ek,i v∆li = v∆l X i Ek,i = v · ∆l · MCO · O2 NA · ACO · XO2 X i (∆XCO)k,i (1) Φk = Z V (∇· Ev)dV = I ∂V =S Ev · dS = X i Ek,i v∆li = v∆l X i Ek,i = v · ∆l · MCO · O2 NA · ACO · XO2 X i (∆XCO)k,i (1) Here, ∆l represents the size of a grid cell and i corresponds to the meridional summation along the respective cross section given by k. The molar mass of carbon monoxide, MCO, is 28.01g mol−1, the Avogadro constant, NA, is 6.022·1023 molec mol−1, the O2 column (in units of molecules per area) depends on the actual mean surface pressure, and the dry air mole fraction of (1) Φk = Z V (∇· Ev)dV = I ∂V =S Ev · dS = X i Ek,i v∆li = v∆l X i Ek,i = NA · ACO · XO2 X i (∆XCO)k,i (1) Here, ∆l represents the size of a grid cell and i corresponds to the meridional summation along the respective cross section given by k. The molar mass of carbon monoxide, MCO, is 28.01g mol−1, the Avogadro constant, NA, is 6.022·1023 molec mol−1, the O2 column (in units of molecules per area) depends on the actual mean surface pressure, and the dry air mole fraction of Here, ∆l represents the size of a grid cell and i corresponds to the meridional summation along the respective cross section given by k. If there are less than five such Φk, this particular day will not be used any further.i From the pool of available days, we select those that fulfill certain criteria (concerning data ground scatter, meridional asymmetry, and wind history), which are listed below, for calculating the averaged long-term emis- 115 sion rate ¯Φ of the respective source region (see Schneising et al. (2020b) for details). To better account for the quasi-point source character of steelworks in contrast to the larger emission regions analysed in Schneising et al. (2020b), we use smaller regions according to Figure 2 (e.g. cross sections of about 100 km length) and the following selection criteria optimised for XCO: at least 50% of the plume, hot spot, and background regions have to be filled with data (additionally at least 20% each of the northern and southern half of the background region), v ∈(1.5m s−1,9m s−1), the coverage and background distri- 120 bution is required to be sufficiently uniform with respect to the equator (nN p > 0.6 · nS p , nS p > 0.6 · nN p , | ¯EN b −¯ES b | < 3ppb, σ(Eb) < 4ppb), where ¯E is the mean enhancement of a region, n is the corresponding number of grid cells, and σ is the standard deviation; ·N,S b,p refers to the northern/southern half of the background/plume region. Additionally, days with wind di- rection changes exceeding 30◦within the analysed wind history of 2 hours are also excluded. There is no criterion preventing negative meridional gradients ( ¯Ep < ¯Eb) and associated negative emissions to ensure an unbiased mean long-term emission 125 estimate ¯Φ. For small emissions, inversion noise can result in negative values, whose suppression would cause an overesti- mation of the mean emission. The calculation method for the uncertainty of the averaged long-term emission rate ¯Φ from the individual daily uncertainties by error propagation has been retained exactly as described in Schneising et al. (2020b). The European Union Emissions Trading System (EU ETS) regulates greenhouse gas emissions of energy-intensive indus- tries and is based on the "cap and trade" principle. The cap limits the amount of greenhouse gases allowed to be emitted by an 130 The European Union Emissions Trading System (EU ETS) regulates greenhouse gas emissions of energy-intensive indus- tries and is based on the "cap and trade" principle. 2 Data and methods To assess the emission, we use the divergence theorem and compute the flux of the vector field Ev through cross 4 3 Results and discussion The steel production sites in Germany that still utilise the conventional Blast Furnace–Basic Oxygen Furnace production route are located in Duisburg, Dillingen/Saar, Salzgitter, Bremen, and Eisenhüttenstadt (ordered by pig iron and steel production from high to low), which together account for approximately 70% of German steel production (Harpprecht et al., 2022). These 145 production sites have been analysed using the cross-sectional flux method to determine CO emissions during the time period 2018-2022. Theil- Sen regression is a robust method, which is insensitive to outliers and influential points by using the median of the slopes of all possible lines formed by pairs of points (Sen, 1968). The corresponding confidence interval is determined by bootstrapping, 140 fitting the Theil-Sen regressor to each resample, and analysing the resulting distribution of regression coefficients. possible lines formed by pairs of points (Sen, 1968). The corresponding confidence interval is determined by bootstrapping, 140 fitting the Theil-Sen regressor to each resample, and analysing the resulting distribution of regression coefficients. The cap limits the amount of greenhouse gases allowed to be emitted by an 130 5 5 3.1 Estimation of site-specific CO emissions The North Rhine-Westphalian city of Duisburg has a long history as a centre of the steel The North Rhine-Westphalian city of Duisburg has a long history as a centre of the steel industry as the region’s proximity The North Rhine-Westphalian city of Duisburg has a long history as a centre of the steel industry as the region s proximity to coal and iron ore reserves made it an ideal location for steel production. The city is home to two of the most prolific steel 150 plants in Germany in service since more than a hundred years: Integriertes Hüttenwerk Duisburg with 4 blast furnaces and Glocke Duisburg with 2 blast furnaces. The averaged multi-year CO enhancement distribution for Duisburg, which exhibits a pronounced plume structure, and the daily emission estimates are displayed in Figure 3. The associated mean CO emission estimate is determined by the daily estimates and amounts to 397 ± 58kt yr−1. The steel industry is one of the most important sectors of the economy in the German federal state of Saarland. Dillinger 155 Hütte is the most significant steel producing site in the region, with production of steel dating back to the 17th century. Today, Dillingen is the only production site for pig iron in the Saarland, which is subsequently further refined into crude steel. Two blast furnaces are operated on the site. Figure 4 illustrates both the average CO enhancement distribution and the daily emission estimates for Dillingen. As in the case of Duisburg, there is a distinct plume shape visible in the long-term wind-rotated mean. The steel industry is one of the most important sectors of the economy in the German federal state of Saarland. Dillinger 155 Hütte is the most significant steel producing site in the region, with production of steel dating back to the 17th century. Today, Dillingen is the only production site for pig iron in the Saarland, which is subsequently further refined into crude steel. Two blast furnaces are operated on the site. Figure 4 illustrates both the average CO enhancement distribution and the daily emission estimates for Dillingen. As in the case of Duisburg, there is a distinct plume shape visible in the long-term wind-rotated mean. The corresponding mean CO emission estimate based on the daily emissions is 157 ± 52kt yr−1. 160 Salzgitter steel works is a Blast Furnace–Basic Oxygen Furnace steel plant operating in Salzgitter, Lower Saxony. https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. installation and is quantified in emission allowances, which can be traded with each other. For each year, the companies op- erating the installations are obligated to surrender sufficient allowances to completely offset their actual emissions. Therefore, industrial installions are required to have an approved monitoring plan for monitoring and reporting annual emissions. These reported emissions data are verified annually by accredited independent verifiers (European Union, 2018). The corresponding information is available on EUETS.INFO (https://www.euets.info/, last access: 14 November 2023) providing verified annual 135 CO2 emissions and surrendered allowances on the level of emitting installations and on country level. installation and is quantified in emission allowances, which can be traded with each other. For each year, the companies op- erating the installations are obligated to surrender sufficient allowances to completely offset their actual emissions. Therefore, industrial installions are required to have an approved monitoring plan for monitoring and reporting annual emissions. These reported emissions data are verified annually by accredited independent verifiers (European Union, 2018). The correspondingi information is available on EUETS.INFO (https://www.euets.info/, last access: 14 November 2023) providing verified annual 135 CO2 emissions and surrendered allowances on the level of emitting installations and on country level. The CO/CO2 emission ratio is determined by Theil-Sen regression of the derived CO emissions for the different sites and the respective verified CO2 emissions from the production of pig iron or steel available from the emission trading data. Theil- Sen regression is a robust method, which is insensitive to outliers and influential points by using the median of the slopes of all The CO/CO2 emission ratio is determined by Theil-Sen regression of the derived CO emissions for the different sites and the respective verified CO2 emissions from the production of pig iron or steel available from the emission trading data. Theil- Sen regression is a robust method, which is insensitive to outliers and influential points by using the median of the slopes of all The CO/CO2 emission ratio is determined by Theil-Sen regression of the derived CO emissions for the different sites and the respective verified CO2 emissions from the production of pig iron or steel available from the emission trading data. 3.1 Estimation of site-specific CO emissions The history of the site can be traced back to the interwar period in the early 20th century. During that time, an initiative aiming The corresponding mean CO emission estimate based on the daily emissions is 157 ± 52kt yr−1. 160 Salzgitter steel works is a Blast Furnace–Basic Oxygen Furnace steel plant operating in Salzgitter, Lower Saxony. The history of the site can be traced back to the interwar period in the early 20th century. During that time, an initiative aiming 6 Figure 3. Mean CO enhancement distribution and associated integrated enhancement along the cross sections (top) as well as daily emission estimates Φ for the steel plants in Duisburg (bottom). The mean CO emission ¯Φ is calculated from the daily emissions. The original daily wind directions, defined as the direction in which the wind blows, are visually represented in the wind rose overlaid in the upper left corner. https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. Figure 3. Mean CO enhancement distribution and associated integrated enhancement along the cross sections (top) as well as daily emission estimates Φ for the steel plants in Duisburg (bottom). The mean CO emission ¯Φ is calculated from the daily emissions. The original daily wind directions, defined as the direction in which the wind blows, are visually represented in the wind rose overlaid in the upper left corner. Figure 3. Mean CO enhancement distribution and associated integrated enhancement along the cross sections (top) as well as daily emission estimates Φ for the steel plants in Duisburg (bottom). The mean CO emission ¯Φ is calculated from the daily emissions. The original daily wind directions, defined as the direction in which the wind blows, are visually represented in the wind rose overlaid in the upper left corner. Figure 4. As Figure 3 but for Dillingen/Saar. Figure 4. As Figure 3 but for Dillingen/Saar. 7 Figure 5. As previous figures but for Salzgitter. at establishing a self-sufficient German steel industry included the construction of a massive steel plant in Salzgitter. After shutdown and recommissioning, the site operates 3 blast furnaces today. The mean CO enhancement distribution is shown https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. Figure 5. As previous figures but for Salzgitter. Figure 5. As previous figures but for Salzgitter. 3.1 Estimation of site-specific CO emissions f S l i Figure 5. As previous figures but for Salzgitter. at establishing a self-sufficient German steel industry included the construction of a massive steel plant in Salzgitter. After shutdown and recommissioning, the site operates 3 blast furnaces today. The mean CO enhancement distribution is shown together with the daily emission estimates in Figure 5. The average CO emission is estimated to be 125 ± 48kt yr−1. 65 at establishing a self-sufficient German steel industry included the construction of a massive steel plant in Salzgitter. After shutdown and recommissioning, the site operates 3 blast furnaces today. The mean CO enhancement distribution is shown together with the daily emission estimates in Figure 5. The average CO emission is estimated to be 125 ± 48kt yr−1. 165 The Bremen steel plant with 2 blast furnaces has its roots in a long history of steel production in the region. The reason for establishing steelworks at this strategic location was the access to key transportation routes, including rivers and ports, that facilitated the import of raw materials and the export of finished steel products. Over the years, the plant underwent several redesigns, mergers and expansions to meet the changing needs of the steel industry. The averaged CO enhancement distribution together with the daily emission estimates in Figure 5. The average CO emission is estimated to be 125 ± 48kt yr−1. 165 The Bremen steel plant with 2 blast furnaces has its roots in a long history of steel production in the region. The reason for establishing steelworks at this strategic location was the access to key transportation routes, including rivers and ports, that facilitated the import of raw materials and the export of finished steel products. Over the years, the plant underwent several redesigns, mergers and expansions to meet the changing needs of the steel industry. The averaged CO enhancement distribution and the daily emission estimates are displayed in Figure 6. The associated mean CO emission estimate is 92 ± 59kt yr−1. 170 The history of the Eisenhüttenstadt plant located in the German federal state of Brandenburg began in the 1950s as the Eisenhüttenkombinat in East Germany producing pig iron with 6 blast furnaces. In the 1980s, a Linz–Donawitz steelworks was installed. After German reunification a new blast furnace was built, which is the only one still in operation today. 3.1 Estimation of site-specific CO emissions Figure 7 illustrates both the average CO enhancement distribution and the daily emission estimates. The corresponding mean CO and the daily emission estimates are displayed in Figure 6. The associated mean CO emission estimate is 92 ± 59kt yr−1. 170 The history of the Eisenhüttenstadt plant located in the German federal state of Brandenburg began in the 1950s as the Eisenhüttenkombinat in East Germany producing pig iron with 6 blast furnaces. In the 1980s, a Linz–Donawitz steelworks was installed. After German reunification a new blast furnace was built, which is the only one still in operation today. Figure 7 illustrates both the average CO enhancement distribution and the daily emission estimates. The corresponding mean CO and the daily emission estimates are displayed in Figure 6. The associated mean CO emission estimate is 92 ± 59kt yr−1. 170 The history of the Eisenhüttenstadt plant located in the German federal state of Brandenburg began in the 1950s as the Eisenhüttenkombinat in East Germany producing pig iron with 6 blast furnaces. In the 1980s, a Linz–Donawitz steelworks was installed. After German reunification a new blast furnace was built, which is the only one still in operation today. Figure 7 illustrates both the average CO enhancement distribution and the daily emission estimates. The corresponding mean CO emission estimate is 48 ± 55kt yr−1. In contrast to the other analysed production sites, the emissions seem to be close to the 175 detection limit because only a rather weak plume is observable in the average CO distribution and there is hardly any variation of the associated sums along the cross-sections. In accordance with this finding, the mean emission estimate is similar in magnitude to the corresponding uncertainty indicating that the derived uncertainties are generally realistic. emission estimate is 48 ± 55kt yr−1. In contrast to the other analysed production sites, the emissions seem to be close to the 175 detection limit because only a rather weak plume is observable in the average CO distribution and there is hardly any variation of the associated sums along the cross-sections. In accordance with this finding, the mean emission estimate is similar in magnitude to the corresponding uncertainty indicating that the derived uncertainties are generally realistic. emission estimate is 48 ± 55kt yr−1. https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. 3.2 Air quality assessment According to German air quality standards, the maximum allowed daily 8-hour mean of ambient CO is 10mg m−3 (Umwelt- 180 bundesamt, 2017). Typical background values in Germany are about 0.2mg m−3 (Umweltbundesamt, 2022). The largest local daily enhancement anomalies occurring in the vicinity of German steelworks reach about 50ppb in very rare cases, which translate to a total column enhancement E of roughly 0.5g m−2. It is assumed that the excess CO from the steel production site is located in the well-mixed boundary layer and that the associated boundary layer concentration anomaly ∆ρbl (in units of mass per volume) can be determined by division by the boundary layer height hbl (Schneising et al 2020a): 185 ∆ρbl = E hbl (2) Assuming a boundary layer height of 500m, the boundary layer anomaly is about 1mg m−3, which is well below the air quality standard of 10mg m−3 even after adding typical background concentrations. The figures in Section 3.1 show that the maximum annual averaged enhancements due to steelworks are of the order of ∆ρbl = E hbl (2) Assuming a boundary layer height of 500m, the boundary layer anomaly is about 1mg m−3, which is well below the air quality standard of 10mg m−3 even after adding typical background concentrations. The figures in Section 3.1 show that the maximum annual averaged enhancements due to steelworks are of the order of Assuming a boundary layer height of 500m, the boundary layer anomaly is about 1mg m−3, which is well below the air quality standard of 10mg m−3 even after adding typical background concentrations. 10ppb locally, which corresponds to an annual mean boundary layer anomaly of about 0.2mg m−3 using the above assump- 190 tions. Adding a typical background value gives a maximum total annual mean concentration at TROPOMI resolution of about 0.4mg m−3 in the vicinity of steel production sites, which is in agreement with actually measured values, e.g. in Dillingen (Umweltbundesamt, 2022). Consequently, the rough calculation has confirmed that the CO emissions from the analysed steel- works are not an air quality issue. 3.1 Estimation of site-specific CO emissions In contrast to the other analysed production sites, the emissions seem to be close to the 175 detection limit because only a rather weak plume is observable in the average CO distribution and there is hardly any variation of the associated sums along the cross-sections. In accordance with this finding, the mean emission estimate is similar in magnitude to the corresponding uncertainty indicating that the derived uncertainties are generally realistic. 8 https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. Figure 6. As previous figures but for Bremen. Figure 7. As previous figures but for Eisenhüttenstadt. 9 Figure 6. As previous figures but for Bremen. Figure 6. As previous figures but for Bremen. Figure 6. As previous figures but for Bremen. Figure 7. As previous figures but for Eisenhüttenstadt. Figure 7. As previous figures but for Eisenhüttenstadt. Figure 7. As previous figures but for Eisenhüttenstadt. 9 9 3.3 Sector-specific CO/CO2 emission ratio 195 3.3 Sector-specific CO/CO2 emission ratio 195 The European Union Emissions Trading System (EU ETS) provides verified annual CO2 emissions on the level of emitting installations. The associated mean emissions of the steel production sites for the time period analysed here (2018-2022) are summarised in Table 1. Figure 8 demonstrates that CO and CO2 emissions from the production of pig iron or steel are highly correlated. It is The European Union Emissions Trading System (EU ETS) provides verified annual CO2 emissions on the level of emitting installations. The associated mean emissions of the steel production sites for the time period analysed here (2018-2022) are summarised in Table 1. Figure 8 demonstrates that CO and CO2 emissions from the production of pig iron or steel are highly correlated. It is g p p g g y assumed that the temporal sampling of available daily CO emission estimates is representative for the actual variability of steel 200 production and associated reported CO2 emissions at the analysed sites. As the data point representing Duisburg is quite far away from the main cluster of data points, it may be an influential point with large impact on the results when performing an ordinary least-squares (OLS) regression, which potentially complicates the interpretation of the fitted coefficients and their uncertainties. This potential issue can be mitigated by using the robust Theil-Sen regression (Sen, 1968), which calculates the assumed that the temporal sampling of available daily CO emission estimates is representative for the actual variability of steel 200 production and associated reported CO2 emissions at the analysed sites. As the data point representing Duisburg is quite far away from the main cluster of data points, it may be an influential point with large impact on the results when performing an ordinary least-squares (OLS) regression, which potentially complicates the interpretation of the fitted coefficients and their uncertainties. This potential issue can be mitigated by using the robust Theil-Sen regression (Sen, 1968), which calculates the assumed that the temporal sampling of available daily CO emission estimates is representative for the actual variability of steel 200 production and associated reported CO2 emissions at the analysed sites. 3.3 Sector-specific CO/CO2 emission ratio 195 As the data point representing Duisburg is quite far away from the main cluster of data points, it may be an influential point with large impact on the results when performing an ordinary least-squares (OLS) regression, which potentially complicates the interpretation of the fitted coefficients and their uncertainties. This potential issue can be mitigated by using the robust Theil-Sen regression (Sen, 1968), which calculates the slope by taking the median of all possible slopes between individual pairs of data points. To compute a confidence interval for 205 the Theil-Sen regression, we use bootstrapping (plus additional random perturbation of the data points in y-direction according to the respective uncertainties of the individual CO emission estimates) to generate multiple resamples of the data and fit the Theil-Sen Regressor to each resample. This results in a set of regression coefficients from which the final regression and the associated 1σ-confidence interval are derived by determining the median of slopes and intercepts as well as the 16th and 84th slope by taking the median of all possible slopes between individual pairs of data points. To compute a confidence interval for 205 the Theil-Sen regression, we use bootstrapping (plus additional random perturbation of the data points in y-direction according to the respective uncertainties of the individual CO emission estimates) to generate multiple resamples of the data and fit the Theil-Sen Regressor to each resample. This results in a set of regression coefficients from which the final regression and the associated 1σ-confidence interval are derived by determining the median of slopes and intercepts as well as the 16th and 84th percentile of the distribution 210 10 https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. Table 1. Mean emissions for the time period 2018-2022. The CO2 emissions from the production of pig iron or steel are obtained from the European Union Emissions Trading System (EU ETS), the CO emissions are estimated in this study as well as extracted from the Thru.de portal (providing key environmental data from industrial facilities in Germany) for comparison. EU ETS This study Thru.de CO2 emissions CO emissions CO emissions Site ID Operator Blast furnaces (Mt yr−1) (kt yr−1) (kt yr−1) Duisburg DU Thyssenkrupp Steel Europe 4 7.75 397 ± 58 315 Hüttenwerke Krupp Mannesmann 2 4.61 Dillingen DI Dillinger Hüttenwerke 2 4.15 157 ± 52 90 Salzgitter SZ Salzgitter Flachstahl 3 3.92 125 ± 48 66 Bremen HB ArcelorMittal Bremen 2 2.30 92 ± 59 63 Eisenhüttenstadt EH ArcelorMittal Eisenhüttenstadt 1 1.48 48 ± 55 40 Figure 8. Theil-Sen regression of the derived CO emissions for the different sites and the respective CO2 emissions according to the European Union Emissions Trading System (EU ETS) to determine the CO/CO2 emission ratio and the associated 1σ-confidence interval. The shaded region surrounding the regression line represents the prediction interval, which is determined by assessing the standard deviation of Theil-Sen regressions from multiple bootstrap samples. R2 is the coefficient of determination of the prediction of the Theil-Sen regression. EU ETS This study Thru.de CO2 emissions CO emissions CO emissions Site ID Operator Blast furnaces (Mt yr−1) (kt yr−1) (kt yr−1) Duisburg DU Thyssenkrupp Steel Europe 4 7.75 397 ± 58 315 Hüttenwerke Krupp Mannesmann 2 4.61 Dillingen DI Dillinger Hüttenwerke 2 4.15 157 ± 52 90 Salzgitter SZ Salzgitter Flachstahl 3 3.92 125 ± 48 66 Bremen HB ArcelorMittal Bremen 2 2.30 92 ± 59 63 Eisenhüttenstadt EH ArcelorMittal Eisenhüttenstadt 1 1.48 48 ± 55 40 Figure 8. Theil-Sen regression of the derived CO emissions for the different sites and the respective Figure 8. Theil-Sen regression of the derived CO emissions for the different sites and the respective CO2 emissions according to the European Union Emissions Trading System (EU ETS) to determine the CO/CO2 emission ratio and the associated 1σ-confidence interval. The shaded region surrounding the regression line represents the prediction interval, which is determined by assessing the standard deviation of Theil-Sen regressions from multiple bootstrap samples. R2 is the coefficient of determination of the prediction of the Theil-Sen regression. A facility is defined as one or more installations at the same site that are run by one operator. For example, a facility in the steel industry (integrated CO/CO2 emission ratio is approximately 2.0%. However, this value cannot be directly compared with ours either, because 230 this activity also comprises other processes than conventional primary steel production. Deriving a sector-specific emission ratio based on Thru.de data is also not straightforward because the reported releases are not provided on the level of emitting installations (in contrast to the European Union Emissions Trading System), but on the facility level. A facility is defined as one or more installations at the same site that are run by one operator. For example, a facility in the steel industry (integrated steelworks) may include a large number of different installations (e.g. coking plant, sintering plant, blast furnace, basic oxygen 235 furnace, rolling mill, power plant), whose combined emissions are then attributed to the so-called main activity of the facility, which is usually the production of pig iron or steel. While the CO emissions are actually mainly attributable to the main activity, the reported CO2 emissions typically also include significant contributions from other sectors such as the energy sector. As a consequence, the facility-based Thru.de CO/CO2 emission ratio underestimates the actually targeted sector-specific emission ratio, just like the other potential comparison data sets discussed so far. However, the extent of underestimation is not even 240 consistent from site to site, but depends on which non-main activities are explicitly carried out additionally at a given facility. It is therefore not possible to obtain a representative CO/CO2 emission ratio from this data set by regressing the individual CO and CO2 emissions of the respective facilities. Nevertheless, the reported Thru.de CO releases can be directly compared with our emission estimates, because only the place of origin and not the exact breakdown by sector is relevant for this pur- ratio, just like the other potential comparison data sets discussed so far. However, the extent of underestimation is not even 240 consistent from site to site, but depends on which non-main activities are explicitly carried out additionally at a given facility. It is therefore not possible to obtain a representative CO/CO2 emission ratio from this data set by regressing the individual CO and CO2 emissions of the respective facilities. regression of the derived CO emissions for the different sites and the respective CO2 emissions accordi Figure 8. Theil-Sen regression of the derived CO emissions for the different sites and the respective CO2 emissions according to the European Union Emissions Trading System (EU ETS) to determine the CO/CO2 emission ratio and the associated 1σ-confidence interval. The shaded region surrounding the regression line represents the prediction interval, which is determined by assessing the standard deviation of Theil-Sen regressions from multiple bootstrap samples. R2 is the coefficient of determination of the prediction of the Theil-Sen regression. The performed robust Theil-Sen regression of CO and CO2 emissions is illustrated in Figure 8. The shaded area around the regression line visually represents the prediction interval, which is determined by the standard deviation of the regressions of the multiple bootstrap samples and effectively reflects the predictive uncertainty of the model. The resulting CO/CO2 emission 11 https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. ratio for the analysed steelworks amounts to 3.24%[2.73−3.89; 1σ]; the corresponding 95%-confidence interval (obtained from the 2.5th an 97.5th percentile of the slope distribution) is [1.90,5.50]. 5 ratio for the analysed steelworks amounts to 3.24%[2.73−3.89; 1σ]; the corresponding 95%-confidence interval (obtained from h h 7 h il f h l di ib i ) i [ ] the 2.5th an 97.5th percentile of the slope distribution) is [1.90,5.50]. 215 This sector-specific estimate can be hardly compared to global inventories such as the Emissions Database for Global Atmo- spheric Research (EDGAR) (Crippa et al., 2020) because the underlying sector discrimination is typically not detailed enough. For example, iron and steel production is part of the EDGAR activity “Industrial combustion and processes” that also in- cludes sectors with significantly less CO emissions than steelworks at comparable CO2 emissions. Consequently, the EDGAR This sector-specific estimate can be hardly compared to global inventories such as the Emissions Database for Global Atmo- spheric Research (EDGAR) (Crippa et al., 2020) because the underlying sector discrimination is typically not detailed enough. For example, iron and steel production is part of the EDGAR activity “Industrial combustion and processes” that also in- cludes sectors with significantly less CO emissions than steelworks at comparable CO2 emissions. Consequently, the EDGAR CO/CO2 emission ratio for the entirety of industrial processes is smaller than our sector-specific estimate for the steel industry 220 and amounts to about 0.5% for Germany. Similar representativeness issues arise when comparing to the estimated CO/CO2 ratios for cities of Wu et al. (2022): their estimate for the Chinese cities with metal production is about 1% (when transformed to a mass ratio) but there are also other sectors, such as energy production, with significantly smaller CO/CO2 emission ratios (significant CO2 emissions, but virtually no CO emissions) contributing to the derived city averages. CO/CO2 emission ratio for the entirety of industrial processes is smaller than our sector-specific estimate for the steel industry 220 and amounts to about 0.5% for Germany. Similar representativeness issues arise when comparing to the estimated CO/CO2 ratios for cities of Wu et al. (2022): their estimate for the Chinese cities with metal production is about 1% (when transformed to a mass ratio) but there are also other sectors, such as energy production, with significantly smaller CO/CO2 emission ratios (significant CO2 emissions, but virtually no CO emissions) contributing to the derived city averages. CO/CO2 emission ratio for the entirety of industrial processes is smaller than our sector-specific estimate for the steel industry 220 and amounts to about 0.5% for Germany. Similar representativeness issues arise when comparing to the estimated CO/CO2 ratios for cities of Wu et al. (2022): their estimate for the Chinese cities with metal production is about 1% (when transformed to a mass ratio) but there are also other sectors, such as energy production, with significantly smaller CO/CO2 emission ratios (significant CO2 emissions, but virtually no CO emissions) contributing to the derived city averages. Another register of emissions from industrial facilities in Germany is the Thru.de portal provided by the Umweltbundesamt 225 (https://thru.de/en/, last access: 14 November 2023) including annual loads of CO and CO2 based on measurements, calcula- tions, or estimates of the operators. The reported values are reviewed for completeness and plausibility by authorities at federal state level, but unlike the emissions trading data used to derive the CO/CO2 emission ratio, no independent verification is required. Using the reported Thru.de mean releases from the German metal industry for the years 2018-2022, the associated Another register of emissions from industrial facilities in Germany is the Thru.de portal provided by the Umweltbundesamt 225 (https://thru.de/en/, last access: 14 November 2023) including annual loads of CO and CO2 based on measurements, calcula- tions, or estimates of the operators. The reported values are reviewed for completeness and plausibility by authorities at federal state level, but unlike the emissions trading data used to derive the CO/CO2 emission ratio, no independent verification is required. Using the reported Thru.de mean releases from the German metal industry for the years 2018-2022, the associated CO/CO2 emission ratio is approximately 2.0%. However, this value cannot be directly compared with ours either, because 230 this activity also comprises other processes than conventional primary steel production. Deriving a sector-specific emission ratio based on Thru.de data is also not straightforward because the reported releases are not provided on the level of emitting installations (in contrast to the European Union Emissions Trading System), but on the facility level. https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. The estimate that is conceptually closest to our estimate is obtained by using the outputs of the sintering plant, blast furnace, and basic oxygen furnace of the comprehensive inventory of a Polish integrated steel plant (Burchart-Korol, 2013) resulting in a CO/CO2 emission ratio of 2.60%. This value is considerably closer to our sector-specific estimate for steel production than 50 the other less representative estimates and within the associated 95%-confidence interval (even near the estimated 1σ-range). This consistency further corroborates the potential feasibility of using CO as a proxy for CO2 emissions from comparable steel production sites The estimate that is conceptually closest to our estimate is obtained by using the outputs of the sintering plant, blast furnace, and basic oxygen furnace of the comprehensive inventory of a Polish integrated steel plant (Burchart-Korol, 2013) resulting in a CO/CO2 emission ratio of 2.60%. This value is considerably closer to our sector-specific estimate for steel production than 250 the other less representative estimates and within the associated 95%-confidence interval (even near the estimated 1σ-range). This consistency further corroborates the potential feasibility of using CO as a proxy for CO2 emissions from comparable steel production sites. a CO/CO2 emission ratio of 2.60%. This value is considerably closer to our sector-specific estimate for steel production than 250 the other less representative estimates and within the associated 95%-confidence interval (even near the estimated 1σ-range). This consistency further corroborates the potential feasibility of using CO as a proxy for CO2 emissions from comparable steel production sites. Nevertheless, the reported Thru.de CO releases can be directly compared with our emission estimates, because only the place of origin and not the exact breakdown by sector is relevant for this pur- pose. The corresponding values are also listed in Table 1. In general, the reported Thru.de CO releases are systematically 245 smaller than our estimates. If the respective uncertainties are taken into account, there is no significant deviation in Bremen and Eisenhüttenstadt, but systematic residual underestimates of less than 20% in the Thru.de data at the other sites. pose. The corresponding values are also listed in Table 1. In general, the reported Thru.de CO releases are systematically 245 smaller than our estimates. If the respective uncertainties are taken into account, there is no significant deviation in Bremen and Eisenhüttenstadt, but systematic residual underestimates of less than 20% in the Thru.de data at the other sites. 12 12 Data availability. The carbon monoxide data product presented in this publication is available at http://www.iup.uni-bremen.de/carbon_ghg/ 275 products/tropomi_wfmd/. 4 Conclusions If locally observed CO emissions are very sector-specific, i.e. the vast majority of CO emissions can be attributed to a single sector, as in the case of pig iron or steel production analysed here, the usage of realistic installation-based bottom-up CO2 the accurate reporting of CO2 emissions within the framework of emissions trading enables a good calibration of the CO/CO2 265 emission ratio, which is thus of significant value to use CO as proxy for CO2 emissions from the steel industry in particular for comparable Linz–Donawitz steel plants, also in less regulated countries with less stringent reporting requirements. If locally observed CO emissions are very sector-specific, i.e. the vast majority of CO emissions can be attributed to a single sector, as in the case of pig iron or steel production analysed here, the usage of realistic installation-based bottom-up CO2 the accurate reporting of CO2 emissions within the framework of emissions trading enables a good calibration of the CO/CO2 265 emission ratio, which is thus of significant value to use CO as proxy for CO2 emissions from the steel industry in particular for comparable Linz–Donawitz steel plants, also in less regulated countries with less stringent reporting requirements. If locally observed CO emissions are very sector-specific, i.e. the vast majority of CO emissions can be attributed to a single sector, as in the case of pig iron or steel production analysed here, the usage of realistic installation-based bottom-up CO2 emission data broken down by activity type simplifies obtaining sector-specific CO/CO2 emission ratios. In contrast, this is 270 difficult to achieve by means of space-based CO2 measurements, because emissions from the sector in question are potentially entangled with atmospheric signals from nearby anthropogenic CO2 emissions associated with other sectors such as electricity production, as well as natural sources and sinks. Future accurate CO2 satellite missions with very high spatial resolution could help to better separate emissions from neighbouring anthropogenic sources belonging to different sectors from space. emission data broken down by activity type simplifies obtaining sector-specific CO/CO2 emission ratios. In contrast, this is 270 difficult to achieve by means of space-based CO2 measurements, because emissions from the sector in question are potentially entangled with atmospheric signals from nearby anthropogenic CO2 emissions associated with other sectors such as electricity production, as well as natural sources and sinks. 4 Conclusions We conducted an analysis of carbon monoxide enhancements originating from German steel plants using the conventional 255 highly CO2-intensive Blast Furnace–Basic Oxygen Furnace production route. This analysis utilised daily measurements in the shortwave infrared spectral range of the TROPOMI instrument on board the Sentinel-5 Precursor satellite to estimate the CO emissions for these steelworks during the 2018-2022 period benefiting from TROPOMI’s distinctive attributes, including its high quality measurements and comprehensive spatio-temporal coverage. These qualities enable us to systematically detect and quantify sufficiently large emission sources during a single satellite overpass 260 We conducted an analysis of carbon monoxide enhancements originating from German steel plants using the conventional 255 highly CO2-intensive Blast Furnace–Basic Oxygen Furnace production route. This analysis utilised daily measurements in the shortwave infrared spectral range of the TROPOMI instrument on board the Sentinel-5 Precursor satellite to estimate the CO emissions for these steelworks during the 2018-2022 period benefiting from TROPOMI’s distinctive attributes, including its high quality measurements and comprehensive spatio-temporal coverage. These qualities enable us to systematically detect and quantify sufficiently large emission sources during a single satellite overpass. 260 Together with the comprehensive availability of verified site-specific CO2 emission data from the production of pig iron or steel available from the European Union Emissions Trading System, an estimate for the associated sector-specific CO/CO2 emission ratio is derived. The high correlation of CO and CO2 emissions suggests that the raw material use and the involved processes are comparable and reproducible for the steelworks studied. The focus on German steel plants has the advantage that and quantify sufficiently large emission sources during a single satellite overpass. 260 Together with the comprehensive availability of verified site-specific CO2 emission data from the production of pig iron or steel available from the European Union Emissions Trading System, an estimate for the associated sector-specific CO/CO2 emission ratio is derived. The high correlation of CO and CO2 emissions suggests that the raw material use and the involved processes are comparable and reproducible for the steelworks studied. The focus on German steel plants has the advantage that the accurate reporting of CO2 emissions within the framework of emissions trading enables a good calibration of the CO/CO2 265 emission ratio, which is thus of significant value to use CO as proxy for CO2 emissions from the steel industry in particular for comparable Linz–Donawitz steel plants, also in less regulated countries with less stringent reporting requirements. https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. Author contributions. OS designed and operated the TROPOMI/WFMD satellite retrievals, performed the data analysis, interpreted the re- sults, and wrote the paper. MB, MR, MW, HeB, JPB, HB made significant contributions to the conception of the analysis and the improvement of the manuscript. All authors discussed the results and commented on the paper. Competing interests. The authors declare that they have no conflict of interest. 280 Competing interests. The authors declare that they have no conflict of interest. 280 280 Acknowledgements. This publication contains modified Copernicus Sentinel data (2018-2022). Sentinel-5 Precursor is an ESA mission implemented on behalf of the European Commission. The TROPOMI payload is a joint development by ESA and the Netherlands Space Office (NSO). The Sentinel-5 Precursor ground-segment development has been funded by ESA and with national contributions from The Netherlands, Germany, and Belgium. We thank the European Centre for Medium-Range Weather Forecasts (ECMWF) for providing the ERA5 reanalysis and acknowledge the use of carbon dioxide emission data from the European Union Emissions Trading System (EU ETS) 285 (https://www.euets.info/, last access: 14 November 2023). Acknowledgements. This publication contains modified Copernicus Sentinel data (2018-2022). Sentinel-5 Precursor is an ESA mission implemented on behalf of the European Commission. The TROPOMI payload is a joint development by ESA and the Netherlands Space Office (NSO). The Sentinel-5 Precursor ground-segment development has been funded by ESA and with national contributions from The Netherlands, Germany, and Belgium. We thank the European Centre for Medium-Range Weather Forecasts (ECMWF) for providing the ERA5 reanalysis and acknowledge the use of carbon dioxide emission data from the European Union Emissions Trading System (EU ETS) 285 ERA5 reanalysis and acknowledge the use of carbon dioxide emission data from the European Union Emissions Trading System (EU ETS) 285 (https://www.euets.info/, last access: 14 November 2023). ERA5 reanalysis and acknowledge the use of carbon dioxide emission data from the European Union Emissions Trading System (EU ETS) 285 (https://www.euets.info/, last access: 14 November 2023). Financial support. The research leading to the presented results received funding from the European Space Agency (ESA) via the projects GHG-CCI+ and MethaneCAMP (ESA contract nos. 4000126450/19/I-NB and 4000137895/22/I-AG) and from the German ministry of education and research (BMBF) within its project ITMS via grant 01 LK2103A. 4 Conclusions Future accurate CO2 satellite missions with very high spatial resolution could help to better separate emissions from neighbouring anthropogenic sources belonging to different sectors from space. emission data broken down by activity type simplifies obtaining sector-specific CO/CO2 emission ratios. In contrast, this is 270 difficult to achieve by means of space-based CO2 measurements, because emissions from the sector in question are potentially entangled with atmospheric signals from nearby anthropogenic CO2 emissions associated with other sectors such as electricity production, as well as natural sources and sinks. 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O., Butz, A., Haun, M., Buijs, H., Shiomi, K., Imai, H., and Kuze, A.: Thermal and near- infrared sensor for carbon observation Fourier transform spectrometer-2 (TANSO-FTS-2) on the Greenhouse gases Observing SATellite-2 (GOSAT-2) during its first year in orbit, Atmos. Meas. Tech., 14, 2013–2039, https://doi.org/10.5194/amt-14-2013-2021, 2021. Tian, Y., Sun, Y., Borsdorff, T., Liu, C., Liu, T., Zhu, Y., Yin, H., and Landgraf, J.: Quantifying CO emission rates of industrial point sources from Tropospheric Monitoring Instrument observations, Environmental Research Letters, 17, 014057, https://doi.org/10.1088/1748- 360 9326/ac3b1a, 2022. from Tropospheric Monitoring Instrument observations, Environmental Research Letters, 17, 014057, https://doi.org/10.1088/1748- 360 9326/ac3b1a, 2022. 360 from Tropospheric Monitoring Instrument observations, Environmental Research Letters, 17, 014057, https://doi.org/10.1088/1748- 360 9326/ac3b1a, 2022. 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U ltb d t Ai d t A l t b l ti (CO) il bl t htt // ltb d t d / /d t / i / i d t / l t b l ti / Umweltbundesamt: Air data: Annual tabulation (CO), available at: https://www.umweltbundesamt.de/en/data/air/air-data/annual-tabulation/ eJxrWpScv9BoUWXqEiMDIyMAMLgFtA== (last access: 14 November 2023), 2022. 365 eJxrWpScv9BoUWXqEiMDIyMAMLgFtA== (last access: 14 November 2023), 2022. 365 eJxrWpScv9BoUWXqEiMDIyMAMLgFtA== (last access: 14 November 2023), 2022. 365 16 Veefkind, J. P., Aben, I., McMullan, K., Förster, H., de Vries, J., Otter, G., Claas, J., Eskes, H. J., de Haan, J. F., Kleipool, Q., van Weele, M., Hasekamp, O., Hoogeveen, R., Landgraf, J., Snel, R., Tol, P., Ingmann, P., Voors, R., Kruizinga, B., Vink, R., Visser, H., and Levelt, P. F.: TROPOMI on the ESA Sentinel-5 Precursor: A GMES mission for global observations of the atmospheric composition for climate, air quality and ozone layer applications, Remote Sensing of Environment, 120, 70–83, https://doi.org/10.1016/j.rse.2011.09.027, 2012. Wu, D., Liu, J., Wennberg, P. O., Palmer, P. I., Nelson, R. R., Kiel, M., and Eldering, A.: Towards sector-based attribution using intra-city 370 variations in satellite-based emission ratios between CO2 and CO, Atmos. Chem. Phys., 22, 14 547–14 570, https://doi.org/10.5194/acp- 22-14547-2022, 2022. https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. https://doi.org/10.5194/egusphere-2023-2709 Preprint. Discussion started: 8 February 2024 c⃝Author(s) 2024. CC BY 4.0 License. Wu, D., Liu, J., Wennberg, P. O., Palmer, P. I., Nelson, R. R., Kiel, M., and Eldering, A.: Towards sector-based attribution using intra-city 370 variations in satellite-based emission ratios between CO2 and CO, Atmos. Chem. Phys., 22, 14 547–14 570, https://doi.org/10.5194/acp- 22-14547-2022, 2022. Wu, D., Liu, J., Wennberg, P. O., Palmer, P. I., Nelson, R. R., Kiel, M., and Eldering, A.: Towards sector-based attribution using intra-city 370 variations in satellite-based emission ratios between CO2 and CO, Atmos. Chem. Phys., 22, 14 547–14 570, https://doi.org/10.5194/acp- 22-14547-2022, 2022. 17 17
https://openalex.org/W2964096549
https://www.researchsquare.com/article/rs-920/v3.pdf?c=1631840480000
English
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Gene expression profile of human T cells following a single stimulation of peripheral blood mononuclear cells with anti-CD3 antibodies
BMC genomics
2,019
cc-by
9,467
Version of Record: A version of this preprint was published on July 19th, 2019. See the published version at https://doi.org/10.1186/s12864-019-5967-8. Research article License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Page 1/28 Version of Record: A version of this preprint was published on July 19th, 2019. See the published version at https://doi.org/10.1186/s12864-019-5967-8. Page 2/28 Abstract Background: Anti-CD3 immunotherapy was initially approved for clinical use for renal transplantation rejection prevention. Subsequently, new generations of anti-CD3 antibodies have entered clinical trials for a broader spectrum of therapeutic applications, including cancer and autoimmune diseases. Despite their extensive use, little is known about the exact mechanism of these molecules, except that they are able to activate T cells, inducing an overall immunoregulatory and tolerogenic behavior. To better understand the effects of anti-CD3 antibodies on human T cells, PBMCs were stimulated, and then, we performed RNA- seq assays of enriched T cells to assess changes in their gene expression profiles. In this study, three different anti-CD3 antibodies were used for the stimulation: two recombinant antibody fragments, namely, a humanized and a chimeric FvFc molecule, and the prototype mouse mAb OKT3. Results: Gene Ontology categories and individual immunoregulatory markers were compared, suggesting a similarity in modulated gene sets, mainly those for immunoregulatory and inflammatory terms. Upregulation of interleukin receptors, such as IL2RA, IL1R, IL12RB2, IL18R1, IL21R and IL23R, and of inhibitory molecules, such as FOXP3, CTLA4, TNFRSF18, LAG3 and PDCD1, were also observed, suggesting an inhibitory and exhausted phenotype. Conclusions: In conclusion, we used a deep transcriptome sequencing method for comparing three anti-CD3 antibodies in terms of Gene Ontology enrichment and immunological marker expression. The present data showed that both recombinant antibodies induced a compatible expression profile, suggesting that they might be candidates for a closer evaluation with respect to their therapeutic value. Moreover, the proposed methodology is amenable to be more generally applied for molecular comparison of cell receptor dependent antibody therapy. Background Immunosuppressive therapies based on monoclonal antibodies (mAbs) started in the 1980s, with the use of Muromonab-CD3 (OKT3), an antihuman CD3 antibody, for attaining long-term graft survival after organ transplantation1. After decades of use, this biopharmaceutical was withdrawn from clinics due to its toxic side effects2. However, the emergence of a new generation of (re)engineered recombinant antibodies has sparked hopes that anti-CD3 antibodies may again be used to induce peripheral tolerance3, renewing the enthusiasm for CD3-targeted therapies. Hence, anti-CD3 therapy is now being tested for several autoimmune and inflammatory diseases4,5. Furthermore, recent clinical data on the use of Teplizumab in type I diabetes6 contribute to this optimism that new anti-CD3 therapies for autoimmunity and transplantation will become available in a foreseeable time. The administration of anti-CD3 antibodies induces the general activation of T cells, which may lead to a state of tolerance not yet fully understood3,7. The proposed mechanism of a peripheral tolerance induction rests upon a potential modulation of regulatory lineages of the CD4 phenotype8,9, even though CD8 regulatory cells were also shown to be affected10,11. Peripherally induced regulatory cells control the activation of T cells, promoting negative feedback in the inflammatory response. The induction of a more regulatory environment by anti-CD3 antibodies could produce antigen-specific tolerance and alleviate the immune response. More recent data on human clinical data suggest that other mechanisms such as T cell Page 3/28 Page 3/28 exhaustion11,12 or the induction of inhibitory receptors on T cells13,14 could also contribute to the suppression of the immune response. The effect of anti-CD3 therapy has been addressed in different studies trying to elucidate its mechanism by assessing the genetic profile of T cells induced by those antibodies. These studies have been performed by microarray analysis15,16,17 or, more recently, by Next Generation Sequencing (NGS)18,19. Nevertheless, in the majority of the investigations, anti-CD3 is not the unique stimulus but is combined with anti-CD28 antibody and/or interleukins, such as IL2. More importantly, these studies are often performed using isolated T cells and thus are in a very different context from the PBMC environment. In the present work, we compared two recombinant antibody fragments, a chimeric fragment and a humanized fragment in an FvFc format, with their prototypic antibody OKT3. The treatment was performed using healthy human donor PBMCs in vitro. The global changes in the transcriptome profile were assessed using RNA-seq. Background Subsequently, their T cell differentiation markers and immunoregulatory signatures were compared. Our data showed that, despite the antibody format, the three anti-CD3 antibodies induced a common pattern of gene expression strongly enriching regulatory genes as well as genes involved in inhibitory signaling. We propose that these comparative analyses could be exploited as a validation tool in designing new and more effective CD3-binding molecules. Global change in the gene expression profile in human T cells induced by anti-CD3 treatments To compare the effects of each of the three anti-CD3 antibodies on human T cells, the gene expression profiles were analyzed. T cells were obtained from 72-hour untreated or treated PBMCs with one of the three anti-CD3 antibodies: OKT3, FvFc M (OKT3 scFv fused to human IgG1 Fc), and a humanized version of this FvFc (FvFc R). Anti-CD3 was used as the sole stimulus. To avoid any further stimulation, T cells were obtained by negative selection, using magnetic beads for cell surface markers. The purity of the T cell population was assessed by flow cytometry and was above 96% (Supplementary Figure S1). The transcriptomes of stimulated and unstimulated T cells from a single individual were obtained by performing sequencing in two replicates. More than 55 million paired-end reads of 150 bp length were obtained. The reads were mapped to the human reference genome (hg19); of the total reads, 84% to 94% were mapped (Table 1). Subsequently, we assessed differentially expressed genes (DEGs) by comparing each anti-CD3 antibody- treated sample with the control of unstimulated T cells. The gene sets found to be differentially expressed in the different treatments are shown as a MA plot in Figure 1A and as a Venn diagram in Figure 1B. OKT3 treatment resulted in a larger set of differentially expressed genes (7089) with a fold change of less than –0.8 or above 0.8, followed by FvFc R treatment with 2425 DEG and FvFc M treatment with 1406 DEG. We found 860 genes that were equally regulated among the treatments, considering a padj ≤ 0.05. Except for FvFc R treatment, DEGs were mostly downregulated. FvFc R Page 4/28 Page 4/28 Page 4/28 induced the most unbalanced DEG dataset, with 58% (1,419) upregulated over 41% (1,006) downregulated DEGs. The gene regulation profile promoted by FvFc R was more similar to OKT3 than FvFc M, even though the cluster analysis suggested a similar DEG profile for each treatment (Figure 1C). Associations of DEGs with Gene Ontology categories Anti-CD3 stimulation was shown to affect different set of genes18,19. Therefore, functional characterization of the differentially expressed genes was performed using GO term enrichment analysis. Anti-CD3 activated and repressed DEGs were separately classified for the GO category “biological process”. Upregulated genes were dominated by terms associated with cell proliferation (Figure 2), reflecting the anti-CD3 associated activation of T cells. To visualize changes in GO term enrichment and coverage (completeness), immune-associated terms were selected among up- and downregulated DEGs for each antibody treatment, focusing on those associated with the immune response and inflammation typically associated with anti-CD3 therapy (Figure 3). All antibodies induced a similar profile of GO term enrichment, coverage and FDR adjusted p-value, shown by radar plots (Figure 3). Among the upregulated genes, the predominance of OKT3-induced GO term coverage was less obvious. Between selected terms, the most enriched GO term among the upregulated genes was the Regulation of Regulatory T Cell Differentiation (GO:0045589), but terms for the regulation of IFNγ (GO:0032729), IL–10 (GO:0032653) and IL–12 production (GO:0032655) were also highlighted. The downregulated DEG set enriched terms reflected categories that fade after antibody treatment. It is notable that, among the GO terms enriched by genes repressed after treatment, the term “regulation of inflammatory response” (GO:0050727), was the most conspicuous. Furthermore, the terms “immune response-regulating signaling pathway” (GO:0002433) and “activation of immune response” (GO:0002253) were also evident (Figure 3). Regulation of cytokines and their receptors by anti-CD3 stimulation Anti-CD3 antibody therapy is strongly associated with an over secretion of cytokines, also known as a “Cytokine Storm”4. The deleterious consequences of the cytokine production are assumed to be promoted by the Fc part of the molecule, and novel humanized antibodies can circumvent these consequences by inducing a nonmitogenic effect. Our data suggest that the in vitro administration of all three anti-CD3 antibodies induce the upregulation of several cytokine genes, including INFG, IL17A, IL17F, LIF and TNF (Figure 4). However, when we analyzed the expression of IL17 in human donors by RT-qPCR, we noticed that even though the IL17A gene expression was consistently expressed along all treatments in the NGS panel, its induction was variable among antibody-treated donor T cells (Figure 5A). The FvFc R and OKT3 treatment also induced upregulation of IL6 and IL32. OKT3 treatment induced additional interleukins such as IL1B, IL2, IL3, IL9, IL13, IL12B, IL21 and IL22 (Figure 4). Page 5/28 Page 5/28 Cytokine receptors were also induced after antibody treatment, including strong upregulation of the IL2 receptor subunit genes, IL2RA and IL2RB (Figure 4). IL2RA expression was also tested in the qPCR panel of treated donor T cells, suggesting that any form of anti-CD3 induces the expression of the IL2 receptor α-chain, also known as CD25 (Figure 5B). Moreover, all antibody treatments induced the expression of IL1R2, IL12RB2, IL18R1, IL21R, IL23R (Figures 4 and 5C). However, as suggested by the NGS panel, anti- CD3-treated T cells increased their sensitivity toward IL1, IL2, IL12, IL18, IL21 and IL23. Anti-CD3 antibody treatment induced the upregulation of several interleukin and interleukin receptors genes, but only a few interleukins and receptors were downregulated due to antibody treatment. IL10 and IL24 expression was significantly repressed after OKT3 and FvFc R treatment, while IL18BP was repressed by OKT3 and FvFc M. In addition, OKT3 treatment also reduced the expression of IL18 (Figure 4). IL10 was further investigated by qPCR. Notwithstanding, the qPCR panel suggested that OKT3 treatment had a variable effect on IL10 expression among treated donor cells, and the FvFc-based antibody had no significant effect (Figure 5D). Downregulation of interleukin receptors makes T cells less sensitive to their cognate cytokine. The NGS panel suggested that OKT3 treatment might interfere with signaling of interleukins IL10, IL11 and IL13, due to the downregulation of IL10RA, IL10RB, IL11RA and IL13RA1 (Figure 4). IL6R was downregulated after treatment with OKT3 and FvFc R. Regulation of cytokines and their receptors by anti-CD3 stimulation The IL17RA codes for IL17A specific receptor and was found to be downregulated after OKT3 treatment, with a barely significant q-value (0.0069); nevertheless, the qPCR panel confirmed this tendency for downregulation after treatment with any of the antibodies (Figure 5E). The IL17RC gene, which codes for a receptor for both IL17A and IL17F, was found to be downregulated after both OKT3 and FvFc M treatment. The receptor for IL7, IL7R, was shown to be downregulated with both FvFc R and OKT3 treatment. The qPCR panel corroborated these results, suggesting that most donor T cells respond to any anti-CD3 antibody format, reducing the IL7R expression levels (Figure 5F). Anti-CD3 stimulation regulates phenotypic marker genes Activation of resting T cells by anti-CD3 antibodies can induce cell differentiation, and indeed, several phenotypic markers are modulated after antibody treatment. Resting T cells can differentiate in several lineages of effector and regulatory phenotypes, and specific genetic markers can characterize these T cell phenotypes. We compared several markers for CD4 and CD8 subpopulations depicted as panels to visualize their possible differentiation (Figure 6). To confirm prototype marker expression levels found in the NGS panel, qPCR analyses were performed using anti-CD3 treated T cells (Figure 7). Some expression markers are key for charactering T cell subpopulations. The Th1 marker TBX21, which codes for the TBET transcription factor, was shown to be significantly induced only with OKT3 treatment in the NGS panel (Figure 4). The qPCR panel corroborated the NGS data (Figure 7A), suggesting a minimal effect of FvFc antibodies on TBX21 expression. STAT4, another Th1 marker, was also only induced by OKT3 in the NGS experiment, but qPCR data suggests that FvFc R could also affect the expression levels of STAT4 in stimulated cells20,21 (Figures 4 and 7B). GATA3, a Th2 phenotypic marker, was not significantly induced Page 6/28 Page 6/28 in NGS or qPCR data (Figures 4 and 7C). However, other characteristic markers of this subtype were induced21,22 (Figure 6). In addition, we also analyzed markers for the Th17 subpopulation23,24 (Figures 4, 5, 6 and 7). The gene that codes for RORϒt, RORC was found to be slightly upregulated after treatment with both OKT3 and FvFc M antibodies (Figure 4), but without significance (padj > 0.01). In the qPCR panel, RORC was shown to be barely activated in all three treatments (Figure 7D). IL17A, known to be produced by Th17 cells, was upregulated in the NGS panel, but these data were not supported by qPCR, which suggests a variable and mild regulation of this gene (Figure 5A). The third marker, STAT3, was found to be induced by OKT3 in the NGS data and was induced by OKT3 and FvFc R treatments, as measured by qPCR (Figure 7E). Interestingly, the FvFc M antibody induced a very contrasting effect on different donors. Half of the donors showed an upregulated profile, while the other half showed a downregulated profile. Interestingly, the FvFc M antibody induced a very contrasting effect on different donors. Half of the donors showed an upregulated profile, while the other half showed a downregulated profile. Anti-CD3 stimulation modulates genes that encode nuclear receptor transcription factors VDR codes for the vitamin D3 receptor, and its overexpression was detected in all antibody treatments by qPCR (Figure 7P). Among the downregulated DEGs, peroxisome proliferator-activated receptor gamma (PPARG), a gene associated with the development of Tregs, was found to be 4- to 9-fold less expressed than that in the unstimulated T cells (Figure 4). Moreover, the THRA gene that codes for thyroid hormone receptor alpha was also repressed in all treatments. Anti-CD3 stimulation regulates phenotypic marker genes T cells can assume a regulatory phenotype, and many regulatory markers were found in this analysis25,26 (Figure 6). FOXP3, a major transcription factor that is associated with the human T regulatory phenotype, was upregulated in the NGS data for all antibody treatments. These data were corroborated by qPCR (Figure 7F). GITR (TNFRSF18) was strongly upregulated by all antibodies (approximately 16-fold, Figure 4), and this effect was also observed for all donors in qPCR (Figure 7G). CTLA4 and LAG3 were similarly upregulated in the NGS (Figure 4), and qPCR data supported this finding (Figures 7H and I), but the effect was less pronounced for FvFc antibodies compared to OKT3. The gene that codes for PD–1, namely, PDCD1, was also consistently induced by all antibody treatments (approximately 5-fold, Figure 4), and qPCR data confirmed this observation (Figure 7J). Modulations of CD8 T cell markers were also observed after anti-CD3 treatment, suggesting changes in the CD8 T cell population27,28 (Figure 6). Among these markers, EOMES and KLRG1 were repressed after all the anti-CD3 treatments, but GMZB was strongly induced by anti-CD3. These three markers were also tested by qPCR, which confirmed the tendency of the NGS data (Figure 7K, L and M). Moreover, markers of regulatory CD8 T cell29, such as IL2RA, were sharply induced by OKT3 and FvFc R but to a lesser extent by FvFc M. CD274 (PD-L1) was only marginally induced in all treatments (Figure 6), and FOXP3 showed a variable profile (Figure 7F). ICOS was weakly induced only by OKT3 and FvFc M (Figure 4). Phenotypic markers associated with T cell activation, cell death and apoptosis pathways were also affected by anti-CD3 treatment. Figure 4 resumes the induction/repression of these markers after anti- CD3 treatment. Overall, OKT3 induced most activation markers except EOMES and AIF1, while FvFc- based antibodies had a milder profile. Among the activation molecules, IFGN, GZMB, IL2RA, TNFRSF4 and TNFRSF9 showed remarkable induction. Cell death was the fate of activated cells, and the FAS/FASLG pathway was induced after T cell activation. The anti-CD3 effect on FAS induction was slight (Figure 6) and variable among donors (Figure 7N), and FASLG was very consistent among donors with the treatment of FvFc R (Figure 7O). GITR, along with PDCD1, was consistently induced by all the treatments (Figures 4, 6, 7G and J). Page 7/28 Page 7/28 Effect of an exclusive anti-CD3 stimulation To compare the global gene expression profile under the effect of anti-CD3 antibodies with that of activated T cells, we paralleled our results with those described by Zhao and colleagues (2014), who probed DEGs of immortalized T cells cultured in the presence of anti-CD3 and anti-CD28 antibodies. Their DEG dataset after 72 hours treatment was compared with NGS data generated in the present work focusing on DEGs regulated after anti-CD3 treatment without the costimulatory anti-CD28 stimulus. Among the 12 most opposite DEG (Supplementary Table 3), three genes were selected for qPCR analysis: AIF1, XCL1 and IDO1 (Figures 7Q, R and S). XCL1 and IDO1 were induced by all of the anti-CD3 treatments, as observed in the qPCR panel, while AIF1 was found to be repressed after anti-CD3 treatment. Anti-CD3 stimulation modulates genes that encode nuclear receptor transcription factors Nuclear receptors integrate a family of transcription factors that respond to hormones and hydrophobic molecules that have been associated with the control of the immune response30. Thus, the PFAM family for Nuclear Receptor (PF00104), was used to probe antibody-induced DEGs. Anti-CD3 treatment induced the expression of PF00104-associated genes. OKT3 induced 7 genes, while FvFc R induced 3 and FvFc M induced 2 genes. The orphan nuclear receptor gene NR4A1 was activated in all treatments at a padj < 10– 5. Three other PF00104 annotated genes were found in two of three treatments: NR4A3, RORC, and VDR (Figure 4). NR4A3 codes for a mitogen-associated nuclear receptor Nuclear receptors integrate a family of transcription factors that respond to hormones and hydrophobic molecules that have been associated with the control of the immune response30. Thus, the PFAM family for Nuclear Receptor (PF00104), was used to probe antibody-induced DEGs. Anti-CD3 treatment induced the expression of PF00104-associated genes. OKT3 induced 7 genes, while FvFc R induced 3 and FvFc M induced 2 genes. The orphan nuclear receptor gene NR4A1 was activated in all treatments at a padj < 10– 5. Three other PF00104 annotated genes were found in two of three treatments: NR4A3, RORC, and VDR (Figure 4). NR4A3 codes for a mitogen-associated nuclear receptor (http://www.uniprot.org/uniprot/Q92570). RORC is mentioned above as a marker for lymphocyte lineages. VDR codes for the vitamin D3 receptor, and its overexpression was detected in all antibody treatments by qPCR (Figure 7P). Nuclear receptors integrate a family of transcription factors that respond to hormones and hydrophobic molecules that have been associated with the control of the immune response30. Thus, the PFAM family for Nuclear Receptor (PF00104), was used to probe antibody-induced DEGs. Anti-CD3 treatment induced the expression of PF00104-associated genes. OKT3 induced 7 genes, while FvFc R induced 3 and FvFc M induced 2 genes. The orphan nuclear receptor gene NR4A1 was activated in all treatments at a padj < 10 5. Three other PF00104 annotated genes were found in two of three treatments: NR4A3, RORC, and VDR (Figure 4). NR4A3 codes for a mitogen-associated nuclear receptor (http://www.uniprot.org/uniprot/Q92570). RORC is mentioned above as a marker for lymphocyte lineages. VDR codes for the vitamin D3 receptor, and its overexpression was detected in all antibody treatments by qPCR (Figure 7P). (http://www.uniprot.org/uniprot/Q92570). RORC is mentioned above as a marker for lymphocyte ineages. Discussion Anti-CD3 antibodies are known to induce immunosuppression and have been proposed for several therapies, including those for different autoimmune diseases and acute transplanted organ rejection. For approximately two decades, Muromonab-CD3 (OKT3) therapy was used as an adjuvant for acute episodes of graft rejection, but its use was discontinued due to pronounced side effects2. However, despite the prolonged clinical use, the mechanism of action of OKT3 is still uncertain. In this study, human T cells were treated with anti-CD3 antibodies in vitro, within the complexity of the PBMC milieu, in an attempt to simulate the natural ambiance that occurs in the intravenous administration of therapeutic Page 8/28 anti-CD3. This in vitro experimental model was used to compare the mouse mAb OKT3 with two recombinant antibody fragments inspired by the mAb: a humanized and a chimeric human IgG1 in the FvFc format (scFv-hinge-CH2-CH3). Currently, most antibody therapies rely on full-sized mAbs, derived from chimeric, humanized or fully human sequences, but new molecular formats may represent technological and economical alternatives. The FvFc format used here represents a novel solution as a single-chained homodimeric molecule that mimics heteromultimeric mAbs31,32,33,34,35,36. The DEG profiles induced by each antibody format were i il j d d f h i h l i d i h l DEG i d d b OKT3 Currently, most antibody therapies rely on full-sized mAbs, derived from chimeric, humanized or fully human sequences, but new molecular formats may represent technological and economical alternatives. The FvFc format used here represents a novel solution as a single-chained homodimeric molecule that mimics heteromultimeric mAbs31,32,33,34,35,36. The DEG profiles induced by each antibody format were very similar as judged from the enrichment analysis, despite the larger DEG set induced by OKT3, especially for the repressed DEG set. The ontology-based classification for up- and downregulated DEGs suggests that all antibody formats induce a very similar profile, marked by a sharp mitotic response (with a low p-value), and a higher, even significant, p-value for “Immune”-related GO. It is noteworthy that FvFc compares positively for several terms, such as regulation of “regulatory T cell” and “interleukin–10 production” and “inflammatory response.” Overall, despite the larger set of OKT3 DEGs, FvFc molecules could enrich GO terms at least similarly. The broader coverage of GO terms of OKT3 DEGs may reflect their greater mitogenic stimulus31, while the humanized FvFc displayed a skewed DEG profile, yet preserving its function. Discussion Among those with the Th17 phenotype, IL17A, IL17F, and IL16 were upregulated, and FOXP3, GITR, LAG3, and CTLA4 were characteristic of the regulatory phenotype. These markers were all observed to some degree in each of treatments but commonly were weakly expressed among donors stimulated with FvFc M. Several regulatory phenotypes have been proposed, along with genes usually associated with a regulatory function44. For CD4 cells, regulatory cells are distinguished from effector cells that are classified as Th1, Th2, and Th17. A TBET signature with high production of IFNγ characterizes Th1 cells, but TBX21, which codes for TBET, is only weakly upregulated by OKT3, in line with previous observations43. Th2 cells do not appear to be induced by anti-CD3 since no significant alteration in GATA3 expression was observed. Beyond that, markers for Th17 and T regulatory cells are predominantly found in anti-CD3-treated cells. Among those with the Th17 phenotype, IL17A, IL17F, and IL16 were upregulated, and FOXP3, GITR, LAG3, and CTLA4 were characteristic of the regulatory phenotype. These markers were all observed to some degree in each of treatments but commonly were weakly expressed among donors stimulated with FvFc M. The anti-CD3 treatment seemed to bias toward a Th17/Treg polarity, as suggested before45,46. However, FOXP3, an important marker of regulatory cells, was only weakly induced after PBMC stimulation. It is possible that by analyzing gene expression after 72 h of anti-CD3 induction, we missed the transient FOXP3 peak kinetics18,19. Moreover, the activation of IRF4, a late effect of FOXP3 activation, represses FOXP3 and may negatively affect its expression47. IRF4 was upregulated in all the anti-CD3-treated cells. Interestingly, anti-CD3-treated cells showed an apparent decrease in the mRNA levels of CD127 (IL7R), the IL–7 receptor, for which downregulation is considered to be a hallmark of a bona fide regulatory phenotype in humans29,48,49. IL10 is a marker for regulatory CD8 and the CD4 (Tr1) phenotype50,51. We found no significant IL10 regulation except for a slight decline due to treatment with OKT3. However, we noted an enrichment of the “regulation of Interleukin–10” GO term, suggesting that the machinery for IL10 production was activated in anti-CD3-treated cells. FvFc R antibody was previously shown to induce a high IL10/IFNγ ratio compared to OKT3 in anti-CD3-stimulated PBMCs31, although no significant induction of IL10 was observed in the present study. Discussion Further analyses suggest that the chimeric molecule FvFc R reproduces the OKT3 DEG profile more accurately than FvFc M, despite the better binding proprieties of the latter molecule. Therefore, the humanization process seems to have preserved the original OKT3 paratope in the recombinant molecules, suggesting them as alternative CD3 binders for clinical anti-CD3 therapy. The mitogenic activity of OKT3 and other anti-CD3 antibodies renders them especially investigated for therapeutics37,38,39,40. The analysis of differentially expressed gene ontology classification suggests that all three anti-CD3 antibodies modulate a distinct number of genes related to cell proliferation and mitosis. This supports a significant impact of anti-CD3 therapy on T cell proliferation as observed for the proliferation marker MKI67 and the T-specific activation marker CD25 (IL2RA). The activation of T cells by OKT3 and other anti-CD3 antibodies is usually associated with the clinical efficacy of this antibody39. However, upregulation of activation markers does not correlate with antibody mitogenic activity, since non mitogenic anti-CD3 antibodies may also induce activation markers in vivo40. Therefore, these data corroborate a previous characterization of the FvFc R antibody, shown to be less mitogenic than OKT331, despite inducing several activation markers, as observed in the present study. Most models for anti-CD3 therapy rely on CD4 regulatory cells41,42,43, but the majority of data supporting it came from mouse models. Recent data on humanized antibodies in clinical trials highlight the role of CD8 cells in tolerance associated with anti-CD3 therapy, suggesting a two-phase model: a short-term depletion of T cells followed by induction of regulatory mechanisms6. A burst of cell activation initially induces mitotic mechanisms. Our data suggest that even after three days of anti-CD3 stimulation, activated T cell DEGs are still dominated by a mitotic signature, as seen by GO term enrichment, but, along with, barely detected emerging immunoregulatory mechanisms. Page 9/28 Several regulatory phenotypes have been proposed, along with genes usually associated with a regulatory function44. For CD4 cells, regulatory cells are distinguished from effector cells that are classified as Th1, Th2, and Th17. A TBET signature with high production of IFNγ characterizes Th1 cells but TBX21, which codes for TBET, is only weakly upregulated by OKT3, in line with previous observations43. Th2 cells do not appear to be induced by anti-CD3 since no significant alteration in GATA3 expression was observed. Beyond that, markers for Th17 and T regulatory cells are predominant found in anti-CD3-treated cells. Discussion Nevertheless, the increase in the IL10/IFNγ ratio observed by Silva and colleagues could be explained in part by a more consistent induction of the IFNG gene in OKT3-treated T cells, or likewise due to a non-lymphocytic origin of the produced IL10 probed in the whole PBMCs31. Clinical data on novel humanized antibodies suggest new mechanisms of anti-CD3 action in humans. In mice, studies have suggested that anti-CD3 therapy induces immunosuppression dependent on CD4 T cells, with stimulated helper cells developing a regulatory phenotype. However, in humans, the CD8 lineage also seems to contribute to the tolerogenic effect of anti-CD3, either by inducing differentiation into CD8 regulatory cells15,29 or by leading CD8 T cells to exhaustion11,12. Data from Teplizumab clinical trials suggested that the immunosuppressive effect of the humanized antibody is due to anergic and exhausted CD8 cells12,52, along with CD8 and CD4 Tregs15. Nonetheless, inhibitory receptors were clearly activated in our model system, including PDCD1, CTLA4, and LAG3, suggesting that inhibition of the immune response and inflammation after 72 h of a proliferative stimulus might have led to an exhausted phenotype14. Otherwise, inhibitory receptors may not indicate exhaustion, but a detuning of CD8 T activation. It is possible that these inhibitory receptors signify the transition from a highly activated T cell Page 10/28 Page 10/28 state toward a differentiation/memory profile11,53. The high and consistent induction of the PDCD1 gene (PD–1) observed here suggests a general detuning of anti-CD3-treated cells, that may underlie the basis of anti-CD3 therapeutic effects. The detuning of T cell following PD–1 expression may contribute to the effect of anti-CD3, but other molecular players may also contribute to immunosuppression. IDO1 is a tryptophan catabolic enzyme known to induce regulatory T cells and immunosuppression54,55. Although usually produced by monocytes, a CD4+IDO+ lymphocyte population had been characterized56. Anti-CD3 treatment induced IDO1 upregulation in T cells, although not uniformly among donors. In this sense, a putative IDO- producing T cell could trigger a profound regulatory effect by locally restricting available tryptophan. This finding may represent an alternative mechanism of T-cell-induced immunosuppression that could be therapeutically exploited. Donors Peripheral blood was collected from seven healthy individuals enrolled in this study (Supplementary Table S1). For NGS a single donor was analyzed and for qPCR assays, seven healthy individuals were enrolled. All human blood experiments were performed in accordance to the Ethics Committee of the University of Brasilia guidelines, which approved the study protocol (CAAE: 32874614.4.0000.0030). A written informed consent was obtained from all human donors. Conclusions Novel therapeutic anti-CD3 antibodies development could focus on regulatory associated GO term enrichment and specific subpopulation markers. The in vitro assay proposed here, based on a simple and economical procedure, seems to be efficient to compare novel antibody molecules before clinical evaluation. Development of new antibodies or novel pharmaceutical association could benefit from this in vitro methodology, allowing a novel discovery pipeline based on a System Biology approach. In conclusion, we used a deep transcriptome sequencing method for comparing three anti-CD3 antibodies regarding Gene Ontology enrichment and immunological marker expression. The present data showed that both recombinant antibodies induced a compatible expression profile, suggesting that they might be candidates for closer evaluation concerning their therapeutic value. Moreover, the proposed methodology is amenable to be more generally applied for molecular comparison purposes. Antibodies OKT3 was purchased from eBioscience (San Diego, CA, USA). The humanized antibody fragment FvFc R is a single-chain FvFc molecule and was previously described (FvFc version R)31. The chimeric FvFc M Page 11/28 contains the original OKT3 VH and VL coding sequences fused to human IgG1 Fc and cloned in the pMIRES expression vector. The FvFc antibody fragments were affinity purified from supernatants of CHO- K1 transfected cells. PBMC stimulation and T cell preparation Fresh PBMCs were isolated using Ficoll-Paque density gradient centrifugation (GE Healthcare, Uppsala, Sweden). PBMCs were cultured in RPMI media (Invitrogen, Carlsbad, CA, USA) supplemented with 4 mM L-glutamine and 10% FBS in the presence or absence of soluble anti-CD3 antibodies. A total of 250 ng of antibody was applied to 1 x 106 PBMC/mL. T cells were isolated after 72 hours of PBMC treatment, using magnetic beads by negative selection (according to the manufacturer´s instructions). Briefly, PBMCs were selectively depleted of CD16, CD19, CD20 cells and were discarded (Dynabeads® Untouched™ Human T Cells Kit, Invitrogen, Carlsbad, CA, USA). The purity of T cell enrichment was checked using flow cytometry (Supplementary Figure S1). RNA extraction Total RNA was extracted from T cells isolated after PBMC stimulation using the miRNeasy® Mini Kit (Qiagen, Valencia, CA, USA) as described before46. RNA integrity and purity were evaluated using a Bioanalyzer 2100 (Agilent Technologies Genomics, Santa Clara, CA, USA). All RNA samples used in this work showed an RIN > 7. Sample sequencing and differential gene expression analysis RNA-seq was performed by Macrogen, Inc. (Seoul, Korea), using the Illumina HiSeq™ 2500 platform (Illumina, San Diego, CA, USA) according to the manufacturer’s standard protocol. The total RNA, up to 1500 ng, was sent in a RNA-stable tube (Biomatrica, Inc., San Diego, CA) to preserve the integrity of the RNA, and Illumina sequencing was performed in a 2 × 150 nt paired-end mode. All sequencing reads produced by Illumina were analyzed for quality control using FASTQC57. The reads were aligned to the human genome GRCh37/hg19 downloaded from the UCSC Genome Browser58 using open source Segemehl, version 0.2.059 with the split read option -S. The aligned files were ordered and indexed using Samtools60 followed by read counts using HTSeq-count61. For a differential gene expression analysis, the reads of CD3 T cell treated and untreated samples uniquely aligned by Segemehl were used. To identify differentially expressed genes (DEGs) for each treatment comparison (treated versus untreated), two replicates per condition were analyzed using the Bioconductor package DESeq262 applying a significance threshold for the adjusted p-values of 0.05. Gene expression analysis by qPCR assays Quantitative PCR was performed as previous described46. Briefly, total RNA isolated from T cells was utilized for cDNA synthesis using an RT2 First Strand Kit (Qiagen, Valencia, CA, USA). The expression genes were quantified using RT² qPCR SYBR Green/ROX MasterMix (Qiagen, Valencia, CA, USA) following the manufacturer’s instructions. The housekeeping gene B2M was used as the endogenous control. qPCR assays were performed using an ABI Step One Plus Real-Time PCR System (Applied Biosystems, Austin, Texas, EUA) and the 2-ΔΔCt method was used to calculate mRNA transcript levels (fold change) using RT2 Profiler PCR Array Data Analysis software (SABiosciences, Frederick, MD, USA for analysis. Three independent experiments were performed in triplicate. Analysis of gene functions The enrichment GO terms for biological processes of DEG were also assessed. For this purpose, upregulated (log2FC >1.2) and downregulated (log2FC <1.2) gene set enrichment analyses were performed using functional categories of the database Gene Ontology (GO). The Panther software63,64 was used to calculate enrichment, p-values and FDR adjusted p-values. The super category “biological process” was used, and within this category, GO terms related to the immune system and inflammatory process were further investigated. The enrichment GO terms for biological processes of DEG were also assessed. For this purpose, upregulated (log2FC >1.2) and downregulated (log2FC <1.2) gene set enrichment analyses were performed using functional categories of the database Gene Ontology (GO). The Panther software63,64 was used to calculate enrichment, p-values and FDR adjusted p-values. The super category “biological process” was used, and within this category, GO terms related to the immune system and inflammatory process were further investigated. Nuclear receptor analysis was performed exclusively for the Pfam family PF00104 of the Pfam database (http://pfam.xfam.org/). Members of PF00104 were searched in the DEG set using regular expression and analyzed individually. Statistical analysis All RNA-seq experiments statistical evaluations were performed using Bioconductor package DESeq262 based in Benjamini-Hochberg method for adjusted p-values. Gene function attribution was performed using adjusted p-values calculated by the Binomial statistic and Mann-Whitney U Test (Wilcoxon Rank- Sum Test) by Panther software63,64. Real Time qPCR p-values were calculated based on Student’s t-test using RT2 Profiler PCR Array Data Analysis software. Funding Research work was supported by FAP-DF (grant number: 193.000.560/2009). This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001. Brazilian Council for Research (CNPq) contributes with fellowship. The funding agencies, CAPES, CNPq and FAP-DF were not involved in the design of the study, collection, analysis, and interpretation of data and in writing the manuscript. Consent for publication Not applicable. Availability of data and material RNA-Seq datasets are available at GEO (www.ncbi.nlm.nih.gov/geo) under the accession number GSE112899. Supplementary informations are in Additional file.pdf Declarations Ethics approval and consent to participate All human blood experiments were performed in accordance to the Ethics Committee of the University of Brasilia guidelines, which approved the study protocol (CAAE: 32874614.4.0000.0030). A written informed consent was obtained from all human donors. The authors declare that they have no competing interests. The authors declare that they have no competing interests. Abbreviations DEGs: Differentially Expressed Genes DEGs: Differentially Expressed Genes FvFc: antibody format - scFv fused to human IgG1 Fc NGS: Next Generation Sequencing FvFc: antibody format - scFv fused to human IgG1 Fc Page 13/28 Page 13/28 Authors’ contributions I. G. S., K. C. R. S., M. M. B. and A. Q. M. designed the experiments. I. G. S., K. C. R. S. and M. A. G. B. processed the blood samples, performed cell culture for recombinant antibodies production and made flow cytometry. I. G. S., K. C. R. S., G. 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PANTHER in 2013: Modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 2013;41(D1):377–86. Page 19/28 Page 19/28 64.Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, et al. Enrichr : interactive and collaborative HTML5 gene list enrichment analysis tool. 2013; 64.Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, et al. Enrichr : interactive and collaborative HTML5 gene list enrichment analysis tool. 2013; Tables Table 1. Read mapping rates and statistics for RNA-seq data. Replicate All Reads Mapped Reads % Mapped Reads Unstimulated (1) 59 623 760 54 990 450 92 Unstimulated (2) 61 444 968 58 149 032 94 FvFc R (1) 57 712 398 54 065 899 93 FvFc R (2) 54 633 094 51 012 088 93 FvFc M (1) 62 274 364 58 117 856 93 FvFc M (2) 65 142 278 60 452 698 92 OKT3 (1) 60 724 236 51 446 623 84 OKT3 (2) 59 435 924 50 336 034 84 Table 1. Read mapping rates and statistics for RNA-seq data. Replicate All Reads Mapped Reads % Mapped Reads Unstimulated (1) 59 623 760 54 990 450 92 Unstimulated (2) 61 444 968 58 149 032 94 FvFc R (1) 57 712 398 54 065 899 93 FvFc R (2) 54 633 094 51 012 088 93 FvFc M (1) 62 274 364 58 117 856 93 FvFc M (2) 65 142 278 60 452 698 92 OKT3 (1) 60 724 236 51 446 623 84 OKT3 (2) 59 435 924 50 336 034 84 Table 1. Read mapping rates and statistics for RNA-seq data. Figures Page 20/28 Page 20/28 Page 20/28 Page 20/28 Page 20/28 Figure 1 Global gene expression profiles in anti-CD3-treated human T cells by RNA-seq data. The transcriptome was obtained in CD3 T cells collected from a healthy donor at two different moments, treated or untreated with anti-CD3 antibodies. Only genes with padj ≤ 0.05 were considered differentially expressed. (A) MA-plot with the global gene expression profile; red dots indicate up- or downregulated genes. (B) Venn diagrams showing an overlap of regulated expressed genes compared to the control, among different anti-CD3 treatments. (C) Clustering analysis and heatmap of gene expression based on fold change data. Cluster analysis was performed with 860 commonly regulated genes (shown in rows) for each sample (columns). Gradient colors from purple to gold represent lower to higher expression (range from −9.27 to 9.22). Global gene expression profiles in anti-CD3-treated human T cells by RNA-seq data. The transcriptome was obtained in CD3 T cells collected from a healthy donor at two different moments, treated or untreated with anti-CD3 antibodies. Only genes with padj ≤ 0.05 were considered differentially expressed. (A) MA-plot with the global gene expression profile; red dots indicate up- or downregulated genes. (B) Venn diagrams showing an overlap of regulated expressed genes compared to the control, among different anti-CD3 treatments. (C) Clustering analysis and heatmap of gene expression based on fold change data. Cluster analysis was performed with 860 commonly regulated genes (shown in rows) for each sample (columns). Gradient colors from purple to gold represent lower to higher expression (range from −9.27 to 9.22). Page 21/28 Figure 2 Gene set enrichment analysis of differentially expressed genes. Gene ontologies associated with upregulated genes in peripheral blood CD3 cells following anti-CD3 treatment. The top twelve enriche biological process categories were calculated using Panther. GO terms associated with cell proliferat Figure 2 Gene set enrichment analysis of differentially expressed genes. Gene ontologies associated with upregulated genes in peripheral blood CD3 cells following anti-CD3 treatment. The top twelve enriched biological process categories were calculated using Panther. GO terms associated with cell proliferation was found to be overrepresented. (A) FvFc M-treated, (B) FvFc R-treated, and (C) OKT3-treated T cells. Gene set enrichment analysis of differentially expressed genes. Gene ontologies associated with upregulated genes in peripheral blood CD3 cells following anti-CD3 treatment. The top twelve enriched biological process categories were calculated using Panther. GO terms associated with cell proliferation was found to be overrepresented. (A) FvFc M-treated, (B) FvFc R-treated, and (C) OKT3-treated T cells. Page 22/28 Page 22/28 Page 22/28 Figure 3 Gene set enrichment analysis of differentially expressed genes associated with immune terms. Radar Plot of the GO term profile enrichment, coverage (completeness) and FDR adjusted p-value of immune- associated terms. The terms were selected among up- and downregulated DEGs for each antibody treatment, accessing those associated with immune response and inflammation typically associated with anti-CD3 therapy. The black line represents OKT3 treatment; the orange line, FvFc R treatment; and the gray line, FvFc M treatment. Figure 3 Figure 3 Gene set enrichment analysis of differentially expressed genes associated with immune terms. Radar Plot of the GO term profile enrichment, coverage (completeness) and FDR adjusted p-value of immune- associated terms. The terms were selected among up- and downregulated DEGs for each antibody treatment, accessing those associated with immune response and inflammation typically associated with anti-CD3 therapy. The black line represents OKT3 treatment; the orange line, FvFc R treatment; and the gray line, FvFc M treatment. Page 23/28 Page 23/28 Figure 4 Differentially expressed genes in treated T cells assessed by RNA-seq data. Individual anti DEG fold changes were grouped according to their biological function. The results are pres mean gene expression fold change from two RNA-seq experiments. The asterisk represent OKT3 (black bars) FvFc R (orange bars) or FvFc M (gray bars) Figure 4 Differentially expressed genes in treated T cells assessed by RNA-seq data. Individual anti-C DEG fold changes were grouped according to their biological function. The results are prese mean gene expression fold change from two RNA-seq experiments. The asterisk represents OKT3 (black bars), FvFc R (orange bars) or FvFc M (gray bars). Figure 4 Figure 4 Differentially expressed genes in treated T cells assessed by RNA-seq data. Individual anti-CD3-induced DEG fold changes were grouped according to their biological function. The results are presented as the mean gene expression fold change from two RNA-seq experiments. The asterisk represents padj < 0.05. OKT3 (black bars), FvFc R (orange bars) or FvFc M (gray bars). Page 24/28 Page 24/28 Figure 5 Cytokines and their receptor genes regulated by anti-CD3 stimulation. qPCR assays were performed with total RNA extracted from T cells, 72 h post anti-CD3 stimulation. The results are expressed as the fold change relative to unstimulated T cells (n = 7; p < 0,05). B2M was used as an internal control for data normalization. (A) IL17A, (B) IL2RA, (C) IL23R, (D) IL10, (E) IL17RA, (F) IL7R, (G) TGFB1. Figure 5 Cytokines and their receptor genes regulated by anti-CD3 stimulation. qPCR assays were performed with total RNA extracted from T cells, 72 h post anti-CD3 stimulation. The results are expressed as the fold change relative to unstimulated T cells (n = 7; p < 0,05). B2M was used as an internal control for data normalization. (A) IL17A, (B) IL2RA, (C) IL23R, (D) IL10, (E) IL17RA, (F) IL7R, (G) TGFB1. Page 25/28 Figure 6 T cell subpopulation signatures. Cluster analysis based on the fold change data of regulated genes (shown in rows) for each sample (columns) and grouped into T cell populations. Only genes with padj ≤  0.05 were considered differentially expressed. Gradient colors from blue to dark brown represent lower to higher expression (range from -2.69 to 9.22). T cell subpopulation signatures. Cluster analysis based on the fold change data of regulated genes (shown in rows) for each sample (columns) and grouped into T cell populations. Only genes with padj ≤  0.05 were considered differentially expressed. Gradient colors from blue to dark brown represent lower to higher expression (range from -2.69 to 9.22). Page 26/28 Page 26/28 Figure 7 Quantitative analysis of T cell marker expression in anti-CD3-treated T cells. qPCR assays were performed with total RNA extracted from T cells, 72 h post anti-CD3 stimulation; the results are expr as fold changes relative to levels in unstimulated T cells (n = 7; p < 0,05). B2M was used as an inter control for data normalization. (A) TBX21, (B) STAT4, (C) GATA, (D) RORC, (E) STAT3, (F) FOXP3, (G Figure 7 Figure 7 Quantitative analysis of T cell marker expression in anti-CD3-treated T cells. qPCR assays were performed with total RNA extracted from T cells, 72 h post anti-CD3 stimulation; the results are expressed as fold changes relative to levels in unstimulated T cells (n = 7; p < 0,05). B2M was used as an internal control for data normalization. (A) TBX21, (B) STAT4, (C) GATA, (D) RORC, (E) STAT3, (F) FOXP3, (G) Page 27/28 Page 27/28 TNFRSF18, (H) CTLA4, (I) LAG3, (J) PDCD1, (K) EOMES, (L) KLRG1, (M) GZMB, (N) FAS, (O) FASLG, (P) VDR, (Q) AIF1, (R) XCL1, (S) IDO1, (T) CD38, (U) GZMM, (V) STAT5A. supplement1.pdf Supplementary Files This is a list of supplementary files associated with this preprint. Click to download. supplement1.pdf supplement1.pdf Page 28/28
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Distribution of graminoids in open habitats in Tajikistan and Kyrgyzstan
Vegetation Classification and Survey
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Vegetation Classification and Survey 3: 273–286 doi: 10.3897/VCS.95767 Abstract Aims: Landscapes of Middle Asia are exposed to human influence due to long-lasting pastoral tradition, and now are largely dominated by non-forest vegetation. Graminoids perform key ecosystem functions, and constitute an important feed source for livestock. We studied the distribution patterns of graminoids cover under climatic and grazing pressure gradients in different open vegetation types. Study area: Tajikistan, Kyrgyzstan. Methods: 1,525 vegetation plots repre­ senting five open vegetation types (mires, salt marshes, tall-forb communities, pseudosteppes and steppes) were extract­ ed from the Vegetation of Middle Asia Database. We assessed the relative cover of graminoid species in each vegetation type. The importance of mean annual temperature, sum of annual precipitation, aridity and livestock density as drivers of relative cover of graminoids contribution patterns in the five vegetation types were explored with use of polynomial functions and commonality analysis. Results: Open ecosystems of Middle Asia are characterized by different graminoid contributions. The highest relative cover of graminoids was found for steppes, pseudosteppes and mires. Comparison of model fits for relationship between the graminoids cover, climatic parameters and livestock pressure indicated advantage of polynomial models. The best-fitting models for pseudosteppes were for mean annual temperature, Aridity Index and livestock density, for steppes mean annual temperature and Aridity Index, and for salt marshes mean annual temperature. For mires and tall-forb communities, the models showed a poor fit or no effect of the variables studied. Conclusions: Our study shows that climate and livestock pressure have an impact on the contribution of graminoids in open vegetation types, but a general pattern is difficult to describe. Ongoing climate change may influence the share of graminoids in salt marshes, steppes and pseudosteppes. Grazing (with a common effect of climatic factors) is the most important factor influencing graminoids contribution on pseudosteppes, confirming the secondary origin of this vegetation type. Taxonomic reference: The nomenclature of the vascular plants follows Plants of the World Online (POWO 2022) and problematic taxonomic issues were based on The World Flora Online (WFO 2022). Nomenclature of Stipa spp. follows Nobis et al. (2020). Distribution of graminoids in open habitats in Tajikistan and Kyrgyzstan 5 Institute of Agroecology and Plant Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland Corresponding author: Sebastian Świerszcz (sebastian.swierszcz@ob.pan.pl) Academic editor: Idoia Biurrun  ♦  Received 28 September 2022  ♦  Accepted 13 December 2022  ♦  Published 20 December 2022 aridity, climate, Cyperaceae, grassland, hot-spot, Juncaceae, Kyrgyzstan, Middle Asia, open habitat, Poaceae, steppe, k International Association for Vegetation Science (IAVS) GRASSLANDS OF ASIA Introduction Graminoids are a major component of open habitats across the world, particularly wetlands and grasslands (Gibbson 2009; Bragina et al. 2018; Nowak et al. 2020a). Graminoids include vascular plants with a grass-like morphology from three groups: grasses (Poaceae), sedges (Cyperaceae) and rushes (Juncaceae). Poaceae, as one of the most species-rich family worldwide, includes around 11,500–12,000 taxa classified to about 770–780 genera (Christenhusz and Byng 2016; Soreng et al. 2017). The second most abundant family of graminoids, Cyperaceae, includes approx. 5,500 species within about 90 genera (Christenhusz and Byng 2016). The most common group are sedges, represented mainly by the genus Carex, which are found in many types of habitats, often as dominants or co-dominants (Spalink et al. 2018). At high altitudes, e.g. the Pamir Plateau, the Tibetan Plateau and the Himalayas, open vegetation is dominated by cold-resistant sedge species such as Kobresia spp. creating dense, low mats (Miehe et al. 2009; Vanselow 2011). Vegetation types dominated by species from Kobre­ sia or Carex are used as winter pastures because they store more nutrients in the cold season, and maintain the nu­ tritional value for livestock longer than other graminoids, e.g. grasses (Vanselow 2011). The third graminoid group, Juncaceae, is less numerous and includes about 460 species within eight genera (Christenhusz and Byng 2016). The most species-rich genus is Juncus, with the majority of the species growing sparsely in wetland habitats.f p g g p y Many grasses, sedges and rushes are effective colo­ nisers, making them cosmopolitan (Spalink et al. 2016; Linder et al. 2018; Martín-Bravo et al. 2019). Grass-dom­ inated ecosystems cover 31–43% of the earth’s surface (Gibbson 2009). Colonisation of new areas and habitats is facilitated by dispersal and establishment ability, broad environmental tolerance and ecological competitiveness of the species (Scheiter et al. 2012; Linder et al. 2018). They are often exposed to extreme environmental conditions such as drought and high salinity and various disturbanc­ es, e.g. intensive herbivory (Coughenour 1985; Gibbson 2009; Borer et al. 2019). Graminoids are intensively used as forage for livestock (Linder et al. 2018). In the course of evolution, graminoids have developed several features that allow them to endure harsh conditions. For example, traits allowing to tolerate drought, which are also useful in adapting to grazing resistance, include basal meri­ stems, rapid growth, high shoot density, nutrient storage and rapid transpiration (Coughenour 1985). Keywords idity, climate, Cyperaceae, grassland, hot-spot, Juncaceae, Kyrgyzstan, Middle Asia, open habitat, Poaceae, steppe, ajikistan aridity, climate, Cyperaceae, grassland, hot-spot, Juncaceae, Kyrgyzstan, Middle Asia, open habitat, Poaceae, steppe, Tajikistan Copyright Sebastian Świerszcz et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC-BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Sebastian Świerszcz et al.: Graminoids in Tajikistan and Kyrgyzstan 274 of plants and vegetation types (Stanyukovich 1982). The landscape of Middle Asia is dominated by open habi­ tats with a high contribution of graminoids as a conse­ quence of thousands of years of pastoralism. Steppes are the most prominent biome in Middle Asia, divided into three types: high altitude arid steppes (Nowak et al. 2018), mountain steppes of semi-arid areas, and dry, thermophi­ lous steppes of montane and subalpine belts (Nowak et al. 2016b, 2018, 2020a). The most abundant plant group of the Middle Asian steppes is Poaceae. Examples of promi­ nent grass genera in the steppe vegetation are Agropyron, Avena, Bromus, Elymus, Elytrigia and Stipa (Nowak et al. 2020a) and the most diverse genus is Stipa with 76 species and subspecies. Contrary to the steppes, pseudosteppes are secondary grassland types that have replaced natural thermophilous open woodlands and scrub vegetation, as a result of clearing and subsequent grazing of the herb lay­ er (Świerszcz et al. 2020; Nowak et al. 2022b). Mesophi­ lous grasslands ranging from the lowlands to the alpine belt form a distinct vegetation type, in which numerous graminoid species occur. At high elevation in the alpine belt, graminoid vegetation is often dominated by Kobresia species (Nowak et al. 2020a). Graminoids are also core species in fen and spring communities, as well as littoral vegetation (Nowak et al. 2014, 2016a). A distinct vegeta­ tion type are salt marshes, which develop on lake shores at high altitudes but also in the colline and foothill belts along rivers, springs and artificial leakages, under harsh saline conditions (Nowak et al. 2020a). In areas of defor­ estation of juniper woods, tall-forb communities domi­ nated by dicotyledonous perennials with a variable pro­ portion of graminoids develop (Nowak et al. 2020b). Introduction Saline and wet habitats promote plants with lower requirements for mechanical support characterized by long rhizomes and short stature (Dolezal et al. 2019).l About 9,300 vascular plant species have been de­ scribed from the Middle Asia region (Khassanov 2015). The vascular flora of Kyrgyzstan consists of ca. 4,000 spe­ cies (Lazkov and Sultanova 2014), of which about 10% are endemics (Lazkov and Umralina 2015). The families Poaceae, Cyperaceae and Juncaceae account for a total of 430 species, and among them 120 species are endemics or sub-endemics (21% of all graminoids; Lazkov and Sul­ tanova 2014). The Tajik flora consists of ca. 4,300 species (see Nowak et al. 2020c), where approx. 30% are known as endemics (Nowak et al. 2011). In Tajikistan, 438 species belong to the Poaceae, Cyperaceae and Juncaceae fami­ lies, 70 of them are endemics or sub-endemics (16% of all graminoids) and 133 are considered endangered at the national level (Nowak et al. 2020c). These numbers show how unique the flora of Middle Asia is, and how abundant graminoids are. In terms of food and economic safety, Middle Asia is al­ most entirely dependent on livestock production. This re­ gion has a long tradition of pastoralism and since ancient times a whole human population consider its welfare with the quality of pasturelands and the number of livestock herds. Besides typical grasslands, there are also other veg­ etation types in Middle Asia such as tall-forb communities, mires, and salt marshes used for grazing in which gram­ inoids are likely key contributors to biomass and diversity. Due to its unique floristic richness, most of the terri­ tory of Tajikistan and Kyrgyzstan is recognized by Con­ servation International as a biodiversity hotspot – Moun­ tains of Central Asia (Mittermeier et al. 2011). The diverse landscape, extreme climate and varied habitat condi­ tions shape the biogeography of Middle Asia (Nowak et al. 2020a; Wagner et al. 2020), offering a high diversity 275 Vegetation Classification and Survey Thus, finding basic patterns of graminoid species abun­ dance and distribution in different vegetation types in Mid­ dle Asia is of high importance. In this paper, we addressed three main questions: (1) How is graminoid species richness shaped in the open vegetation types of Tajikistan and Kyr­ gyzstan? (2) Is there a general pattern of graminoid occur­ rence in different open vegetation types? (3) How do climate and livestock density affect the proportion of graminoids? Introduction The region is characterized by a very long elevational gradient ranging from 287 to 7,495 m a.s.l, which makes this territory particularly diverse in terms of climate, land relief and geomorphology. The geological profile is com­ plex with a predominance of limestone, marble, dolomite, dolomitic shale, clay shale, phyllitic schist, siltstone, and argillaceous slates of Carboniferous, Cambrian, Siluri­ an, and Early Cretaceous origin. However, the specific geological conditions of this region are still under study (Leven 1981; Budanov and Pashkov 1988; Lohr 2001).hfi Study area The study area is difficult to characterize in terms of climatic conditions. The climate differs spatially in terms of its continentality, topographic complexity, and orogra­ phy. However, according to Latipova (1968), Narzikulov and Stanyukovich (1968), and Safarov (2003), four main climatic regions can be distinguished. The study area is placed between two main biogeographic regions, Ira­ no-Turanian and Central Asiatic, with climatic influences from the Indo-Indochinese region in the south and the Euro-Siberian region in the north. The specific conditions of the regions are as follows (Figure 1):h The study was conducted within the administrative bor­ ders of Tajikistan and Kyrgyzstan (Figure 1). The land­ scape of the area is dominated by diverse open habitats, which are shaped by the strongly varied environment, landscape, and human activity, grazing of sheep, goats, cattle and horses in particular. The study area is main­ ly dominated by steppes and chasmophytic vegetation. However, hay meadows also contribute importantly to the landscape at intermediate altitudes (ca. 2,000–3,000 m a.s.l.). Alpine swards in subalpine and alpine belts are used as summer pastures, and Kobresia mats at the highest al­ titudes are used as winter pastures. Additionally, the wide terraces of lowland river valleys and floodplains of the alpine rivers offer suitable habitats for grassland develop­ ment. Salt marshes develop under harsh saline conditions. The studied vegetation types differ considerably in terms of topographic and edaphic conditions as well as altitude. The warm and continental Irano-Turanian region (Fer­ gana Valley and south-western Tajikistan) is character­ ized by low annual precipitation with the sum of ca. 200– 250 mm, and the peak in March (ca. 80 mm). During the summer months (from June to August) the precipitation is scarce, with the sum of 0–10 mm per month. Snow and frost occur only in winter (from December to February). Temperatures strongly vary during the year; in the warmest Figure 1. Distribution of plots in the study area (n = 1,525). Figure 1. Distribution of plots in the study area (n = 1,525). 276 Sebastian Świerszcz et al.: Graminoids in Tajikistan and Kyrgyzstan The final data set consisted of 1,525 vegetation-plot re­ cords of open habitats (Table 1). Plots were sampled from 2006 to 2019 in Tajikistan and Kyrgyzstan (Figure 1). Vegetation data preparation ( g ) Based on the coordinates, we derived the mean annual temperature and the sum of annual precipitation from the CHELSA dataset, with a resolution of 0.00833 decimal de­ grees (30 arc sec; Karger et al. 2017a, 2017b). Global Arid­ ity Index (hereinafter referred to as Aridity Index) was obtained from the Global-PET geospatial dataset available on the CGIAR-CSI GeoPortal (Zomer et al. 2022). Arid­ ity Index values are unitless and decrease with more arid conditions (Zomer et al. 2022). Livestock density data were obtained from the Gridded Livestock of the World database at a spatial resolution of 0.083333 decimal degrees (approxi­ mately 10 km at the equator) (GLW v3.1; Gilbert et al. 2018). For this study, we selected population densities (the average number of animals per km2) of the most common and in­ fluential livestock species: sheep, goats and cattle combined. The primary source of data was the Vegetation of Mid­ dle Asia database (Nowak et al. 2017; GIVD ID: AS-00- 003) containing 4,649 vegetation plots (relevés) stored in TURBOVEG (Hennekens and Schaminée 2001). Plots that were previously classified as natural or semi-natural vegetation of open habitats were extracted. We removed plots with a shrub layer > 50% and also those that are not typically used for grazing. At this stage, we obtained a data set representing five types of vegetation (Table 1; Figure 2). Because of the low number of records from meadows in our database (26 vegetation plots), they were excluded. The plant identification was based on the ten-volume flora of Tajikistan (Ovchinnikov 1957, 1963, 1968, 1975, 1978, 1981; Chukavina 1984; Kochkareva 1986; Kinzikaeva 1988; Rasulova 1991) and the ten-vol­ ume study of the flora of the former Soviet part of the Middle Asia (Conspectus Florae Asiae Mediae; Kova­ levskaya 1968–1993). B temp CHE gree ity I obta on t ity I cond obta at a s mate For num fluen Sta All s (R C noid Junc by w ‘ggri W annu Inde Table 1. Number of plots for each open vegetation type (n = 1,525). Vegetation types Number of plots Plot size range (m2) Mires 489 2–30 Tall-forb communities 168 10 Pseudosteppes 150 10 Salt marshes 191 10–100 Steppes 527 10–30 The primary source of data was the Vegetation of Mid­ dle Asia database (Nowak et al. 2017; GIVD ID: AS-00- 003) containing 4,649 vegetation plots (relevés) stored in TURBOVEG (Hennekens and Schaminée 2001). Study area Each plot contains a full list of vascular plant species recorded in a plot, often also a list of bryophytes, and estimates of the cover-abundance of species in each layer in the Braun-Blan­ quet or percentage scale. For each plot, geographical co­ ordinates were measured using a GPSMAP 60CSx device with an accuracy of ± 5 m, and the WGS84 reference frame. In the case when the Braun-Blanquet scale was used, we transformed to the percentage scale (r: 1%, +: 2%, 1: 3%, 2: 13%, 3: 38%, 4: 63%, 5: 88%). Then we calculated the rel­ ative cover of each species within each plot. Relative cover was calculated by dividing the cover of each species by the total vegetation cover of all species in the plot. To deter­ mine the relative cover of graminoids, we summed the rel­ ative cover of each species in this group in the plot. months, they reach from 20°C (May) to 34°C (June, July, August). In winter, the mean temperature is no lower than -3°C with extreme values reaching -27°C in some years.h months, they reach from 20°C (May) to 34°C (June, July, August). In winter, the mean temperature is no lower than -3°C with extreme values reaching -27°C in some years. The warm, humid and continental region includes the Tian Shan and Pamir-Alai ranges. The sum of annual pre­ cipitation ranges from ca. 500 mm in northern slopes to ca. 1000 mm in southern slopes. In June, the mean tem­ perature in colline and montane belts reaches ca. 22°C while in alpine belts, it reaches up to 10°C. The cold, semi-arid region includes the Issyk-Kul ba­ sin, central and western parts of the Alai Valley, as well as foothills and plateaus in the colline, montane and subal­ pine belts. The area is characterized by low precipitation, with the sum of ca. 200–400 mm per year. The precipita­ tion reaches a peak of 70 mm per month in spring (from May to July). The annual mean temperature is ca. 10°C, it exceeds 20°C only in the summer months.h The cold and arid climate region includes the eastern­ most sections of the Alai Valley and the eastern Pamirian Plateau. The sum of annual precipitation is extremely low and does not exceed 100 mm. Only in May and August the monthly sum of precipitation is ca. 20 mm. Environmental variables We assessed the importance of mean annual temperature, sum of annual precipitation, aridity, and livestock density (surrogate of grazing intensity) as drivers of the relative cover of graminoids. Mean annual temperature and sum of annual precipitation are two key climate factors that de­ termine plant distribution (Whittaker 1975). Aridity and grazing are factors that promote species with grazing re­ sistance traits (Coughenour 1985; Milchunas et al. 1988). Vegetation data preparation Plots that were previously classified as natural or semi-natural vegetation of open habitats were extracted. We removed plots with a shrub layer > 50% and also those that are not typically used for grazing. At this stage, we obtained a data set representing five types of vegetation (Table 1; Figure 2). Because of the low number of records from meadows in our database (26 vegetation plots), they were excluded. The plant identification was based on the ten-volume flora of Tajikistan (Ovchinnikov 1957, 1963, 1968, 1975, 1978, 1981; Chukavina 1984; Kochkareva 1986; Kinzikaeva 1988; Rasulova 1991) and the ten-vol­ ume study of the flora of the former Soviet part of the Middle Asia (Conspectus Florae Asiae Mediae; Kova­ levskaya 1968–1993). Study area The annual mean temperature is slightly above 0°C, with a minimum of ca. -30°C from January to February. Statistical analyses All statistical analyses were performed in R environment (R Core Team 2022). The relative cover (%) of all grami­ noids in the plots as well as of Poaceae, Cyperaceae and Juncaceae was presented by density curves computed by weighted kernel density smoothing functions using ‘ggridges’ package (Wilke 2021).f Table 1. Number of plots for each open vegetation type (n = 1,525). Vegetation types Number of plots Plot size range (m2) Mires 489 2–30 Tall-forb communities 168 10 Pseudosteppes 150 10 Salt marshes 191 10–100 Steppes 527 10–30 We used linear models to explore the effects of the mean annual temperature, sum of annual precipitation, Aridity Index and livestock density for the patterns of graminoid 277 Vegetation Classification and Survey Figure 2. Photos of the open vegetation types: (a) steppe (Kosh-Dobo, Kyrgyzstan), (b) salt marsh (Zoogvand, Tajik­ istan), (c) pseudosteppe (on the right site of the photo; Khoja Mumin Mt. near Vose, Tajikistan), (d) tall-forb commu­ nity (near Rabot, Tajikistan), (e) mire near Jelondy (Tajikistan) and (f) overgrazing – one of the main human-driven threats to grasslands in Middle Asia leading to land degradation. Figure 2. Photos of the open vegetation types: (a) steppe (Kosh-Dobo, Kyrgyzstan), (b) salt marsh (Zoogvand, Tajik­ istan), (c) pseudosteppe (on the right site of the photo; Khoja Mumin Mt. near Vose, Tajikistan), (d) tall-forb commu­ nity (near Rabot, Tajikistan), (e) mire near Jelondy (Tajikistan) and (f) overgrazing – one of the main human-driven threats to grasslands in Middle Asia leading to land degradation. abundance in open habitats. We performed linear models and evaluated the relevance of a quadratic term (polynomi­ al) to account for potential curvilinear relationships. We built models for each vegetation type and explanatory variable separately. The best model among the linear and quadratic ones was evaluated by their coefficient of determination (R2) and root mean-squared error (RMSE) with the compare_per­ formance function in the R package ‘performance’ version 0.8.0 (Lüdecke et al. 2021). Results of linear and polynomial models performance are presented in Suppl. material 1.i of relative cover of graminoids. To do this, we decom­ posed the variance of R2 into unique and common effects of predictors. Unique effects indicate how much variance is uniquely accounted for by a single predictor and com­ mon effects indicate how much variance is common to a predictor set (Ray-Mukherjee et al. 2014). Statistical analyses The sum of unique and common effects (total) represents the total contribution of a predictor to the dependent variable irrespective of collinearity with other variables (Pru­ nier et al. 2015). Commonality analysis was conducted with commonalityCoefficients function in ‘yhat’ package (Nimon et al. 2008). Additionally, we used commonality analysis to find the most important factors influencing the contributions Sebastian Świerszcz et al.: Graminoids in Tajikistan and Kyrgyzstan 278 munities. Mires and salt marshes had the lowest number of shared graminoid species among all pair-wise compa­ risions. The most common species were Calamagrostis pseudophragmites and Poa bulbosa (Suppl. material 2).h Results In total, we recorded 255 graminoid species within all vegetation types. Graminoid-richest vegetation types were steppes (136 species – 53.3% of the total graminoid flora) and pseudosteppes (94 species – 36.9% of the total grami­ noid flora) (Table 2). Lower number of graminoid species was recorded in mires (77), salt marshes (74) and tall-forb communities (57). The observed number of shared spe­ cies between vegetation types and the proportion of the observed species varied between the pairs of vegetation types (Table 2). The highest number of shared species was found for steppes and pseudosteppes, steppes and tall- forb communities, and pseudosteppes and tall-forb com­ The highest relative cover of graminoids was found for steppes (median: 47.8%), mires (median: 43.06%) and pseudosteppes (median: 39%). However, a particular density peak cannot be distinguished because the relative cover of graminoids is evenly distributed along the entire range within these vegetation types (Figure 3a). The dis­ tribution of the relative cover of Poaceae is similar to the distribution of relative cover of all graminoids (Figure 3b) indicating the apparent dominance of species from this family. The only exception was mires, where Cyperaceae Figure 3. Density curves representing the distribution of relative cover (%) for all graminoids together (a) and split by family (b, c, d) within open habitat types at plot level. The vertical red line shows the median value of relative graminoid cover within each vegetation type. On the y-axis, the distributions are represented by relative values with the maximum density of each group standardized to 1. Figure 3. Density curves representing the distribution of relative cover (%) for all graminoids together (a) and split Figure 3. Density curves representing the distribution of relative cover (%) for all graminoids together (a) and split by family (b, c, d) within open habitat types at plot level. The vertical red line shows the median value of relative graminoid cover within each vegetation type. On the y-axis, the distributions are represented by relative values with the maximum density of each group standardized to 1. Vegetation Classification and Survey 279 hump-shaped with the highest values of graminoids be­ tween ca. 0 and 10°C (Figure 4).h were dominating, with a median relative cover of 31% (Figure 3c). The relative cover of Juncaceae was lowest in all vegetation types (Figure 3d). Results The model showed that sum of annual precipitation had statistically significant effect on all vegetation types, although with a low model fit (R2 = 0.05–0.1; Table 3). The effect of this variable in pseudosteppes and tall- forb communities was negative and in salt-marshes and steppes was positive. The highest unique effect of this factor was found in tall-forb communities (68.4%). No clear pattern was found for mires (Figure 4). The models of Aridity Index and domestic animal pressure measured by livestock density showed a statistically sig­ nificant effect on the relative cover of graminoids in all vegetation types except tall-forb communities (Table 3). Model comparison showed that polynomial models provided a better fit for the relationship between gram­ inoid relative cover and predictor variables (Table 3). The model of mean annual temperature showed a significant pattern of the relative cover of graminoids for salt marsh­ es, pseudosteppes and steppes with the best fit and high unique effect for salt marshes (R2 = 0.32 and 65.3% of the regression effect; Table 3). The relative cover of gram­ inoids increased in pseudosteppes, and decreased in salt marshes with increasing mean annual temperature. The effect of the mean annual temperature in steppes was Figure 4. The relationship between graminoids relative cover and mean annual temperature (MAT), sum of annual precipitation (AP), Aridity Index and livestock density for open vegetation types in Tajikistan and Kyrgyzstan. Lines are predictions of fitted polynomial models (for a comparison of linear and polynomial models see Suppl. material 1). Only significant models at p < 0.05 level are shown. Figure 4. The relationship between graminoids relative cover and mean annual temperature (MAT), sum of annual precipitation (AP), Aridity Index and livestock density for open vegetation types in Tajikistan and Kyrgyzstan. Lines are predictions of fitted polynomial models (for a comparison of linear and polynomial models see Suppl. material 1). Only significant models at p < 0.05 level are shown. Sebastian Świerszcz et al.: Graminoids in Tajikistan and Kyrgyzstan 280 Table 2. Graminoid species cumulative number in each open vegetation type and the quantitative proportion of graminoids in relation to the graminoid flora (255 species). Grey-shaded cells show the number and percentage val­ ue (in brackets) of shared graminoid species between pairs of vegetation types. The darker the cell, the higher the number of shared graminoid species between pairs of vegetation types. Results Total graminoid species richness = 255 Mires Tall-forb communities Pseudosteppes Salt marshes Steppes Mires 77 (30.2) 10 (3.9) 24 (9.4) 22 (8.6) 13 (5.1) Tall-forb communities 57 (22.4) 41 (16.1) 15 (5.9) 40 (15.7) Pseudosteppes 94 (36.9) 30 (11.8) 61 (23.9) Salt marshes 74 (29) 26 (10.2) Steppes 136 (53.3) Table 3. Results of the polynomial regression models and commonality analysis for the effect of mean annual tem­ perature, sum of annual precipitation, Aridity Index and livestock density on graminoids relative cover for open veg­ etation types. The significant values are shown in bold. Commonality analysis output represents a unique, common and total contribution of each predictor variable to the regression effect. The proportion of variance explained by the predictor is presented in parenthesis as a percentage of R2. Table 3. Results of the polynomial regression models and commonality analysis for the effect of mean annual tem­ perature, sum of annual precipitation, Aridity Index and livestock density on graminoids relative cover for open veg­ etation types. The significant values are shown in bold. Commonality analysis output represents a unique, common and total contribution of each predictor variable to the regression effect. The proportion of variance explained by the predictor is presented in parenthesis as a percentage of R2. The best-fitted models for Aridity Index were found for pseudosteppes (R2 = 0.16) and steppes (R2 = 0.14). The highest unique effect of Aridity Index was found for mires (46.2%), however the highest common effect for this factor was recorded for steppes (62.1%) and pseu­ dosteppes (43 9%) In pseudosteppes and mires relative However, the unique effect of livestock density is rela­ tively low (7.4%), but the common effect with other fac­ tors is the highest among all the open vegetation types analysed (57.4%). The highest graminoids relative cover values on pseudosteppes was found at a density of ca. Results 9,000 animals per km2 Similar hump-shape pattern Explanatory variable F p-value R2 Commonality analysis Unique Common Total Mires Mean annual temperature 1.20 0.303 0.005 0.001 (0.8%) 0.004 (5.8%) 0.005 (6.6%) Sum of annual precipitation 13.30 < 0.001 0.052 0.003 (4.6%) 0.016 (22.3%) 0.019 (27%) Aridity Index 16.23 < 0.001 0.063 0.033 (46.2%) 0.028 (39.9%) 0.061 (86.1%) Livestock density 12.25 < 0.001 0.048 0.003 (4.8%) 0.025 (35%) 0.028 (39.7%) Tall-forb communities Mean annual temperature 0.82 0.441 0.010 0.003 (5.4%) 0.005 (9.7%) 0.008 (15.2%) Sum of annual precipitation 4.26 0.016 0.049 0.037 (68.4%) 0.003 (6%) 0.04 (74.3%) Aridity Index 1.16 0.316 0.014 0.013 (25.1%) -0.002 (-2.8%) 0.012 (22.3%) Livestock density 0.88 0.417 0.011 0.004 (7.7%) -0.004 (-7.3%) 0.0002 (0.4%) Pseudosteppes Mean annual temperature 13.31 < 0.001 0.153 0.029 (11.1%) 0.123 (46.4%) 0.152 (57.5%) Sum of annual precipitation 8.55 < 0.001 0.104 0.004 (1.5%) 0.07 (26.6%) 0.074 (28.1%) Aridity Index 14.40 < 0.001 0.164 0.045 (17%) 0.116 (43.9%) 0.161 (60.9%) Livestock density 22.69 < 0.001 0.236 0.02 (7.4%) 0.152 (57.4%) 0.172 (64.9%) Salt marshes Mean annual temperature 43.51 < 0.001 0.316 0.239 (65.3%) 0.068 (18.6%) 0.307 (83.9%) Sum of annual precipitation 7.56 < 0.001 0.074 0.001 (0.2%) 0.044 (11.9%) 0.044 (12.1%) Aridity Index 10.91 < 0.001 0.104 0.004 (1.2%) 0.078 (21.2%) 0.082 (22.4%) Livestock density 8.25 < 0.001 0.081 0.031 (8.4%) -0.003 (-0.8%) 0.028 (7.6%) Steppes Mean annual temperature 43.02 < 0.001 0.141 0.0001 (0.1%) 0.001 (0.4%) 0.001 (0.5%) Sum of annual precipitation 33.03 < 0.001 0.112 0.013 (9.6%) 0.085 (63.3%) 0.098 (73%) Aridity Index 42.06 < 0.001 0.138 0.036 (26.6%) 0.083 (62.1%) 0.119 (88.6%) Livestock density 25.31 < 0.001 0.088 0.001 (0.7%) 0.0002 (0.1%) 0.001 (0.8%) The best-fitted models for Aridity Index were found for pseudosteppes (R2 = 0.16) and steppes (R2 = 0.14). The highest unique effect of Aridity Index was found for mires (46.2%), however the highest common effect for this factor was recorded for steppes (62.1%) and pseu­ dosteppes (43.9%). In pseudosteppes and mires relative cover of graminoids decreased with increasing Aridity Index (and therefore increasing moisture availability, see the Methods), and in steppes and salt marshes, relative cover of graminoids increased with increasing Aridi­ ty Index (Figure 4). For livestock density, the best-fit­ ted model was found for pseudosteppes (R2 = 0.24). Graminoids are not always the dominant group in broadly-defined grasslands of Tajikistan and Kyrgyzstan Grasslands are generally described as vegetation dominat­ ed by graminoids, which typically have > 25% coverage (Dengler et al. 2014). Referring to the definition of Allen et al. (2011) the vegetation of grassland is broadly consid­ ered because a variety of plant groups are present includ­ ing grasses, legumes and other forbs, with no or scarce occurrence of woody plants. The results of our research showed that the analysed types of vegetation, which can be broadly classified as grasslands (steppes, pseudosteppes, mires, salt marshes and tall-forb vegetation), are charac­ terized by different proportions of graminoids (Figure 2). It is not surprising that the highest proportion of grami­ noids was recorded in steppes, mires and pseudosteppes. These are vegetation types that are shaped by the livestock grazing. The area of Middle Asia is characterized by long pastoral tradition, which for many years influenced the formation of plant communities consisting of grazing tolerant species (Wesche and Treiber 2012; Spengler et al. 2014). In grassland vegetation occurring in Tajikistan and Kyrgyzstan, species from Poaceae dominate or constitute a significant share. An important component of steppe veg­ etation are species from the genus Stipa (Wesche and Trei­ ber 2012); in this study 33 Stipa taxa (species and subspe­ cies) were found within the study area. Pseudosteppes are secondary grassland types developed in habitats primarily dominated by shrublands. This vegetation type occurs in lowlands (Figure 2c), in the southern regions of Middle Asia characterized by relatively high annual precipitations and high temperatures (Świerszcz et al. 2020). Similarly to steppes, they are characterized by a constant and sig­ nificant share of species from the Poaceae, including the most frequently recorded Poa bulbosa. Also, some pseu­ dosteppes are characterized by a higher frequency and cover of annual species, e.g. Aegilops triuncialis, Avena sterilis subsp. ludoviciana, Bromus lanceolatus, or Vulpia persica (Suppl. material 2). Results However, the unique effect of livestock density is rela­ tively low (7.4%), but the common effect with other fac­ tors is the highest among all the open vegetation types analysed (57.4%). The highest graminoids relative cover values on pseudosteppes was found at a density of ca. 9,000 animals per km2. Similar hump-shape pattern was found for steppes with the highest graminoids rel­ ative cover values at a density of ca. 4,000 animals. On the other hand, for salt marshes and mires we found a U-shaped pattern with the lowest relative cover of gram­ inoids at level of ca. 1,500 and 2,500 domestic animals per km2 respectively (Figure 4). 281 Vegetation Classification and Survey spp. (Świerszcz et al. 2021) to vegetation with a negligi­ ble share of graminoids, e.g. communities dominated by stem succulent С3 chenopods of the genera Salicornia, Halopeplis, and Suaeda (Akhani 2004). Our study showed that the number of graminoid species is relatively low in salt marshes of Middle Asia (74 taxa; Suppl. material 2); however, they are used as pasture, mostly in the harsh conditions of the Pamirs (Świerszcz et al. 2021). Tall-forb communities are also characterized by a low graminoid abundance. They are dominated by tall forbs, such as species from the Apiaceae (e.g. Prangos pabularia, Feru­ la kuhistanica, and Heracleum lehmannianii; Nowak et al. 2020b). Similar results were obtained by Wagner (2009) in meadow-forb vegetation in the western Tian Shan, where non-graminoid species dominate while only 19 graminoid species were recorded. The low number and contribution of graminoids in tall-forb vegetation can be explained by their close relationship with juniper forests, xerophyt­ ic shrubs, or screes in which graminoids occur with low abundance (Nowak et al. 2020b, 2022a; Świerszcz et al. 2022). Moreover, tall-forb communities are used as pas­ tures, but grazing animals use sward selectively because the vegetation includes tasteless or even poisonous spe­ cies (e.g. Prangos pabularia, species of the genus Ferula). This phenomenon causes a strong growth and dominance of these plants and simultaneously inhibits the growth of grasses and sedges (Figure 2d). Grazing-induced changes in graminoids abun­ dance The vegetation cover of open habitats in Tajikistan and Kyr­ gyzstan is strongly affected by livestock grazing, which re­ sulted in changes in graminoid abundance. However, our study shows that not all analysed vegetation types respond to grazing in terms of graminoid contribution. We obtained the best-fitted model for pseudosteppes, where the proportion of graminoids increases with increasing livestock density to the highest point of all vegetation types analysed. The results confirm that pseudosteppes are a secondary vegetation type created after the cutting of pistachio groves (Nowak et al. 2022b). Intensive grazing, mainly by sheep and goats, results in the appearance of a high abundance of species resistant to grazing (e.g. Poa bulbosa, Carex pachystylis, Cynodon dac­ tylon) and characterized by animal-induced diaspore dis­ persal (e.g. Aegilops triuncialis, Avena sterilis subsp. ludovi­ ciana, Taeniatherum caput-medusae subsp. crinitum; Suppl. material 2). Many of them are ephemeral species (Toderich et al. 2013) also resistant to aridity and high temperatures. Milchunas et al. (1988) showed that arid conditions pro­ mote grazing resistance traits. It appears that semi-natural pseudosteppes are associated with a long evolutionary his­ tory of grazing, strongly linked to climatic conditions (e.g. seasonally dry soils; Guarino et al. 2020). Similar relation­ ships have been confirmed in other parts of the world, e.g. the Patagonian steppes of southern Argentina (Adler et al. 2004; Guarino et al. 2020). On the other hand, in the steppes, which are characterized by similar vegetation physiognomy and land use type, according to our results, the variation in relative graminoid cover is mainly related to climatic con­ ditions. Grazing has a much smaller effect on their share of patches in the vegetation; moreover, grazing intensification may lead to a reduction in the proportion of graminoids at the expense of other grazing-tolerant species, e.g. species of the genus Astragalus (= Tragacantha, Astracantha). The contribution of graminoids in salt marshes also varied along climatic gradients. The highest graminoid cover was found on sites with a low mean annual tempera­ ture, high precipitation and less arid conditions. Middle Asian salt marshes vary according to geobotanical regions. In south-western Tajikistan and in the Ferghana Valley salt vegetation inhabits e.g. shallow ponds and around riv­ erbeds. The most common graminoid species is Aeluropus littoralis, however, it does not make a significant contribu­ tion to the vegetation. The high-elevation salt marshes in the Eastern Pamir are different. Effects of climatic factors on the abundance of graminoids Pseudo­ steppes develop in zones with high average temperatures with dry periods during the summer, when the entire grasslands sesonally dry up (Guarino et al. 2020). High pre­ cipitation in spring and autumn and dry summers promote periodically drought-tolerant species that increase in abun­ dance seasonally. Due to arid climatic conditions, high live­ stock pressure, and soil erosion, the vegetation has a greater contribution of graminoids, especially annual grasses, e.g. Avena sterilis subsp. ludoviciana, Bromus lanceolatus, and Vulpia persica (Suppl. material 2; Świerszcz et al. 2020). This secondary vegetation within the shrubland zone (Figure 2c) is similar to the thermo-mesomediterranean grasslands oc­ curring in the Mediterranean Region (San Miguel 2008; Guarino et al. 2020; Świerszcz et al. 2020).h bioclimatic variables studied poorly explained patterns of graminoids contribution. This may be explained by plant species composition in tall-forb communities, which de­ pends on specific microclimatic and soil conditions, not examined in this study. For example, Central European tall- forb communities with a high abundance of graminoids are associated with acidic soils and/or excessive depositions of atmospheric nitrogen (Świerkosz and Reczyńska 2022). Grazing-induced changes in graminoids abun­ dance The vegetation is shaped by extremely harsh conditions and is species poor. How­ ever, a common feature of graminoid species found in salt marshes, as in steppes, is their longevity and low resistance to soil drought. Many vegetation patches are dominated by graminoids adapted to the high salt content in the soil, e.g. species of the genus Puccinellia (Nowak et al. 2020a). Although our results show some patterns in the propor­ tions of graminoids with regard to precipitation and the Aridity Index in mires, the models show a poor fit. The lack of a clear climatic gradient may be due to the fact that sedges are the main component of this type of vegetation (Spalink et al. 2018; Martín-Bravo et al. 2019). Mires are hydrogenic habitats, fed mainly by seeping groundwater (Nowak et al. 2016a), thus they buffer the surplus of water supplied by rain­ fall. However, the highest share of graminoids in this type of vegetation, mainly species from Cyperaceae, is recorded in the driest areas (with low Aridity Index values). In the case of Middle Asia, such conditions prevail mainly in high al­ titudes of the Pamir Mountains, where long-rhizomatous graminoids typical for high alpine vegetation are promoted (Dolezal et al. 2019). Also, aridity facilitates the development of other plant features, e.g. grazing‐resistance traits (Adler et al. 2004). These features, combined with resistance to cold, radiation, drought and strong wind are very important from the point of view of livestock production, especially as winter pastures (Göbel et al. 2019; Can et al. 2020). Effects of climatic factors on the abundance of graminoids Grasslands in Middle Asia, despite having similar phys­ iognomy, show high variation in species composition (Wesche and Treiber 2012). Grasslands, similarly to other vegetation types, change along environmental gradients in relation to climatic variables such as precipitation, tem­ perature, and aridity. The altitudinal gradient influenc­ es the structure, phenology and species composition of grasslands in this strongly mountainous region (Wagner et al. 2020). Steppes are typical grassland vegetation and constitute an important feature of the diverse landscape in Middle Asia. Our study showed strong response of graminoids relative cover to climatic gradients in these steppes. We observed a sharp decrease of graminoids at low average annual temperatures at altitudes above 3,000 m a.s.l. (own observations). With the increasing altitude and harsh­ er environmental conditions, graminoids are replaced by resilient semi-desert taxa adapted to high elevations, e.g. Artemisia skorniakovii, Astragalus chomutowii or Braya pamirica (Nowak et al. 2018; Świerszcz et al. 2020). Low proportion of graminoids is also noted in the more ther­ mophilic steppes in the colline and montane belts, where the vegetation may consist mainly of dwarf shrubs (Nowak et al. 2016b). A possible explanation for this may be that the graminoids involved in the formation of the steppe vegeta­ tion have a long life span and are less resistant to aridity and The vegetation type with the highest proportion of graminoids are mires, which occur mostly in the moun­ tainous areas of Middle Asia. Harsh environmental condi­ tions at high elevational zones together with an intensive grazing promote species from the Cyperaceae. An increas­ ing abundance of Cyperaceae representatives with increas­ ing altitude was also found in the Himalayas (Dolezal et al. 2019). However, despite analogous relationships in the proportion of graminoids in the altitudinal gradient our results do not show any clear pattern in sedges-dominated mires related to elevation (data not shown). Salt marshes and tall-forb vegetation had a low contri­ bution of graminoids (median relative coverage < 25%, Figure 3). Halophytic vegetation is quite diverse in terms of dominant plant groups: from graminoid-dominat­ ed communities with Aeluropus littoralis or Puccinellia Sebastian Świerszcz et al.: Graminoids in Tajikistan and Kyrgyzstan 282 low annual precipitation. The opposite pattern was found for pseudosteppes, where a higher contribution of gram­ inoids was recorded in a more arid environment. Author contributions S.Ś. planned the research. S.Ś., G.S, and S.N. collected part of the field data. S.Ś. prepared the final dataset, performed statistical analyses and led the writing. G.S., M.R., and S.N. critically revised and edited the manuscript. References Adler PB, Milchunas DG, Lauenroth WK, Sala OE, Burke IC (2004) Functional traits of graminoids in semi-arid steppes: A test of graz­ ing histories. Journal of Applied Ecology 41: 653–663. https://doi. org/10.1111/j.0021-8901.2004.00934.x Christenhusz MJM, Byng JW (2016) The number of known plants spe­ cies in the world and its annual increase. Phytotaxa 261: 201–217. https://doi.org/10.11646/phytotaxa.261.3.1 Christenhusz MJM, Byng JW (2016) The number of known plants spe­ cies in the world and its annual increase. Phytotaxa 261: 201–217. https://doi.org/10.11646/phytotaxa.261.3.1 Chukavina AP (1984) Flora Tadzhikskoi SSR. T. VII. Zontichnye – Ver­ benovye [Flora of the Tajik SSR. T. VII. Umbelliferae – Verbenaceae]. Izdatelstvo Nauka, Leningrad, RU. [In Russian] Chukavina AP (1984) Flora Tadzhikskoi SSR. T. VII. Zontichnye – Ver­ benovye [Flora of the Tajik SSR. T. VII. Umbelliferae – Verbenaceae]. Izdatelstvo Nauka, Leningrad, RU. [In Russian] Akhani H (2004) Halophytic vegetation of Iran: Towards a syntaxonomi­ cal classification. Annali di Botanica 4: 65–82. https://rosa.uniroma1. it/rosa04/annali_di_botanica/article/view/9168/9093 Coughenour MB (1985) Graminoid responses to grazing by large herbivores: adaptations, exaptations, and interacting processes. Annals of the Mis­ souri Botanical Garden 72: 852–863. https://doi.org/10.2307/2399227 Allen VG, Batello C, Berretta EJ, Hodgson J, Kothmann M, Li X, McIvor J, Milne J, Morris C, … Sanderson M (2011) An international ter­ minology for grazing lands and grazing animals. Grass and Forage Science 66: 2–28. https://doi.org/10.1111/j.1365-2494.2010.00780.x Dengler J, Janišová M, Török P, Wellstein C (2014) Biodiversity of Pa­ laearctic grasslands: A synthesis. Agriculture, Ecosystems & Environ­ ment 182: 1–14. https://doi.org/10.1016/j.agee.2013.12.015 Borer ET, Lind EM, Firn J, Seabloom EW, Anderson TM, Bakker ES, Bie­ derman L, La Pierre KJ, MacDougall AS, … Stevens CJ (2019) More salt, please: global patterns, responses and impacts of foliar sodium in grass­ lands. Ecology Letters 22: 1136–1144. https://doi.org/10.1111/ele.13270 Dolezal J, Klimes A, Dvorsky M, Riha P, Klimesova J, Schweingruber F (2019) Disentangling evolutionary, environmental and morphological drivers of plant anatomical adaptations to drought and cold in Himalayan graminoids. Oikos 128: 1576–1587. https:// doi.org/10.1111/oik.06451 Bragina TM, Wagner V, Nowak A, Vanselow KA (2018) Grasslands of Kazakhstan and Middle Asia: the ecology, conservation and use of a vast and globally important area. In: Squires VR, Dengler J, Feng H, Hua L (Eds) Grasslands of the world: diversity, management and conservation. CRC Press Taylor & Francis Group, Boca Raton, Lon­ don, New York, UK, US, 139–167. Gibbson DJ (2009) Grasses and Grassland Ecology. Oxford University Press, Oxford, UK, 305 pp. Acknowledgements We are grateful to Idoia Biurrun, Arkadiusz Nowak, and anonymous Reviewers for the valuable comments that improved the quality of the manuscript. We also thank Firuza Illarionova from the Dushanbe Nature Protection Team for her assistance and help in organizing field ex­ peditions. The project was partially supported by the Na­ tional Science Centre, Poland, no. 2020/04/X/NZ8/00032. Data availability Primary data are stored in the Vegetation of Middle Asia database (http://www.givd.info/ID/AS-00-003) (Nowak et al. 2017). Conclusions Our study shows that the largest number of graminoid species is associated with steppes, which are the most common vegetation type in Middle Asia. However, there is no universal pattern for graminoid distribution along the climatic and grazing gradient, but such relationships were found for particular vegetation types. Strong but not con­ sistent relationships were found in steppes, pseudosteppes Tall-forb communities are not typical graminoid veg­ etation. In most cases, graminoids do not dominate in these communities, although there is great variability with­ in this type of vegetation (Nowak et al. 2020b). However, Vegetation Classification and Survey 283 and salt marshes. These differences result mainly from bi­ ogeographic features of the study area. But it is important to bear in mind that current and upcoming climate change may contribute to the potential extinction of some grami­ noid species, including endemics (Vintsek et al. 2022). Grazing showed to be the strongest variable influencing the proportion of graminoids in pseudosteppes, pointing to their anthropogenic origin. The mountainous land­ scape and the history of human activity, especially grazing by sheep, cattle and horses, create favourable habitats for various types of graminoid communities. It is worth not­ ing that major changes in open ecosystems are related to expanding human and livestock populations, resulting in pastures that are often overgrazed, which can lead to more serious problems related to soil erosion, among others (Figure 2f). As Middle Asia is an area where the human food and economic safety is largely depended on graz­ ing animals, research on group of plants is necessary and should be continued, also for vegetation types important for grazing but not covered by our analyses (e.g. alpine meadows, Kobresia mats). The knowledge about relative cover patterns of graminoids and their underlying factors increases our understanding of ecological patterns in the open vegetation of Middle Asia. References https://doi.org/10.2989/10220111003703542 Gilbert M, Nicolas G, Cinardi G, Van Boeckel TP, Vanwambeke SO, Wint GRW, Robinson TP (2018) Global distribution data for cattle, buffa­ loes, horses, sheep, goats, pigs, chickens and ducks in 2010. 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Scheiter S, Higgins SI, Osborne CP, Bradshaw C, Lunt D, Ripley BS, Tay­ lor LL, Beerling DJ (2012) Fire and fire-adapted vegetation promoted Scheiter S, Higgins SI, Osborne CP, Bradshaw C, Lunt D, Ripley BS, Tay­ lor LL, Beerling DJ (2012) Fire and fire-adapted vegetation promoted Sebastian Świerszcz et al.: Graminoids in Tajikistan and Kyrgyzstan 286 Ecological Indicators 144: e109419. https://doi.org/10.1016/j. ecolind.2022.109419 Werger MJA, Staalduinen MA van (Eds) Eurasian Steppes. Ecolog­ ical Problems and Livelihoods in a Changing World. Springer, Dor­ drecht, NL, 3–43. https://doi.org/10.1007/978-94-007-3886-7_1 Wagner V (2009) Eurosiberian meadows at their southern edge: Patterns and phytogeography in the NW Tien Shan. E-mail and ORCID Sebastian Świerszcz (Corresponding author, sebastian.swierszcz@ob.pan.pl), ORCID: https://orcid.org/0000-0003- 2035-0035 Grzegorz Swacha (grzegorz.swacha@uwr.edu.pl), ORCID: https://orcid.org/0000-0002-6380-2954 Małgorzata W. Raduła (malgorzata.radula@upwr.edu.pl), ORCID: https://orcid.org/0000-0002-9578-6135 Sylwia Nowak (snowak@uni.opole.pl), ORCID: https://orcid.org/0000-0003-2867-9839 Supplementary material Supplementary material Supplementary material 1 Comparison of models performance used in our study Link: https://doi.org/10.3897/VCS.95767.suppl1 Supplementary material 2 A list of graminoid species recorded in the study area Link: https://doi.org/10.3897/VCS.95767.suppl2
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English
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Cross-Protective Potential and Protection-Relevant Immune Mechanisms of Whole Inactivated Influenza Virus Vaccines Are Determined by Adjuvants and Route of Immunization
Frontiers in immunology
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Citation for published version (APA): Bhide, Y., Dong, W., Gribonika, I., Voshart, D., Meijerhof, T., de Vries-Idema, J., Norley, S., Guilfoyle, K., Skeldon, S., Engelhardt, O. G., Boon, L., Christensen, D., Lycke, N., & Huckriede, A. (2019). Cross- Protective Potential and Protection-Relevant Immune Mechanisms of Whole Inactivated Influenza Virus Vaccines Are Determined by Adjuvants and Route of Immunization. Frontiers in Immunology, 10, Article 646. https://doi.org/10.3389/fimmu.2019.00646 University of Groningen University of Groningen Cross-Protective Potential and Protection-Relevant Immune Mechanisms of Whole Inactivated Influenza Virus Vaccines Are Determined by Adjuvants and Route of Immunization Bhide, Yoshita; Dong, Wei; Gribonika, Inta; Voshart, Danielle; Meijerhof, Tjarko; de Vries- Idema, Jacqueline; Norley, Stephen; Guilfoyle, Kate; Skeldon, Sarah; Engelhardt, Othmar G. Published in: Frontiers in Immunology Bhide, Yoshita; Dong, Wei; Gribonika, Inta; Voshart, Danielle; Meijerhof, Tjarko; de Vries- Idema, Jacqueline; Norley, Stephen; Guilfoyle, Kate; Skeldon, Sarah; Engelhardt, Othmar G. Published in: Frontiers in Immunology DOI: 10.3389/fimmu.2019.00646 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF also known as Version of record Document Version Publisher's PDF, also known as Version of record Publication date: 2019 Publication date: 2019 Publication date: 2019 Link to publication in University of Groningen/UMCG research database Download date: 24-10-2024 Edited by: Cecil Czerkinsky, Institut National de la Santé et de la Recherche Médicale (INSERM), France Yoshita Bhide 1, Wei Dong 1, Inta Gribonika 2, Daniëlle Voshart 1, Tjarko Meijerhof 1, Jacqueline de Vries-Idema 1, Stephen Norley 3, Kate Guilfoyle 4†, Sarah Skeldon 4, Othmar G. Engelhardt 4, Louis Boon 5, Dennis Christensen 6, Nils Lycke 2 and Anke Huckriede 1* Reviewed by: Baik Lin Seong, Yonsei University, South Korea Huan Huu Nguyen, Arizona State University, United States 1 Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands, 2 Department of Microbiology and Immunology, Institute of Biomedicine, Gothenburg University, Gothenburg, Sweden, 3 Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany, 4 Division of Virology, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare products Regulatory Agency (MHRA), Potters Bar, United Kingdom, 5 Bioceros, Utrecht, Netherlands, 6 Adjuvant Research, Department of Infectious Diseases Immunology, Statens Serum Institut (SSI), Copenhagen, Denmark *Correspondence: Anke Huckriede a.l.w.huckriede@umcg.nl Adjuvanted whole inactivated virus (WIV) influenza vaccines show promise as broadly protective influenza vaccine candidates. Using WIV as basis we assessed the relative efficacy of different adjuvants by carrying out a head-to-head comparison of the liposome-based adjuvants CAF01 and CAF09 and the protein-based adjuvants CTA1-DD and CTA1-3M2e-DD and evaluated whether one or more of the adjuvants could induce broadly protective immunity. Mice were immunized with WIV prepared from A/Puerto Rico/8/34 (H1N1) virus intramuscularly with or without CAF01 or intranasally with or without CAF09, CTA1-DD, or CTA1-3M2e-DD, followed by challenge with homologous, heterologous or heterosubtypic virus. In general, intranasal immunizations were significantly more effective than intramuscular immunizations in inducing virus-specific serum-IgG, mucosal-IgA, and splenic IFNγ-producing CD4 T cells. Intranasal immunizations with adjuvanted vaccines afforded strong cross-protection with milder clinical symptoms and better control of virus load in lungs. Mechanistic studies indicated that non-neutralizing IgG antibodies and CD4 T cells were responsible for the improved cross-protection while IgA antibodies were dispensable. The role of CD4 T cells was particularly pronounced for CTA1-3M2e-DD adjuvanted vaccine as evidenced by CD4 T cell-dependent reduction of lung virus titers and clinical symptoms. Thus, intranasally administered WIV in combination with effective mucosal adjuvants appears to be a promising broadly protective influenza vaccine candidate. Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Bhide, Y., Dong, W., Gribonika, I., Voshart, D., Meijerhof, T., de Vries-Idema, J., Norley, S., Guilfoyle, K., Skeldon, S., Engelhardt, O. G., Boon, L., Christensen, D., Lycke, N., & Huckriede, A. (2019). Cross- Protective Potential and Protection-Relevant Immune Mechanisms of Whole Inactivated Influenza Virus Vaccines Are Determined by Adjuvants and Route of Immunization. Frontiers in Immunology, 10, Article 646. https://doi.org/10.3389/fimmu.2019.00646 Citation for published version (APA): Bhide, Y., Dong, W., Gribonika, I., Voshart, D., Meijerhof, T., de Vries-Idema, J., Norley, S., Guilfoyle, K., Skeldon, S., Engelhardt, O. G., Boon, L., Christensen, D., Lycke, N., & Huckriede, A. (2019). Cross- Protective Potential and Protection-Relevant Immune Mechanisms of Whole Inactivated Influenza Virus Vaccines Are Determined by Adjuvants and Route of Immunization. Frontiers in Immunology, 10, Article 646. https://doi.org/10.3389/fimmu.2019.00646 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. 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For technical reasons the number of authors shown on this cover page is limited to 10 maximum. ORIGINAL RESEARCH published: 29 March 2019 doi: 10.3389/fimmu.2019.00646 Keywords: whole inactivated virus (WIV) influenza vaccines, liposome-based adjuvants, protein-based adjuvants, cross protection, non-neutralizing serum antibodies, CD4 T cells †Present Address: Kate Guilfoyle, Viroclinics Biosciences B.V, Rotterdam, Netherlands Viroclinics Biosciences B.V, Rotterdam, Netherlands Specialty section: This article was submitted to Mucosal Immunity, a section of the journal Frontiers in Immunology Received: 27 September 2018 Accepted: 11 March 2019 Published: 29 March 2019 INTRODUCTION Furthermore, CAF05, a predecessor adjuvant was successfully administered via mucosal route (39). This motivated us to administer CAF09 via intranasal route. CTA1-DD is a fusion protein consisting of the enzymatically active A1 subunit of cholera toxin and a dimer of an Ig binding element from Staphylococcus aureus protein A. It targets cells of the innate immune system which results in strongly enhanced humoral and cellular immune responses (27–29). Contrary to whole cholera toxin the mucosal CTA1-DD adjuvant is safe and non-toxic as found in non-human primates and it does not accumulate in the olfactory bulb and nerve following administration intranasally (i.n.) and, hence, cannot cause Bell’s palsy (40). CTA1-3M2e-DD harbors an insert of three copies of the exterior domain of the M2 protein of influenza virus, M2e (26, 30). Vaccination is the cornerstone for the prevention of influenza (1). Current influenza vaccines predominantly mediate strain specific protection by eliciting neutralizing antibody responses to the globular head region of hemagglutinin (HA), one of the surface glycoproteins of the virus. They do not provide protective immunity against strains not included in the vaccine (1, 2). New virus strains regularly emerge through antigenic drift, the phenomenon responsible for recurrent epidemics. Moreover, zoonotic influenza virus subtypes pose a serious pandemic threat, as exemplified by pandemic H1N1(2009) and the potentially pandemic subtypes H5N1, H7N9, H10N8, or H5N6 (3–6). There is therefore an urgent need for broadly protective influenza vaccines which can prevent or at least mitigate infection by virus strains not included in the vaccine. p We compared these adjuvants head-to-head to assess their relative potency in stimulating cross-reactive and cross- protective anti-influenza immunity in mice. In order to mimick the situation of antigenic drift and antigenic shift, mice were immunized intramuscularly (i.m.) or i.n. with A/Puerto Rico/8/34 (PR8) WIV with or without the different adjuvants and 2 weeks after the final immunization mice were challenged with homologous PR8, heterologous (H1N1)pdm09 or heterosubtypic X-31 (H3N2) virus to assess protection and several immune parameters. We observed that WIV administered i.n. with the mucosal adjuvants conferred much stronger cross-protection than parenterally administered WIV with or without adjuvant. Studies into the significance of different immune mechanisms for protection revealed that non-neutralizing serum antibodies and CD4 T cells were important for cross-protection while IgA, even when present in high levels, did not play a critical role. Thus, WIV administered i.n. Citation: Citation: Bhide Y, Dong W, Gribonika I, Voshart D, Meijerhof T, de Vries-Idema J, Norley S, Guilfoyle K, Skeldon S, Engelhardt OG, Boon L, Christensen D, Lycke N and Huckriede A (2019) Cross-Protective Potential and Protection-Relevant Immune Mechanisms of Whole Inactivated Influenza Virus Vaccines Are Determined by Adjuvants and Route of Immunization. Front. Immunol. 10:646. doi: 10.3389/fimmu.2019.00646 March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 1 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. INTRODUCTION in combination with effective mucosal adjuvants provided the strongest cross- protection against heterosubtypic influenza virus infections and appears to be a promising candidate for a broadly protective influenza vaccine. Whole inactivated virus (WIV) vaccines contain all the structural viral proteins and retain the conformation of native virus particles and as such make a promising basis for an influenza vaccine. Moreover, WIV has an intrinsic ability to activate innate immune responses, e.g., antigen presenting cells via Toll-like receptor 7 (TLR7) signaling (7). Although WIV was the first vaccine to be used, it was later replaced by split and subunit vaccines that were considered safer (8), despite WIV being superior at inducing immune responses in mice and naïve human beings (7, 9–12). Interest has recently refocused on WIV vaccines as studies have shown them capable of inducing a certain degree of cross-protection upon parenteral and mucosal vaccination (3, 13–16). However, a large amount of antigen was required to achieve protection and/or virus challenge was only performed shortly after immunization in these studies (16). One approach to reduce the dose of WIV needed would be to use adjuvants that might also improve the breadth of the immune responses (17–19). p There are various adjuvants under investigation for improving the immunogenicity of influenza vaccines (20). In this study, we compared the liposome-based adjuvants CAF01 and CAF09 and the protein-based adjuvants CTA1-DD and CTA1-3M2e- DD. These adjuvants were chosen because they were previously used successfully with several vaccine candidates, including influenza vaccines and are ready for or currently evaluated in clinical trials (21–38). The cationic adjuvant formulations, CAF01 and CAF09, are liposomes consisting of N,N′-dimethyl- N,N′-dioctadecylammonium (DDA) as delivery vehicle. For CAF01, α,α′-trehalose 6,6′-dibeheneate (TDB) acts as an immunomodulator and liposome-stabilizer, while CAF09 is stabilized and adjuvanted with monomycoloyl glycerol (MMG)- 1 and contains the TLR3 ligand Poly(I:C) as an additional immunomodulator (21, 24). CAF01 and CAF09 have been shown to generate strong T cell and antibody responses, with particularly high IgG2a responses for CAF01 (21, 22, 37). CAF09 is furthermore capable of inducing potent CD8+ T cell responses against protein and peptide based antigens (24, 33, 37, 38). CAF01 can be administered parenterally while CAF09 is mainly administered intraperitoneally (i.p.,). However, there has been a number of studies which showed promising results when CAF09 was given mucosally (Christensen et al. unpublished data). Viruses and Vaccines Viruses and Vaccines Live influenza viruses PR8 (H1N1), A/California/7/2009 (H1N1)pdm09, and X-31 (H3N2) (a reassortant strain carrying the HA of A/Aichi/2/68 and the internal proteins of PR8) were propagated in embryonated chicken eggs and were titrated on MDCK cells and in CB6F1 mice. Whole inactivated virus vaccines (WIV) were prepared from these viruses by inactivation with beta-propiolactone. Beta-propiolactone was removed in down-stream processing by concentration of the allantoic fluid and purification using sucrose gradient centrifugation. The WIV HA content (µg/ml) was determined by using Lowry protein assay and SDS-PAGE (colloidal blue staining) to establish total protein content and percentage HA, respectively, the HA content was then calculated. Quality and quantity of HA were confirmed by single radial immunodiffusion assay (41). Frontiers in Immunology | www.frontiersin.org CD4 T Cell Depletion Anti-CD4 antibody (200 µg/injection, clone GK 1.5 Bioceros, Utrecht, The Netherlands) was used for in vivo CD4 depletion, which was assessed by staining with FITC-labeled anti-CD4 (clone RM 4.4, Thermo Scientific). Female CB6F1 mice (aged 6–8 weeks) were immunized as described above (groups 1, 4, 5, 7 from Table 1) followed by a heterosubtypic challenge with X- 31 virus (105.5 TCID50/mouse). Mice were injected i.p. with the anti-CD4 antibody 1 day before, 1 and 7 days after challenge. Six animals/group were sacrificed on day 3 post challenge for assessment of lung virus titers while the remaining animals were followed for 14 days for clinical symptoms using the scoring system described above. Adjuvant Comparison Study j p y Female CB6F1/OlaHsd (C57Bl/6 x BALB/c F1) mice aged 6– 8 weeks were purchased from Envigo (The Netherlands). The mice were distributed randomly and housed in groups of six within individually ventilated cages (IVC) at the animal facility, receiving standard water and diet. Group sizes were determined using Piface software aiming at a power of 80%. Mice were vaccinated three times with 0.5 µg HA of PR8 (with or without the adjuvants) on days 0, 10, and 20 as described in Table 1. Mice from groups 1–3 received 50 µl PBS or vaccine i.m., 25 µl per hindlimb. Mice from groups 4–7 received respective vaccines i.n. in a volume of 40 µl, divided between the two nostrils. Vaccination and virus challenge were carried out under Isoflurane/O2 anesthesia. Three weeks after the 3rd vaccination (day 41), six mice from each group (of 18) were sacrificed to determine vaccine-induced immune responses. The remaining mice were challenged with 104.4 TCID50/mouse of homologous PR8 virus, 103.3 TCID50/mouse of heterologous (H1N1)pdm09 or 105.5 TCID50/mouse of heterosubtypic X-31 (titers were chosen on the basis of titration experiments in CB6F1 mice). Six mice from each experimental group were sacrificed on day 3 post challenge to assess protection against virus replication in the lungs. The remaining six mice were observed until day 10 post challenge to assess clinical symptoms such as weight loss, ruffled fur and activity. The humane endpoint was set to a loss of >20% of the original weight from the day of challenge. Additionally, for the mechanistic experiments, a score sheet was used to follow the animals. Parameters such as weight loss, appearance (degree of ruffled fur, hunched back) and behavior of the animals (slow movements, difficulty in walking, circling, response to external stimulus) were recorded. These parameters were given scores IgA Knockout Experiment IgA knock-out mice (IgA KO; BALB/c background, males and females) were obtained from Margaret Conner, Baylor College of Medicine, Houston, TX, US and bred at EBM in Gothenburg, Sweden. The mice were immunized as described in Table 1, groups 1, 4, 5, and 7 and challenged with X-31 virus on day 41. Female BALB/c mice were used as wild-type (wt) controls. Clinical symptoms were assessed for 14 days using the scoring system described earlier. Adoptive Serum Transfer Serum samples were collected from mice mock-immunized with PBS, or immunized with PR8 WIV i.n., WIV+ CAF09 or WIV+CTA1-3M2e-DD as described above. Two hundred microliter of pooled sera were administered i.p. to naïve mice. Mice were then challenged with 105.5 TCID50/mouse of heterosubtypic X-31 virus 1 day post adoptive transfer. Mice from positive control group received serum samples from mice immunized with PR8 WIV and were challenged with PR8 live virus. Animals were followed for 14 days and clinical symptoms were assessed using the scoring system described above. Animal Experiments All animal experiments were approved by the Institutional Animal Care and Use Committee of the University of Groningen (IACUC-RUG, DEC 6923), or the Central Committee for Animal Experiments CCD of the Netherlands (AVD105002016599), the Animal Welfare and Ethics Review Body (AWERB) of the National Institute for Biological Standards and Controls (NIBSC), Potters Bar, UK (PPL 80/2537), or the IACUC of the University of Gothenburg, Sweden. Adjuvants The liposomal adjuvants CAF01 and CAF09 were produced as described previously (42). The dose for both adjuvants was 300 March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 2 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. µg per 50 µl for i.m. and 300 µg per 40 µl for i.n. administration. The protein adjuvants, CTA1-DD and CTA1-3M2e-DD, were produced by MIVAC Development AB, Sweden. The latter construct carried three copies of the extracellular domain of the influenza virus M2 protein (SLLTEVETPIRNEWGSRSNDSSD). Briefly, the fusion proteins were expressed in E. coli DH5 cells, transformed with the expression vector for the fusion protein, and grown in 500 ml cultures overnight in SYPPG medium with 100 ug/ml carbenicillin, at 37◦C, as previously described (30). Endotoxin levels were below 100 EU/mg as verified by use of the Endosafe R⃝testing system (Charles River). For both protein adjuvants, the concentration was 5 µg per 40 µl WIV. Filtered Dulbecco’s phosphate buffered saline containing CaCl2 and MgCl2 (DPBS, GIBCO by Life TechnologiesTM) was used as a diluent. from 1 to 4 for least to most severe. A cumulative score for a given day of 10 was considered to be the humane endpoint. Sample Collection From Mice p Before sacrifice, blood was drawn by cheek puncture for determining IgG, IgA and neutralizing antibody titers. Nasal and lung washes were taken using 1 ml PBS (pH 7.4) with Complete R⃝ protease inhibitor cocktail (Roche, Almere, The Netherlands) for determining IgA titers. Lungs were collected in 1 ml complete EPISERF medium (100 U/ml penicillin, 100 mg/ml streptomycin, 12.5 ml of 1 M HEPES, 5 ml of 7.5% sodium bicarbonate for 500 ml medium, Thermo Fisher Scientific, Bleisweijk, Netherlands) for determination of viral load. Spleens were collected in 1 ml Iscove’s Modified Dulbecco’s Medium (IMDM) (Thermo Fisher Scientific, Bleisweijk, Netherlands) containing 10% v/v FBS (Lonza, Basel, Switzerland), 100 U/ml penicillin, 100 mg/ml streptomycin and 50 µM 2-mercaptoethanol (Invitrogen, Breda, The Netherlands) to assess cellular immune responses. Frontiers in Immunology | www.frontiersin.org Assessment of Antibody Responses y p Titers of influenza-specific IgG, IgG1, IgG2a, IgA, anti-NP, anti- M2e and neutralizing antibodies were determined in blood serum samples taken on day 41, i.e., the day of challenge. IgA was determined in mucosal samples immediately after sample collection. ELISAs were performed as described previously using WIV prepared from each of the challenge viruses, subunit vaccine (SU) prepared from X-31, NP protein, or M2e protein for coating (44). To determine whether the serum antibodies were (cross-)neutralizing, microneutralization (MN) assays were performed using infectious PR8, (H1N1)pdm09 or X-31 virus as described previously (45). LoD for IgG was determined by calculating the log10 of the 1st dilution while LoD for MN titers was calculated using Log2 of the 1st dilution. Lung Virus Titration Limit of detection (LoD) was determined by calculating the log10 of the 1st dilution and the negative values were given half the value of the LoD. Lung Virus Titration Virus titration was performed as described previously (43). Briefly, the lungs were homogenized in 1 ml EPISERF March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org Frontiers in Immunology | www.frontiersin.org 3 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. TABLE 1 | Vaccination and challenge scheme. Groups Vaccine (D 0, 10, 20) Route Vaccine dose (µg HA) adjuvant dose (µg) injection volume (µl) Challenge D 41 1 PBS i.m. – – 50 2 WIV i.m. 0.5 – 50 3 WIV+ CAF01 i.m. 0.5 300 50 4 WIV i.n. 0.5 – 40 5 WIV+ CAF09 i.n. 0.5 300 40 A/PR/8/34 6 WIV+ CTA1-DD i.n. 0.5 5 40 (H1N1)pdm09 7 WIV+ CTA1-3M2e-DD i.n. 0.5 5 40 X-31 TABLE 1 | Vaccination and challenge scheme. ASNENMDAM for X-31 (University Medical Center Leiden, The Netherlands) in the presence of co-stimulatory anti- CD28 antibody for 16 h. For each mouse, non-stimulated control cells were used to measure the baseline expression of the cytokines. After 12 h of incubation, protein transport inhibitor (Thermo Scientific, Netherlands) was added to stop the transport of proteins out of the Golgi apparatus. Cell stimulation cocktail containing PMA-ionomycin (Thermo Scientific, The Netherlands) was used as a positive control stimulant. Next day, cells were washed once with FACS buffer and stained for surface markers (anti-CD3-Alexa-fluor 700, anti-CD4-FITC, anti-CD8a PerCP-efluor720, all purchased from Thermo Scientific, The Netherlands) for 45 min at 4◦C, followed by rinsing with cold PBS and staining with the fixable viability dye eFluor 780 for 30 min at 4◦C. After two washes with FACS buffer, cells were fixed with fixation buffer and then permeabilized with FACS permeabilization buffer (Thermo Scientific). For intracellular cytokine staining (ICS), antibodies (anti-IFNγ-PE-Cy7, anti-IL2-PE, anti-TNFα eFluor 450 and anti-IL4 APC, Thermo Scientific) were added to the cells and incubated for 45 min. Ultracomp beads (Thermo Scientific, The Netherlands) were used to prepare compensation controls. Events were acquired on an LSRII flow cytometer (BD Biosciences) and FlowJo software (Tree Star) was used for analysis. medium and centrifuged at 1,200 rpm for 10 min to collect the supernatant. These supernatants were used to infect MDCK cells with serial 2 fold dilutions of the lung supernatants to determine lung virus titers as described before (43). Viral titers are presented as log10 titer of 50% tissue culture infectious dose per gram of lung. Immuno-Profiling Reveals Strong Correlation Between Survival and Serum Antibodies, Mucosal IgA and IFNγ+ CD4 T Cells To determine which immune mechanisms correlated with the observed cross-protection and to what degree these mechanisms would differ for the different adjuvanted vaccines, various immunological assays were performed. Sera, nasal and lung washes were collected 3 weeks after the 3rd immunization for antibody titer assessments, while T cell responses against heterologous (H1N1)pdm09 and heterosubtypic X-31 virus were determined using spleens of vaccinated animals 3 days post heterosubtypic challenge. The results of immunoprofiling for the heterologous and heterosubtypic challenge experiments are summarized as heatmaps (Figures 2A,B) to reveal patterns which correlate with protection; the individual data can be found in the Supplementary Information (Figures S1–S5). When infected with PR/8 virus, all mock immunized mice reached the defined humane endpoint (>20% weight loss) and were sacrificed by day 6 post challenge. In contrast, mice from all groups immunized three times with WIV, with or without adjuvants, were protected from weight loss post challenge with homologous PR8 virus (Figures 1A,D). Furthermore, all but one (with low titer) of the vaccinated mice were completely protected from virus replication in the lungs (Figure 1G). Immunization with PR8 WIV i.m. reliably induced neutralizing antibodies against the homologous virus, especially when administered with adjuvant (Figure S1A). By contrast, i.n. immunizations poorly stimulated neutralizing antibodies, even in the presence of adjuvants. Importantly, we found no neutralizing antibodies against heterologous (H1N1)pdm09 or heterosubtypic X-31 virus irrespective of the immunization route or adjuvant used (Figures 2A,B and Figures S1B,C). However, all immunized mice developed serum IgG antibodies reactive with homologous, as well as heterologous and heterosubtypic virus and these titers were of identical magnitude for all three virus strains (Figures 2A,B and Figures S1D–F). The addition of adjuvants to i.m. and i.n WIV immunizations enhanced cross-reactive serum IgG resulting in similar endpoint titers. CAF01 and CAF09 affected IgG titers most strongly and enhanced both IgG1 and IgG2a. CTA1-DD and CTA1-3M2e-DD were comparatively less effective in stimulating IgG and IgG1 and had only minor effects on IgG2a levels (Figures 2A,B and Figures S2A,B). Challenge with heterologous (H1N1)pdm09 virus resulted in gradual weight loss in mock immunized animals gradually necessitating euthanasia on day 6 or 7 post infection. Animals vaccinated with non-adjuvanted WIV i.m. showed some weight loss but all survived until the end of the study. Surprisingly, mice immunized i.m. with CAF01 adjuvanted vaccine lost more weight and 2 out of 6 mice had to be sacrificed (Figures 1B,E). WIV Combined With Mucosal Adjuvants Provides Best Cross-Protection WIV Combined With Mucosal Adjuvants Provides Best Cross-Protection In order to determine the relative efficacy of WIV vaccines combined with different adjuvants, mice were vaccinated three times via the most suitable route of administration with WIV derived from PR8 virus alone or mixed with CAF01, CAF09, CTA1-DD or CTA1-3M2e-DD, followed by challenge with homologous PR8, heterologous H1N1pdm09 (same virus subtype as PR8 but different strain) or heterosubtypic X-31 (different virus subtype but same internal viral proteins). To assess the protective efficacy of the tested vaccines, challenged mice were observed for weight loss and clinical symptoms for a period of 10 days or until they reached defined humane endpoint. Percent weight loss was calculated (Figures 1A–C) and survival curves were plotted (Figures 1D–F). Furthermore, to assess viral loads in the lungs, mock vaccinated and WIV vaccinated animals were sacrificed 3 days after homologous, heterologous or heterosubtypic virus challenge (Figures 1G–I). Statistics To assess the contribution of influenza-specific T cells in protection, a multifunctional T cell assay was performed which involved staining for intracellular cytokines IFNγ, TNFα, IL2, and IL4 expressed by CD3+CD4+ and CD3+CD8+ T lymphocytes. All reagents, buffers and antibodies were purchased from eBioscience, The Netherlands. For statistical analysis of intracellular cytokine levels, the numbers of cytokine positive and cytokine negative cells in the stimulated cell populations were compared with paired unstimulated controls using MIMOSA (Mixture Models for Single-Cell Assays) for IFNγ, TNFα, IL2 and IL4 (46). A false discovery rate of q ≤0.01 was accepted. A Chi-Squared test was used to compare the number of responders between groups. P ≤0.05 were considered significant. Spleens collected in IMDM were immediately processed and single cell suspensions were obtained using GentleMACS C tubes and GentleMACS dissociator (Miltenyi Biotec, Leiden, The Netherlands). Cell suspensions were then forced through a cell strainer (BD Bioscience, Breda, The Netherlands) and erythrocytes lysed using ACK lysis buffer (0.83% NH4Cl, 10 mM KHCO3, 0.1 mM EDTA). Cells were re-stimulated with a final concentration of 10 µg/ml PR8, (H1N1)pdm09 or X-31 (H3N2) WIV plus 10 µg/ml of NP366 peptide, ASNENMETM for PR8, ASNENVETM for (H1N1)pdm09 or The non-parametric Mann-Whitney U test was used to test if the differences between two groups with respect to different parameters were significant. A p < 0.05 was considered significant. Significance is represented as ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.0001. Statistical analyses were performed using GraphPad Prism version 5 for Windows (GraphPad Sofware, La Jolla, California, USA www.graphpad.com). March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 4 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. RESULTS i.n. immunization with CAF09, CTA1-DD or CTA1-3M2e- DD adjuvanted WIV stimulated significantly broader protection compared to systemic immunizations with WIV alone or WIV plus i.m. CAF01 adjuvant. Frontiers in Immunology | www.frontiersin.org Immuno-Profiling Reveals Strong Correlation Between Survival and Serum Antibodies, Mucosal IgA and IFNγ+ CD4 T Cells Animals vaccinated with WIV i.n. exhibited little weight loss except for one animal which reached the humane endpoint on day 5 post challenge. Mice vaccinated with WIV plus mucosal adjuvants presented the best cross-protection against heterologous virus challenge: they showed little or no weight loss and all animals survived to day 10 post challenge (Figures 1B,E). Although not significant, lung virus titers were somewhat higher in well protected than in unprotected, mock-immunized mice (Figure 1H). Furthermore, we wanted to identify the antigens targeted by the cross-reactive IgG. Use of subunit vaccine for coating revealed that vaccine-evoked, cross-reactive antibodies readily bound to viral surface proteins. These antibodies were found in all mice immunized i.m., but were present in mice immunized i.n. only when adjuvanted vaccine was used (Figures 2A,B, Figure S2C). Anti-NP antibodies were detected only in mice vaccinated with WIV plus CAF01 and one mouse from the WIV plus CAF09 group (Figures 2A,B and Figure S2D). Anti-M2e antibodies were induced only by WIV adjuvanted with CTA1-3M2e-DD (Figures 2A,B and Figure S2E). Vaccination, especially when done with adjuvanted vaccines, therefore induced cross-reactive antibodies which mainly targeted the viral surface proteins. The levels of these antibodies correlated with protection from severe In the heterosubtypic X-31 challenge experiment, all animals, whether vaccinated or not, initially showed a similar trend in weight loss (Figure 1C). However, from day 3 onwards, all the mice immunized mucosally with adjuvanted WIV recovered. In contrast, mock-immunized, parenterally immunized and mice immunized i.n. with WIV alone continued to lose weight and most animals had to be sacrificed, except for 4 out of 6 mice immunized i.m. with non-adjuvanted WIV (Figure 1F). Only mice mucosally immunized with adjuvanted WIV demonstrated significant reduction in lung viral titers as compared to mock-immunized control mice. CTA1-DD and CTA1-3M2e-DD adjuvanted vaccines afforded the largest reduction in lung viral titers (Figure 1I). Thus, March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 5 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. FIGURE 1 | Adjuvanted i.n. administered vaccine provides best protection. CB6F1 mice were vaccinated thrice 10 days apart with PBS, non-adjuvanted or adjuvanted WIV vaccines. Three weeks after the last vaccination, 6 mice/group were challenged with homologous PR8 (H1N1) (A,D,G), heterologous A/California/7/2009 (H1N1)pdm09 (B,E,H) or heterosubtypic X-31 (H3N2) viruses (C,F,I). Six animals/group were followed for 10 days for weight loss (A–C) and survival (D–F). Immuno-Profiling Reveals Strong Correlation Between Survival and Serum Antibodies, Mucosal IgA and IFNγ+ CD4 T Cells Three days post challenge 6 mice/group were sacrificed for determining lung viral load (G–I). Groups are represented as in Table 1: 1: PBS, 2: WIV i.m., 3: WIV+CAF01 i.m., 4: WIV i.n., 5: WIV+ CAF09 i.n., 6: WIV+ CTA1-DD i.n., 7: WIV+ CTA1-3Me-DD i.n. Dashed line indicates Limit of detection (LoD) (G–I). Virus titers are represented as log10 titers/gram of lung tissue with level of significance as *p < 0.05 and **p < 0.01 calculated using Mann-Whitney U-test. FIGURE 1 | Adjuvanted i.n. administered vaccine provides best protection. CB6F1 mice were vaccinated thrice 10 days apart with PBS, non-adjuvanted or adjuvanted WIV vaccines. Three weeks after the last vaccination, 6 mice/group were challenged with homologous PR8 (H1N1) (A,D,G), heterologous A/California/7/2009 (H1N1)pdm09 (B,E,H) or heterosubtypic X-31 (H3N2) viruses (C,F,I). Six animals/group were followed for 10 days for weight loss (A–C) and survival (D–F). Three days post challenge 6 mice/group were sacrificed for determining lung viral load (G–I). Groups are represented as in Table 1: 1: PBS, 2: WIV i.m., 3: WIV+CAF01 i.m., 4: WIV i.n., 5: WIV+ CAF09 i.n., 6: WIV+ CTA1-DD i.n., 7: WIV+ CTA1-3Me-DD i.n. Dashed line indicates Limit of detection (LoD) (G–I). Virus titers are represented as log10 titers/gram of lung tissue with level of significance as *p < 0.05 and **p < 0.01 calculated using Mann-Whitney U-test. disease, except in the group with CAF01-adjuvanted vaccine delivered i.m. WIV demonstrated that mice immunized i.m and mice immunized i.n. with non-adjuvanted WIV developed no or very low levels of IFNγ-producing CD4 T cells. Mice immunized i.n. with adjuvanted WIV demonstrated enhancement of IFNγ- producing cells, with CTA1-3M2e-DD being most potent. In addition to IFNγ, we also measured IL2 and TNFα responses in CD4+ T cells, but although restimulation with WIV and peptides increased the numbers of T cells producing these cytokines, the percentages were low and no significant differences between immunized and mock-immunized animals were observed (results not shown). The large majority of vaccine- specific CD4 T cells produced IFNγ, while very few cells were multifunctional, also producing other cytokines (Figure S5). In contrast to CD4+ T cells, CD8+ T cells were not induced in significant numbers by any of the vaccines (Figures 2A,B and Figures S4C,D). Frontiers in Immunology | www.frontiersin.org Immuno-Profiling Reveals Strong Correlation Between Survival and Serum Antibodies, Mucosal IgA and IFNγ+ CD4 T Cells In conclusion, IFNγ-producing CD4 T cells were the only T cell population induced and their numbers Determination of influenza specific mucosal IgA revealed that mice from the PBS control group as well as mice immunized i.m. with non-adjuvanted or CAF01-adjuvanted WIV developed no or very low mucosal IgA responses (in nose and lungs) against any of the viruses (Figures 2A,B and Figures S3A,B,C). In contrast, all miceimmunized i.n. with adjuvanted WIV produced significant levels of specific IgA antibodies in both nose and lungs against all three virus strains, and these levels were significantly higher than in mice immunized i.n. with non-adjuvanted WIV. Therefore, mucosal immunization in the presence of adjuvant was required for successful induction of cross-reactive mucosal IgA (Figures 2A,B and Figures S3A,B,C). IgA titers strongly correlated with protection from weight loss (Figures 2A,B). We next assessed vaccine-induced T cell responses. In vitro re- stimulation of splenocytes with heterologous or heterosubtypic March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 6 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. FIGURE 2 | Immunoprofiling against heterologous and heterosubtypic viruses. Animals were vaccinated 3 times with the vaccines indicated in Table 1. After 3 vaccinations, sera, nasal, and lung washes and spleens were collected to determine systemic, mucosal and cell mediated immune responses (n = 6). Some animals were challenged with heterologous (A) and heterosubtypic (B) virus to determine protection, lung viral load (n = 6) and survival (n = 6). Generated data was used as input and conditional formatting was performed in Ms Excel to plot heatmaps. Each column represents one animal. Survival is shown with different color scheme as these are different animals compared to the rest. Dark blue indicates worst survival while light blue indicates best survival. For other parameters, heatmaps range from red (lowest response) to green (best response). GURE 2 | Immunoprofiling against heterologous and heterosubtypic viruses. Animals were vaccinated 3 times with the vaccines indicated in Table 1. After 3 accinations, sera, nasal, and lung washes and spleens were collected to determine systemic, mucosal and cell mediated immune responses (n = 6). Some animals ere challenged with heterologous (A) and heterosubtypic (B) virus to determine protection, lung viral load (n = 6) and survival (n = 6). Generated data was used as FIGURE 2 | Immunoprofiling against heterologous and heterosubtypic viruses. Immuno-Profiling Reveals Strong Correlation Between Survival and Serum Antibodies, Mucosal IgA and IFNγ+ CD4 T Cells Animals were vaccinated 3 times with the vaccines indicated in Table 1. After 3 vaccinations, sera, nasal, and lung washes and spleens were collected to determine systemic, mucosal and cell mediated immune responses (n = 6). Some animals were challenged with heterologous (A) and heterosubtypic (B) virus to determine protection, lung viral load (n = 6) and survival (n = 6). Generated data was used as input and conditional formatting was performed in Ms Excel to plot heatmaps. Each column represents one animal. Survival is shown with different color scheme as these are different animals compared to the rest. Dark blue indicates worst survival while light blue indicates best survival. For other parameters, heatmaps range from red (lowest response) to green (best response). serum followed by a homologous challenge with PR8 virus served as positive control group. Mice were observed daily for clinical symptoms using the score sheet described previously. We found that PR8 immune serum completely protected mice against PR8 virus infection. Serum from mice immunized i.n. with PR8 WIV without adjuvant did not provide protection against infection with heterosubtypic X-31 virus and the mice transfused with this serum exhibited high clinical scores and reduced survival (Figures 3A,B). By contrast, serum from mice immunized with WIV plus CAF09 or CTA1-3M2e-DD protected partially and clinical scores were reduced by 50% compared to unimmunized control mice. Thus, non-neutralizing serum IgG antibodies from mice immunized i.n. with CAF09 or CTA1-3M2e-DD adjuvanted WIV appeared to partially protect against heterosubtypic X-31 virus challenge. were enhanced significantly by adjuvanted WIV administered i.n. Protection from weight loss correlated well with the number of IFNγ-producing CD4 T cells (Figures 2A,B and Figures S4A,B). Frontiers in Immunology | www.frontiersin.org Dissecting the Mechanisms of Protection The mice were followed for survival (A) and clinical symptoms (B) assessed using a score based on weight, appearance and behavior. the well immunized animals. Yet, CD4 T cell depletion had a significant effect on lung virus titers in animals immunized with WIV and CTA1-3M2e-DD while all other immunization protocols showed comparable lung virus titers irrespective of CD4 depletion (Figure 4I). Therefore, CD4 T cells appeared to play a role in protection against heterobsubtypic challenge only in the CTA1-3M2e-DD group. these would be vaccine-specific. The results indicate that i.n. administered WIV combined with a mucosal adjuvant provided enhanced cross-protection compared to WIV administered i.m. with or without adjuvant and non-adjuvanted WIV administered i.n.. We observed that non-neutralizing serum IgG, mucosal IgA and IFNγ-producing CD4 T cells were significantly higher for mice immunized i.n. with WIV plus adjuvant than for the other, less well protected groups. While non-neutralizing serum IgG antibodies and CD4 T cells were contributing to protection, our experiments in IgA KO mice were less conclusive, but there was a trend toward a protective effect of local IgA on the clinical symptoms. Finally, we addressed whether cross-reactive local IgA antibodies impacted on protection against infection in the mice immunized i.n. by repeating the immunization/challenge experiment in IgA KO mice. In line with reports in literature, we found that mock-immunized IgA KO mice were more susceptible to influenza infection than mock-immunized wt BALB/c mice, demonstrated by higher clinical scores and survival post challenge (47). Wild-type BALB/c mice immunized with non-adjuvanted WIV demonstrated reduced clinical scores as compared to non-immunized BALB/c mice but this was not the case for IgA KO mice indicating a role for IgA in protection (Figures 5A,E and Figures 5B,F). When immunized with WIV and any of the mucosal adjuvants, wt and IgA KO mice developed protective immunity and survived the challenge infection (Figures 5C,D,G,H). Clinical scores of IgA KO mice immunized with CAF09 adjuvanted vaccine were higher than those of wt mice (Figure 5G). Mice immunized with CTA1- 3M2e-DD adjuvanted WIV developed the lowest clinical scores with little difference between wt and IgA KO mice (Figure 5H). These results suggest that local IgA antibodies exerted some protection from severe disease but were not critical for survival in this model. Dissecting the Mechanisms of Protection Dissecting the Mechanisms of Protection From the heat maps it can be deduced that animals which were completely protected from heterosubtypic challenge had high levels of serum IgG and mucosal IgA and high numbers of IFNγ-producing CD4 T cells. We next performed a series of experiments in order to determine whether any of these factors was critical for protection from heterosubtypic virus infection. For these experiments we focused on CAF09 and CTA1-3M2e-DD as the most successful adjuvants from the previous experiment and used PBS and non-adjuvanted WIV as controls. Next, we studied the role of CD4+ T cells in protection. Depletion of CD4 T cells was achieved through anti-CD4 Mab- treatment of mice and resulted in reduction of CD4 T cell numbers in peripheral blood by >95% (data not shown). We found that CD4 depletion did not affect survival (Figures 4A–D) or clinical scores (Figures 4E–H) upon X-31 virus infection in To assess if serum antibodies can mediate cross-protection, mice were passively immunized via the i.p. route with serum collected from animals which had been mock-immunized with PBS or immunized with WIV, WIV+CAF09 or WIV+CTA1- 3M2e-DD i.n. One day later they were challenged with heterosubtypic X-31 virus. Animals which received PR8 immune March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 7 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. FIGURE 3 | Serum antibodies induced by mucosally adjuvanted WIV might induce cross-protection. Serum was collected from animals vaccinated thrice with PBS i.n., non-adjuvanted WIV i.n., WIV+ CAF09 i.n., or WIV+ CTA1-3M2e-DD i.n. and was administered passively in naïve mice (n = 6) via the i.p. route. One day after passive immunization animals were challenged with heterosubtypic X-31 virus. Animals from the positive control group received PR8 immune sera and were challenged with homologous PR8 virus. The mice were followed for survival (A) and clinical symptoms (B) assessed using a score based on weight, appearance and behavior. FIGURE 3 | Serum antibodies induced by mucosally adjuvanted WIV might induce cross-protection. Serum was collected from animals vaccinated thrice with PBS i.n., non-adjuvanted WIV i.n., WIV+ CAF09 i.n., or WIV+ CTA1-3M2e-DD i.n. and was administered passively in naïve mice (n = 6) via the i.p. route. One day after passive immunization animals were challenged with heterosubtypic X-31 virus. Animals from the positive control group received PR8 immune sera and were challenged with homologous PR8 virus. Dissecting the Mechanisms of Protection Mucosal immunization has been shown to be superior to parenteral immunization for stimulating local immunity and resident memory T cells in the lung (48–50) and to provide cross-protection against heterosubtypic virus challenge (14, 51). In agreement with these studies, we found that i.n. immunization with adjuvanted WIV afforded stronger cross- protection than parenteral immunizations. This was the case even though serum anti-viral IgG levels appeared quite comparable for mice immunized i.m. or i.n. with adjuvanted vaccines. Upon heterologous infection with (H1N1)pdm09 virus, clinical symptoms and survival correlated poorly with virus replication in the lungs while for heterosubtypic infection with X-31 virus we observed a clear correlation between clinical scores and lung virus titers. We chose day 3 to assess the lung viral load because we wanted to check if the vaccination has any impact on the replicating virus at a stage where the replication is at peak which in mice is on day 3 (52, 53). From experience we assume that in successfully immunized mice virus titers resolved more quickly than in mock immunized mice (45). Frontiers in Immunology | www.frontiersin.org DISCUSSION Mice (n = 12/group) were vaccinated thrice i.n. with PBS (A,E), non-adjuvanted WIV (B,F), WIV+ CAF09 (C,G) or WIV+ CTA1-3M2e-DD (D,H) followed by heterosubtypic challenge. On day−1, 1 and 7 relative to the challenge, anti-CD4 antibody or PBS was administered i.p.. Mice were followed for 14 days for survival (A–D) and clinical symptoms (E–H). Dotted lines in E-H indicate the humane endpoint. Six animals/group were sacrificed on day 3 post challenge to determine lung virus titers (I). LoD is indicated by dashed line. Mock depletion is presented by filled symbols with—and CD4 depletion is represented by open symbols with +. Virus titers are represented as log10 titers /gram of lung with level of significance as *p < 0.05 calculated using Mann-Whitney U-test. lungs and nose of mice. IgA has been shown to be more cross-reactive than IgG (61, 62). Moreover, Maurer et al have recently shown that IgA antibodies can also neutralize influenza virus in an antigen-aspecific manner by providing sialic acid in the glycosylated Fc part which serves as a decoy receptor not only for influenza virus but also for other viruses using sialic acid as a receptor (63). However, in our study adjuvanted WIV administered i.n. completely protected IgA KO mice from reaching the humane endpoint post heterosubtypic challenge, similar to wt BALB/c mice, indicating that IgA was not crucial for protection. Nevertheless, we cannot exclude that local IgA antibodies exerted some protective function, as reflected in the higher clinical scores in immunized and challenged IgA KO mice compared to the wt mice. Whether local IgA plays a role in cross-protection induced by adjuvanted WIV administered i.n. or not is controversial. For example, Zhang et al. (64) showed that i.n. immunization with a CTB/CT-adjuvanted subunit vaccine in line with recent observations in humans that also indicate that many influenza-specific antibodies, whether measured before or after vaccination, are cross-reactive (54, 55). Although serum antibodies induced by adjuvanted WIV were cross-reactive they could not neutralize heterologous and heterosubtypic virus in vitro, which was according to expectations (45, 56). Nevertheless, when transferred to naïve animals these antibodies provided partial protection against X-31 challenge. It has been shown that anti-influenza antibodies can mediate cross-protection via non- neutralizing mechanisms such as antibody dependent cellular cytotoxicity (ADCC), antibody dependent cellular phagocytosis, or complement mediated cytotoxicity (CDC) (57–60). DISCUSSION Adjuvanted WIV vaccines induced significantly higher systemic immune responses compared to non-adjuvanted WIV. Interestingly, the levels of serum IgG antibodies reacting with homologous, heterologous and heterosubtypic WIV in ELISA assays were similar, suggesting that most of the IgG antibodies induced by immunization with WIV were cross-reactive. This is In this study, we compared liposome and protein adjuvants head-to-head to assess their relative efficacy in inducing cross- reactive immunity in mice, when combined with i.m. and i.n. administered WIV. In addition, we dissected which immune parameters contributed to protection and to what extent March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 8 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. FIGURE 4 | CD4 depletion does not affect protection but affects virus growth. Mice (n = 12/group) were vaccinated thrice i.n. with PBS (A,E), non-adjuvanted WIV (B,F), WIV+ CAF09 (C,G) or WIV+ CTA1-3M2e-DD (D,H) followed by heterosubtypic challenge. On day−1, 1 and 7 relative to the challenge, anti-CD4 antibody or PBS was administered i.p.. Mice were followed for 14 days for survival (A–D) and clinical symptoms (E–H). Dotted lines in E-H indicate the humane endpoint. Six animals/group were sacrificed on day 3 post challenge to determine lung virus titers (I). LoD is indicated by dashed line. Mock depletion is presented by filled symbols with—and CD4 depletion is represented by open symbols with +. Virus titers are represented as log10 titers /gram of lung with level of significance as *p < 0.05 calculated using Mann-Whitney U-test. FIGURE 4 | CD4 depletion does not affect protection but affects virus growth. Mice (n = 12/group) were vaccinated thrice i.n. with PBS (A,E), non-adjuvanted WIV (B,F), WIV+ CAF09 (C,G) or WIV+ CTA1-3M2e-DD (D,H) followed by heterosubtypic challenge. On day−1, 1 and 7 relative to the challenge, anti-CD4 antibody or PBS was administered i.p.. Mice were followed for 14 days for survival (A–D) and clinical symptoms (E–H). Dotted lines in E-H indicate the humane endpoint. Six animals/group were sacrificed on day 3 post challenge to determine lung virus titers (I). LoD is indicated by dashed line. Mock depletion is presented by filled symbols with—and CD4 depletion is represented by open symbols with +. Virus titers are represented as log10 titers /gram of lung with level of significance as *p < 0.05 calculated using Mann-Whitney U-test. FIGURE 4 | CD4 depletion does not affect protection but affects virus growth. Frontiers in Immunology | www.frontiersin.org DISCUSSION From our observations, we think that mucosal IgA, though not being crucial on its own, works in concert with other mechanisms to provide the observed cross-protection. IFNγ-producing cross-reactive CD4 positive T cells increased significantly upon mucosal vaccination, especially in mice immunized with WIV plus CTA1-3M2e-DD. This could be due to the fact that M2e contains an MHC class II restricted CD4 helper epitope (26). CD4 depletion shortly before and after challenge did not affect survival, but impaired the control of lung virus growth in animals vaccinated with WIV plus CTA1-3M2e- DD, indicating a role of CD4 T cells in controlling virus growth rather than controlling clinical symptoms and in turn survival. CAF09-adjuvanted WIV did not induce significant numbers of CD4 T cells and accordingly, depletion of CD4 T cells during infection did not affect clinical scores or lung virus titers. Although WIV plus CAF01 induced the highest levels of cross-reactive antibodies, mice in the respective experimental group showed severe clinical symptoms and reduced survival post challenge. One thing which distinguished the CAF01 vaccinated mice group from the other groups was the induction of anti-NP antibodies. In a pre-clinical study in pigs by Ricklin et al. NP vaccination produced a strong immune response but induced lung inflammation and immunized pigs were not protected (68). In murine models the situation is not entirely clear. Although it has been shown that anti-NP antibodies can confer resistance to influenza virus infection (69–72) (contrary to our results), a previous study from our group demonstrated that mice vaccinated with NP adjuvanted with MPLA (which developed NP-specific antibodies) showed more rapid weight loss in the initial phase of infection than mock vaccinated mice (73). Furthermore, animals receiving a virosomal vaccine without NP showed fewer signs of illness compared to mice receiving a virosomal vaccine with NP. We did not observe IFNγ-producing CD8 T cells induced by vaccination. This was somewhat unexpected since at least CAF01, CAF09, and CTA1-DD are known to support induction of CD8 T cells (24, 33, 37, 66). Failure to detect CD8 T cells in our experiments might be because they were indeed absent or because we missed them due to the timing of the experiments. We assessed CD8 T cell responses on day 25 after the last immunization, by which time the cells were already through the retraction phase and the numbers might therefore have been too low to detect. DISCUSSION Which of these mechanisms, if any, is involved in protection afforded by WIV adjuvanted with CAF09 or CTA1-3M2e-DD remains to be elucidated. Vaccination with WIV plus mucosal adjuvants also led to remarkably enhanced levels of cross-reactive local IgA in the March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 9 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. FIGURE 5 | IgA antibodies are not critical in cross-protection. IgA KO mice and BALB/c mice were vaccinated thrice i.n. with PBS (A,E), non-adjuvanted WIV (B,F), WIV+CAF-09 (C,G) or WIV+CTA1-3M2e-DD (D, H) followed by heterosubtypic challenge. The mice were followed for survival (A–D) and development of clinical symptoms (E–H) for a period of 14 days. IgA KO mice are represented by dashed lines with open symbols while BALB/c wt mice are represented by solid lines with filled symbols. Dotted lines indicate humane endpoint. FIGURE 5 | IgA antibodies are not critical in cross-protection. IgA KO mice and BALB/c mice were vaccinated thrice i.n. with PBS (A,E), non-adjuvanted WIV (B,F), WIV+CAF-09 (C,G) or WIV+CTA1-3M2e-DD (D, H) followed by heterosubtypic challenge. The mice were followed for survival (A–D) and development of clinical symptoms (E–H) for a period of 14 days. IgA KO mice are represented by dashed lines with open symbols while BALB/c wt mice are represented by solid lines with filled symbols. Dotted lines indicate humane endpoint. ELISPOT assay for the detection of CD8 T cells. Despite the fact that we did not find them, we cannot categorically rule out that CD8 T cells contributed to protection. It is known that lung tissue resident memory (TRM) CD8 T cells have an important role in protection from influenza infection (66, 67). These cells might indeed have been induced in our experiments, but as parts of the lungs had to be used for other purposes and the remaining tissues were insufficient for isolating the required numbers of lymphocytes, we were unable to investigate them. Follow up studies will address this issue. stimulated equally efficient control of virus growth in wt and IgA KO mice. Yet, using mice deficient in the poly Ig receptor and thus unable to transport IgA across the respiratory epithelium, Asahi et al demonstrated that mucosal IgA is critical, in particular for protection from heterologous virus challenge (65). Frontiers in Immunology | www.frontiersin.org DISCUSSION Furthermore, we used intracellular cytokine staining, a method which allows simultanous determination of multiple cell populations and cytokines but is not as sensitive as One of the limitations of the study is the use of X-31 virus for heterosubtypic challeng. X-31 is a ressortant between PR8 and A/HK/68 and thus contains internal genes derived from PR8 virus. In future studies it would be ideal to March 2019 | Volume 10 | Article 646 10 Bhide et al. Cross-Protection by Mucosally Adjuvanted WIV use a wild type H3N2 virus for challenge and further also performing challenge experiments with avian influenza viruses to assess the breadth of protection afforded by the adjuvanted vaccines. Another limitation is the fact that heterologous virus challenge was performed 3 weeks after the last immunization when adjuvant-induced innate immune responses might still have been present. However, for CAF09 little induction of (systemic) innate immunity has been observed (Christensen et al. unpublished observations) while for CTA1-DD a low level of antigen-independent protection was observed independent of the time period (2, 4, or 6 weeks) between immunization and challenge (Lycke et al. unpublished observations). Thus, while we cannot completely rule out an effect of adjuvant-induced innate responses we consider it unlikely that these are the major reason for the observed cross-protection. Future experiments devoted to assessing the durability of the induced immune responses by increasing the period between immunization and challenge will clarify this point definitely. by mucosal vaccination with adjuvanted WIV and optimal protection thus requires a combination of different mechanisms. by mucosal vaccination with adjuvanted WIV and optimal protection thus requires a combination of different mechanisms. SUPPLEMENTARY MATERIAL The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fimmu. 2019.00646/full#supplementary-material ACKNOWLEDGMENTS We would like to thank central animal facility of the UMCG and Gothenburg university for animal caretaking and help with vaccinations. Further, we would like to thank the European Union Seventh Framework Program 19 (FP7/2007-2013) and Universal Influenza Vaccines Secured (UNISEC) consortium under grant agreement no. 602012 and also, Federation of European Microbiological Societies (FEMS) research grant for funding this research. We would like to dedicate this work to late Dr. Stephen Norley whose help in the project was very valuable. The results of our head-to-head comparison of different vaccines underline that mucosal immunization with adjuvanted WIV is indeed a promising approach for developing a broadly protective influenza vaccine. These vaccines induce a plethora of immune responses including mucosal IgA, cross-reactive (though not cross-neutralizing) systemic IgG, and CD4 Th cells. Each of these seems to play a role in cross-protection but neither appeared to be crucial. This indicates that, several immune mechanisms contribute to the cross-protection induced AUTHOR CONTRIBUTIONS YB, AH, NL, and DC designed the study. YB, WD, IG, and TM performed the animal experiments. YB, JdV-I, DV, and SN performed assays and analysis of data. KG, SS, and OE produced live and inactivated viruses and characterized them. LB provided CD4 depletion antibody. YB and AH wrote the manuscript. YB, AH, NL, and DC designed the study. YB, WD, IG, and TM performed the animal experiments. YB, JdV-I, DV, and SN performed assays and analysis of data. KG, SS, and OE produced live and inactivated viruses and characterized them. LB provided CD4 depletion antibody. YB and AH wrote the manuscript. 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The cationic liposomal adjuvants CAF01 and CAF09 formulated with the major outer membrane protein elicit robust protection in mice against a Chlamydia muridarum respiratory challenge. Vaccine. (2017) 35:1705–11. doi: 10.1016/j.vaccine.2017.02.020 40. Lycke N, Lebrero-Fernández C. ADP-ribosylating enterotoxins as vaccine adjuvants. Curr Opin Pharmacol. (2018) 41:42–51. doi: 10.1016/j.coph.2018.03.015 41. Wood JM, Schild GC, Newman RW, Seagroatt V. An improved single- radial-immunodiffusion technique for the assay of influenza haemagglutinin antigen: application for potency determinations of inactivated whole virus and subunit vaccines. J Biol Stand. (1977) 5:237–47. 24. Korsholm KS, Hansen J, Karlsen K, Filskov J, Mikkelsen M, Lindenstrøm T, et al. Induction of CD8+ T-cell responses against subunit antigens by the novel cationic liposomal CAF09 adjuvant. Vaccine. (2014) 32:3927–35. doi: 10.1016/j.vaccine.2014.05.050 25. Eriksson AM, Schön KM, Lycke NY. The cholera toxin-derived CTA1-DD vaccine adjuvant administered intranasally does not cause inflammation or accumulate in the nervous tissues. J Immunol. (2004) 173:3310–9. doi: 10. 4049/jimmunol.173.5.3310 42. Schmidt ST, Pedersen GK, Neustrup MA, Korsholm KS, Rades T, Andersen P, et al. Induction of cytotoxic T-lymphocyte responses upon subcutaneous administration of a subunit vaccine adjuvanted with an emulsion containing the toll-like receptor 3 ligand poly(I: C). Front Immunol. (2018) 9:1–12. doi: 10.3389/fimmu.2018.00898 26. Eliasson DG, Omokanye A, Schön K, Wenzel UA, Bernasconi V, Bemark M, et al. M2e-tetramer-specific memory CD4 T cells are broadly protective against influenza infection. Mucosal Immunol. (2017) 11:273–89. doi: 10.1038/mi.2017.14 43. Audouy SAL, van der Schaaf G, Hinrichs WLJ, Frijlink HW, Wilschut J, Huckriede A. Development of a dried influenza whole inactivated virus vaccine for pulmonary immunization. Vaccine. 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(2007) 25:8707–17. doi: 10.1016/j.vaccine.2007.10.035 32. Hansen J, Jensen KT, Follmann F, Agger EM, Theisen M, Andersen P. Liposome delivery of Chlamydia muridarum major outer membrane protein primes a Th1 response that protects against genital chlamydial infection in a mouse model1. J Infect Dis. (2008) 198:758–67. doi: 10.1086/590670 33. Gram GJ, Karlsson I, Agger EM, Andersen P, Fomsgaard A. A novel liposome- based adjuvant CAF01 for induction of CD8+ cytotoxic T-lymphocytes (CTL) to HIV-1 minimal CTL peptides in HLA-A∗0201 transgenic mice. PLoS ONE. (2009) 4:2–6. doi: 10.1371/journal.pone.0006950 50. Bhide Y, Tomar J, Dong W, de Vries-Idema J, Frijlink HW, Huckriede A, et al. Pulmonary delivery of influenza vaccine formulations in cotton rats: site of deposition plays a minor role in the protective efficacy against clinical isolate of H1N1pdm virus. Drug Deliv. (2018) 25:533–45. doi: 10.1080/10717544.2018.1435748 34. REFERENCES Genetic diversity of avian influenza A (H10N8) virus in live poultry markets and its association with human infections in China. Sci Rep. (2015) 5:1–8. doi: 10.1038/srep07632 5. Liu M, Li X, Yuan H, Zhou J, Wu J, Bo H, et al. Genetic diversity of avian influenza A (H10N8) virus in live poultry markets and its association with human infections in China. Sci Rep. (2015) 5:1–8. doi: 10.1038/srep07632 14. Quan F-S, Compans RW, Nguyen HH, Kang S-M. Induction of heterosubtypic immunity to influenza virus by intranasal immunization. J Virol. (2008) 82:1350–9. doi: 10.1128/JVI.01615-07 6. Pan M, Gao R, Lv Q, Huang S, Zhou Z, Yang L, et al. Human infection with a novel, highly pathogenic avian influenza A (H5N6) virus: virological and clinical findings. J Infect. (2016) 72:52–9. doi: 10.1016/j.jinf.2015.06.009 15. Budimir N, de Haan A, Meijerhof T, Waijer S, Boon L, Gostick E, et al. Critical role of TLR7 signaling in the priming of cross-protective cytotoxic T lymphocyte responses by a whole inactivated influenza virus vaccine. PLoS ONE. (2013) 8:e63163. doi: 10.1371/journal.pone.0063163 7. Geeraedts F, Goutagny N, Hornung V, Severa M, De Haan A, Pool J, et al. Superior immunogenicity of inactivated whole virus h5n1 influenza vaccine is primarily controlled by toll-like receptor signalling. PLoS Pathog. (2008) 4:e1000138. doi: 10.1371/journal.ppat.1000138 16. Budimir N, de Haan A, Meijerhof T, Gostick E, Price DA, Huckriede A, et al. Heterosubtypic cross-protection induced by whole inactivated influenza virus vaccine in mice: influence of the route of vaccine administration. Influenza Other Respi Viruses. (2013) 7:1202–9. doi: 10.1111/irv. 12142 8. Al-Mazrou A, Scheifele DW, Soong T, Bjornson G. Comparison of adverse reactions to whole-virion and split-virion influenza vaccines in hospital personnel. Cmaj. (1991) 145:213–8. 8. Al-Mazrou A, Scheifele DW, Soong T, Bjornson G. Comparison of adverse reactions to whole-virion and split-virion influenza vaccines in hospital personnel. Cmaj. (1991) 145:213–8. 9. Geeraedts F, Bungener L, Pool J, ter Veer W, Wilschut J, Huckriede A. Whole inactivated virus influenza vaccine is superior to subunit vaccine 17. Khurana S, Chearwae W, Castellino F, Manischewitz J, King LR, Honorkiewicz A, et al. Vaccines with MF59 adjuvant expand the antibody repertoire to target Frontiers in Immunology | www.frontiersin.org March 2019 | Volume 10 | Article 646 11 Cross-Protection by Mucosally Adjuvanted WIV Bhide et al. HIV-1 vaccine based on 18 T-cell minimal epitope peptides applying a novel cationic adjuvant CAF01. Vaccine. (2011) 29:7067–74. REFERENCES Fomsgaard A, Karlsson I, Gram G, Schou C, Tang S, Bang P, et al. 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Glycosylation of human IgA directly inhibits influenza A and other sialic- acid-binding viruses. Cell Rep. (2018) 23:90–9. doi: 10.1016/j.celrep.2018. 03.027 Copyright © 2019 Bhide, Dong, Gribonika, Voshart, Meijerhof, de Vries-Idema, Norley, Guilfoyle, Skeldon, Engelhardt, Boon, Christensen, Lycke and Huckriede. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. 64. Zhang Y, Pacheco S, Acuna CL, Switzer KC, Wang Y, Gilmore X, et al. Immunoglobulin A-deficient mice exhibit altered T helper 1-type immune responses but retain mucosal immunity to influenza virus. Immunology. (2002) 105:286–94. doi: 10.1046/j.0019-2805.2001.01368.x March 2019 | Volume 10 | Article 646 Frontiers in Immunology | www.frontiersin.org 13
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Decreased plasma concentrations of BDNF and IGF-1 in abstinent patients with alcohol use disorders
PloS one
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S1 Table. Plasma concentrations of BDNF, IGF-1 and IGFBP-3 in the alcohol group according to psychiatric comorbidity ANCOVA revealed no significant main effects or interaction using comorbidity and sex as factors and controlling for age Data represented in the table are the estimated marginal means and 95%CI for levels of comorbidity. (*) BDNF concentrations are the back-transformed means and 95% CI from logarithmic data. Variable Alcohol (N=91) Psychiatric comorbidity Comorbid substance use disorders Comorbid mental disorders No (N=20) Yes (N=71) No (N=54) Yes (N=37) No (N=30) Yes (N=61) BDNF (*) [mean (95% CI)] 121.14 (72.70-201.86) 108.13 (78.00-149.89) 98.00 (68.71-137.21) 139.62 (91.25-213.63) 125.41 (78.86-199.44) 105.02 (74.63-147.78) IGF-1 [mean (95% CI)] 103.61 (82.55-130.05) 113.00 (97.40-131.09) 103.05 (88.06-120.58) 123.38 (102.21-148.93) 109.62 (89.08-134.89) 110.94 (94.86-129.75) IGFBP-3 [mean (95% CI)] 4.22 (3.48-4.97) 4.65 (4.16-5.14) 4.40 (3.87-4.92) 4.77 (4.13-5.39) 4.41 (3.73-5.10) 4.60 (4.09-5.12) S1 Table. Plasma concentrations of BDNF, IGF-1 and IGFBP-3 in the alcohol group according to psychiatric comorbidity ANCOVA revealed no significant main effects or interaction using comorbidity and sex as factors and controlling for age Data represented in the table are the estimated marginal means and 95%CI for levels of comorbidity. (*) BDNF concentrations are the back-transformed means and 95% CI from logarithmic data. Variable Alcohol (N=91) Psychiatric comorbidity Comorbid substance use disorders Comorbid mental disorders No (N=20) Yes (N=71) No (N=54) Yes (N=37) No (N=30) Yes (N=61) BDNF (*) [mean (95% CI)] 121.14 (72.70-201.86) 108.13 (78.00-149.89) 98.00 (68.71-137.21) 139.62 (91.25-213.63) 125.41 (78.86-199.44) 105.02 (74.63-147.78) IGF-1 [mean (95% CI)] 103.61 (82.55-130.05) 113.00 (97.40-131.09) 103.05 (88.06-120.58) 123.38 (102.21-148.93) 109.62 (89.08-134.89) 110.94 (94.86-129.75) IGFBP-3 [mean (95% CI)] 4.22 (3.48-4.97) 4.65 (4.16-5.14) 4.40 (3.87-4.92) 4.77 (4.13-5.39) 4.41 (3.73-5.10) 4.60 (4.09-5.12) S1 Table. Plasma concentrations of BDNF, IGF-1 and IGFBP-3 in the alcohol group according to psychiatric comorbidity ANCOVA revealed no significant main effects or interaction using comorbidity and sex as factors and controlling for age Data represented in the table are the estimated marginal means and 95%CI for levels of comorbidity. (*) BDNF concentrations are the back-transformed means and 95% CI from logarithmic data. Variable Alcohol (N=91) Psychiatric comorbidity Comorbid substance use disorders Comorbid mental disorders No (N=20) Yes (N=71) No (N=54) Yes (N=37) No (N=30) Yes (N=61) BDNF (*) [mean (95% CI)] 121.14 (72.70-201.86) 108.13 (78.00-149.89) 98.00 (68.71-137.21) 139.62 (91.25-213.63) 125.41 (78.86-199.44) 105.02 (74.63-147.78) IGF-1 [mean (95% CI)] 103.61 (82.55-130.05) 113.00 (97.40-131.09) 103.05 (88.06-120.58) 123.38 (102.21-148.93) 109.62 (89.08-134.89) 110.94 (94.86-129.75) IGFBP-3 [mean (95% CI)] 4.22 (3.48-4.97) 4.65 (4.16-5.14) 4.40 (3.87-4.92) 4.77 (4.13-5.39) 4.41 (3.73-5.10) 4.60 (4.09-5.12) ANCOVA revealed no significant main effects or interaction using comorbidity and sex as factors and controlling for age Data represented in the table are the estimated marginal means and 95%CI for levels of comorbidity. (*) BDNF concentrations are the back-transformed means and 95% CI from logarithmic data.
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Frequency Change of Clear-Air Turbulence over the North Pacific under 2 K Global Warming – Ensemble Projections Using a 60-km Atmospheric General Circulation Model
Kisho shushi. Dai1shu/Kisho shushi. Dai2shu/Journal of the Meteorological Society of Japan
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Abstract Future changes in the climatological distribution of clear-air turbulence (CAT) and its seasonality over the North Pacific are estimated on the basis of an ensemble of climate projections under warming for the globally averaged surface air temperature of 2 K relative to preindustrial levels, which includes over 3000 years of ensem- bles using a 60 km atmospheric general circulation model (AGCM). The AGCM outputs are interpolated to a 1.25° horizontal resolution, and the climatological CAT frequency is computed. The CAT broadly decreases in the mid- latitude central to western North Pacific along with the anticyclonic (south) side of its present-day high-frequency band extending from Japan to the eastern North Pacific. Meanwhile, large relative increases are found outside the band, implying an increased risk of CAT encounters. Uncertainty in future CAT changes due to uncertainties in the spatial pattern of sea surface temperature (SST) change is addressed for the first time using six selected Coupled Model Intercomparison Project Phase 5 (CMIP5) climate models. The uncertainty is greatest in the boreal winter and spring over the central North Pacific and is associated with an uncertainty in future changes in the jet stream and upper-level synoptic-scale disturbances. Keywords  clear air turbulence; climate change; ensemble projection database Citation  Watanabe, S., M. Fujita, S. Kawazoe, S. Sugimoto, Y. Okada, R. Mizuta, and M. Ishii, 2019: Frequency change of clear-air turbulence over the North Pacific under 2 K Global Warming – Ensemble projections using a 60- km atmospheric general circulation model. J. Meteor. Soc. Japan, 97, 757–771, doi:10.2151/jmsj.2019-038. Meteorological Research Institute of Japan Meteorological Agency, Tsukuba, Japan (Manuscript received 25 September 2018, in final form 9 Febuary 2019) (Manuscript received 25 September 2018, in final form 9 Febuary 2019) 757 757 S. WATANABE et al. une 2019 ournal of the Meteorological Society of Japan, 97(3), 757−771, 2019. doi:10.2151/jmsj.2019-038 Ryo MIZUTA and Masayoshi ISHII Ryo MIZUTA and Masayoshi ISHII rological Research Institute of Japan Meteorological Agency, Tsukuba, Japan Corresponding author: Shingo Watanabe, Japan Agency for Marine-Earth Science and Technology, 3173-25, Showa- machi, Kanazawa-ku, Yokohama, Kanagawa 236-0001, Japan E-mail: wnabe@jamstec.go.jp J-stage Advance Published Date: 13 March 2019 @j g jp J-stage Advance Published Date: 13 March 2019 Corresponding author: Shingo Watanabe, Japan Agency for Marine-Earth Science and Technology, 3173-25, Showa- machi, Kanazawa-ku, Yokohama, Kanagawa 236-0001, Japan E-mail: wnabe@jamstec.go.jp 1.  Introduction Clear-air turbulence (CAT) accompanies vertical airflows greater than or equal to the size of an aircraft, that is, tens to 2000 m. Aircraft often experience CAT in the tropopause region near jet streams, where environmental conditions frequently satisfy those re- quired for Kelvin–Helmholtz instability. Since CAT is not explicitly resolved by current numerical weather Corresponding author: Shingo Watanabe, Japan Agency for Marine-Earth Science and Technology, 3173-25, Showa- machi, Kanazawa-ku, Yokohama, Kanagawa 236-0001, Japan E-mail: wnabe@jamstec.go.jp ©The Author(s) 2019. This is an open access article published by the Meteorological Society of Japan under a Creative Commons Attribution 4.0 International (CC BY 4.0) license (https://creativecommons.org/licenses/by/4.0). Journal of the Meteorological Society of Japan 758 Vol. 97, No. 3 Vol. 97, No. 3 forecast models, several CAT indices have been devel- oped to diagnose the potential for CAT to occur using synoptic or mesoscale grid point parameters output from forecast models (see Sharman et al. (2006) and the references therein). In a recent paper by Kim et al. (2018), they described the latest development of the Global Graphical Turbulence Guidance (G-GTG), which considers CAT and mountain wave turbulence diagnostics. ensemble projection data from 270 years of six-hourly output for each of the six ΔSSTs. For the CAT indices, we select four from the 20 presented by Storer et al. (2017), which showed a striking dissimilarity with each other, to consider future changes in CAT patterns over the North Pacific. The data and methodology are described in Section 2, followed by an analysis of the results in Section 3 and a summary and discussion in Section 4. From a climatological perspective, Jaeger and Sprenger (2007) reported the climatological distri- butions of CAT indices in the Northern Hemisphere tropopause region derived from the ERA-40 reanal- ysis dataset, which was interpolated from a 125 km horizontal resolution to a 1° horizontal resolution, and discussed their relevance to synoptic-scale dynamical and thermal environments (e.g., jet streams and frontal structures near the tropopause). They also discovered an increasing trend in the CAT frequency in the North Atlantic sector. Williams and Joshi (2013) were the first to conduct a study using a coupled atmosphere– ocean climate model to project future changes in the CAT and reported an increase in the CAT in the winter­time North Atlantic sector. Their atmospher- ic model has a horizontal resolution of 2° × 2.5° in latitude and longitude. Later, Storer et al. 2.  Data and methodology In the present study, we use the database for Policy Decision Making for Future Climate Change (d4PDF), produced with a 60 km horizontal resolution AGCM, MRI-AGCM3.2 (Mizuta et al. 2012, 2017). This database includes an ensemble transient historical sim- ulation of the recent past (PAST experiment) and an ensemble time-slice 2 K warming simulation (referred to as the +2 K experiment hereafter). Here, +2 K denotes the 2 K warming of the globally averaged surface air temperature relative to the preindustrial level in the context of the Paris Agreement. See Mizu- ta et al. (2017) and Fujita et al. (2019) for a detailed experimental design. The ensembles are generated by adding small perturbations to the observed (PAST) or detrended (+2 K) SSTs. To capture the uncertainty in future climate change projections arising from differ- ences between models, the AGCM’s +2 K experiment is forced with six different ΔSSTs obtained from se- lected CMIP5 climate model results. These models are abbreviated as CC (CCSM4: Community Climate Sys- tem Model version 4), GF (GFDL-CM3: Geophysical Fluid Dynamics Laboratory Climate Model version 3), HA (HadGEM2-AO: Hadley Centre Global Environ- mental Model version 2 AO), MI (MIROC5: Model for Interdisciplinary Research on Climate version 5), MP (MPI-ESM-MR: Mixed Resolution version of the Max Planck Institute for Meteorology Earth System Model), and MR (MRI-CGCM3: Meteorological Re- search Institute Coupled Atmosphere–Ocean General Circulation Model version 3). Following these earlier studies, in the present paper, we report several new aspects of future changes in the CAT frequency. We focus on the geographical patterns of frequency changes in the North Pacific sector, which have not been addressed in detail in previous climate change studies. Unlike earlier studies that compared climates under the preindustrial and double the preindustrial concentrations of CO2 (Williams and Joshi 2013) or the preindustrial and the late 21st century in the RCP8.5 scenario (Storer et al. 2017), we compare the present-day climate and the climate under 2 K global warming with the preindustrial lev- el. Unlike earlier studies where only a single climate model was considered, we present future CAT changes projected by an atmospheric general circulation model (AGCM) forced with six different SST change pat- terns (ΔSSTs) obtained from CMIP5 climate models. 1.  Introduction (2017) ex- tended this study to estimate the global change in the CAT frequency for all four seasons, as diagnosed by 20 different CAT indices, which were projected using a higher 1.25° × 1.875° horizontal resolution climate model. More recently, Storer et al. (2018) presented a detailed review on aviation turbulence, including its response to climate change. 2.  Data and methodology Averaging these different projections of changes in CAT frequencies diagnosed by different CAT indices may limit our understanding of future changes in aviation risks. Therefore, the present paper focuses on the individual CAT indices. As a first step, we limit the number of CAT indices to the four mentioned above (i.e., TI1, Sv , DEF, and rNBE), which we selected from the 20 con- sidered by Storer et al. (2017). Pacific is considered in detail. In Fig. 2 of Storer et al. (2017), the CAT index associated with the deforma- tion of the horizontal flow (DEF), which potentially leads to the spontaneous generation of gravity waves, increases between 30°N and 50°N in the North Pacific. The magnitude of the residuals of the nonlinear bal- ance equation (rNBE), which is a common diagnostic method for the spontaneous generation of gravity waves (e.g., Zhang et al. 2000; Plougonven and Zhang 2014), increases in the same latitude band as the DEF, but its increase in the western Pacific sector is less pronounced. In contrast, the vertical shear magnitude of the horizontal wind (Sv), which is related to the intensity of the CAT, generally decreases in the North Pacific. Variant 1 of Ellrod’s turbulence index (TI1), which is defined as the product of the DEF and Sv and has been proven to be skillful in capturing pilot- reported CAT (Ellrod and Knapp 1992), increases between latitudes of 30 – 35°N around Japan and the central to eastern North Pacific. Averaging these different projections of changes in CAT frequencies diagnosed by different CAT indices may limit our understanding of future changes in aviation risks. Therefore, the present paper focuses on the individual CAT indices. As a first step, we limit the number of CAT indices to the four mentioned above (i.e., TI1, Sv , DEF, and rNBE), which we selected from the 20 con- sidered by Storer et al. (2017). Table 1. 99.6th percentile values for CAT indices calculat- ed in the North Pacific sector. Table 1. 99.6th percentile values for CAT indices calculat- ed in the North Pacific sector. Table 1. 99.6th percentile values for CAT indices calculat- ed in the North Pacific sector. CAT indices in the individual simulations are calcu- lated using nine ensemble simulations with 30 years of six-hourly data, which consists of about 10 5 time steps per season at each grid point. 2.  Data and methodology This is one or two orders of magnitude greater than in previous studies. The larger time steps provide a smoother geographical distribution of CAT frequency and a more reliable es- timation of its future change. g Following Williams (2017), the probability distri- bution of the magnitude of the CAT indices sampled over the target period and the grid points involved in the target horizontal domain are calculated, and the threshold values for the severity classes of the CAT are obtained accordingly. As stated by Storer et al. (2017), moderate or greater (MOG) CAT is defined as values exceeding the 99.6th percentile for each CAT index over the entire 270 years of PAST experimental ensembles, and the same threshold value is applied to the +2 K experiment to diagnose the occurrence of MOG CAT. Table 1 shows the threshold values for the four CAT indices, which are larger than those in ear- lier studies based on lower-resolution climate model data (e.g., Williams 2017). These threshold values are only valid for a particular model and spatial resolu- tion. The present study focuses on the climatological frequency of MOG CAT, which is represented as a percentage, that is, 100 × (number of MOG CAT)/(total time steps). These calculations are conducted at each grid point for four seasons, that is, December–Febru- ary (DJF), March–May (MAM), June–August (JJA), and September–November (SON), each of which in- cludes about 360 time steps per year. By definition, a CAT frequency of around 0.28 % (1/360) corresponds to a single occurrence of a MOG CAT event at the 200 hPa level in a season. We investigate the relative change in the PAST and +2 K experimental data to understand the response of the CAT frequency to cli- mate change. By definition, Sv , DEF, and rNBE are independent of each other, whereas TI1 is correlated with Sv and DEF. These CAT indices are calculated for the 200 hPa level, using the last 30 years of PAST and +2 K experimental results for d4PDF. 2.  Data and methodology Unlike earlier studies where 20 years of daily means or 30 years of six-hourly output were used, we use The present study uses six-hourly instantaneous three-dimensional horizontal winds in the upper tro- posphere–lower stratosphere levels, which are inter- polated to a 1.25° horizontal resolution to reduce the data volume. The target domain, the North Pacific sector, is defined as 30 – 75°N and 120°E – 120°W and covers the main North Pacific flight routes and some of the domestic flight routes over Japan (Fig. 1). This domain contains 37 × 97 = 3,589 grid points. Here, the disagreement among the changes in the projected patterns of the CAT indices in the North 759 June 2019 June 2019 S. WATANABE et al. Fig. 1. Climatological distribution of CAT frequency at 200 hPa in the PAST experiment as diagnosed by TI1, Sv , DEF, and rNBE (from top to bottom) in DJF, MAM, JJA, and SON (from left to right), respectively. Journal of the Meteorological Society of Japan 760 Vol. 97, No. 3 Vol. 97, No. 3 Table 1. 99.6th percentile values for CAT indices calculat- ed in the North Pacific sector. CAT index TI1 (10 −9 s −2) Sv (10 −3 s −1) DEF (10 −6 s −1) rNBE (10 −12 s −2) 99.6 percentile 833.3 10.7 116.7 8750 Pacific is considered in detail. In Fig. 2 of Storer et al. (2017), the CAT index associated with the deforma- tion of the horizontal flow (DEF), which potentially leads to the spontaneous generation of gravity waves, increases between 30°N and 50°N in the North Pacific. The magnitude of the residuals of the nonlinear bal- ance equation (rNBE), which is a common diagnostic method for the spontaneous generation of gravity waves (e.g., Zhang et al. 2000; Plougonven and Zhang 2014), increases in the same latitude band as the DEF, but its increase in the western Pacific sector is less pronounced. In contrast, the vertical shear magnitude of the horizontal wind (Sv), which is related to the intensity of the CAT, generally decreases in the North Pacific. Variant 1 of Ellrod’s turbulence index (TI1), which is defined as the product of the DEF and Sv and has been proven to be skillful in capturing pilot- reported CAT (Ellrod and Knapp 1992), increases between latitudes of 30 – 35°N around Japan and the central to eastern North Pacific. 3.2  Changes in +2 K climate 3.2  Changes in +2 K climate Figure 5 shows the horizontal distribution of the percentage change of the CAT frequency diagnosed by the TI1 in the +2 K experiment with the six CMIP5 ΔSSTs, relative to the PAST experiment, that is, 100 × (+2 K − PAST)/PAST. Figures 6, 7, and 8 show a similar percentage change in the distributions of Sv , DEF, and rNBE, respectively. First, we overview the characteristic morphology of the change in the projected patterns. For TI1 and Sv , the most prominent feature is a decrease of over 25 % in the midlatitude central to western North Pacific along with the anticy- clonic (south) side of the present-day maximum (Figs. 5, 6). In contrast, the DEF and rNBE show a broad increase of 25 – 100 % in the eastern North Pacific, which is outside the present-day high-frequency band (Figs. 7, 8). Large relative increases are commonly seen for all CAT indices surrounding the present-day envelope of the CAT frequency maximum (e.g., sub- tropical, coastal, and continental regions). To allow a more practical evaluation of these large relative increases, which may be exaggerated by the relatively low frequency observed in the PAST experiment, the light (dark) gray shading in Figs. 5 – 8 indicates regions where the CAT frequency diagnosed by each index is less than 0.1 % (0.01 %) in the +2 K experi- ment, roughly corresponding to once every three (30) years. The CAT frequency diagnosed by the four indices shows a distinct seasonal variation; TI1 and Sv peak in the boreal spring and autumn and have their minima in the summer, whereas the DEF (rNBE) peaks in the summer (winter). The seasonal variations in TI1 and Sv in the PAST experiment seem to be associated with variations in the activity of upper-level synoptic-scale disturbances, which are diagnosed by the eddy kinetic energy (EKE) due to the 2 – 8-day component at the same 200 hPa level (Fig. 3). We define EKE as 0.5 (u¢ 2 + v ¢ 2), the 2 – 8-day eastward and northward wind components are extracted using a temporal filter following Inatsu and Hoskins (2004). Here, we assume that EKE cascades into turbulence through a wide variety of processes around the meandering jet- front system. TI1 and Sv have broad peaks coinciding with the cyclonic side of the EKE maximum, which migrates northward from DJF to SON. 2.  Data and methodology Sv is calculated by combining the vertical finite differences among the 150, 200, and 250 hPa horizontal winds as Sv u u z z u u z z v = ( )     − − + − − + 1 2 1 2 150 200 150 200 200 250 200 250 2 150− − + − − ( )     v z z v v z z 200 150 200 200 250 200 250 2 , where the subscripts denote the pressure levels and u, v, and z denote the eastward wind component, the northward wind component, and the log-pressure height, respectively. The coarse vertical resolution prohibits the exact estimation of Sv above and below the jet axis, a common deficiency when using pressure level outputs from AGCM and global reanalysis products. Sv u u z z u u z z v = ( )     − − + − − + 1 2 1 2 150 200 150 200 200 250 200 250 2 150− − + − − ( )     v z z v v z z 200 150 200 200 250 200 250 2 , where the subscripts denote the pressure levels and u, v, and z denote the eastward wind component, the northward wind component, and the log-pressure height, respectively. The coarse vertical resolution prohibits the exact estimation of Sv above and below the jet axis, a common deficiency when using pressure level outputs from AGCM and global reanalysis products. To reduce the uncertainty in the projections aris- ing from natural climate variability, nine ensemble members of the PAST experiment are used in the cal- culation of the CAT indices. Similarly, nine ensemble members from the +2 K experiment are used for each of the six ΔSST patterns. Thus, the time series of the The climatological CAT frequency at each grid point is derived from the PAST experimental ensem- ble (270 years) and the +2 K experimental ensembles forced by the six ΔSSTs (6 × 270 years), respectively. The horizontal distribution of the climatological CAT frequency in the PAST experimental ensemble cal- S. WATANABE et al. 761 June 2019 synoptic-scale disturbances are reproduced by the 60 km resolution AGCM, which is an advantage of using the d4PDF to study the CAT in this region. 2.  Data and methodology The wintertime peak rNBE band extends from Japan to the eastern North Pacific and migrates northward from DJF to SON. rNBE is closely related to the spontaneous generation of gravity waves in the jet- front system (e.g., Zhang et al. 2000; Plougonven and Zhang 2014), and its seasonal variation is strongly associated with the strength and location of the subtropical jet (Fig. 4). In addition, divergent flows associated with large-scale mountain waves enlarge the rNBE, generating hot spots over mountains. Be- cause the accuracy of the resolved mountain waves in the AGCM is limited because of its horizontal resolution and the downsampling (i.e., 1.25° by 1.25°), we avoid discussions on future changes in rNBE over land. culated as above is validated against that calculated using 30 years (from 1 December 1979 to 30 Novem- ber 2009) of the Japanese 55-year Reanalysis (JRA- 55) data (Kobayashi et al. 2015; Harada et al. 2016). The AGCM used in JRA-55 has the same 60 km hori- zontal resolution as that used in the present study, and the outputs are interpolated to the same 1.25° horizon- tal resolution (Japan Meteorological Agency 2013). culated as above is validated against that calculated using 30 years (from 1 December 1979 to 30 Novem- ber 2009) of the Japanese 55-year Reanalysis (JRA- 55) data (Kobayashi et al. 2015; Harada et al. 2016). The AGCM used in JRA-55 has the same 60 km hori- zontal resolution as that used in the present study, and the outputs are interpolated to the same 1.25° horizon- tal resolution (Japan Meteorological Agency 2013). 3.1  Present-day climatology of CAT distributions Figures 1 and 2 compare the climatological seasonal evolution of the CAT frequency at 200 hPa diagnosed by the TI1, Sv , DEF, and rNBE derived from the PAST experiment and JRA-55, respectively. The geograph- ical distributions of the CAT frequency in the PAST experiment generally agree with those in JRA-55 and are smoother owing to the larger sample size. The TI1 distribution shown here qualitatively agrees with that shown by Jaeger and Sprenger (2007), although some differences are apparent since they analyzed a longer period and included multiple altitudes near the tropo- pause. 3.  Results 3.1  Present-day climatology of CAT distributions 3.2  Changes in +2 K climate In particular, Sv exhibits a maximum in the midlatitude central to eastern North Pacific where synoptic-scale meander- ing of the jet stream frequently occurs. In contrast, the DEF peaks over the subtropical western North Pacific and aligns with the cyclonic side of the subtropical jet (Fig. 4). It is revealed from a six-hourly diagnosis that the DEF shows a distinct peak in the summer over Japan and further downstream in the jet stream, because of the frequent passage of sub-synoptic-scale disturbances associated with the Baiu front accompa- nying large DEF and relatively small Sv. These sub- There are several interesting features in the season- ality of the projected CAT change and its dependency on the SST change. The most striking ΔSST depen- dency can be found in DJF, when two or three of the six ΔSST ensembles, depending on the index, project 762 Vol. 97, No. 3 Journal of the Meteorological Society of Japan Fig. 2. Same as Fig. 1 but for JRA-55 data. Fig. 2. Same as Fig. 1 but for JRA-55 data. 763 S. WATANABE et al. June 2019 Fig. 3. Top row: climatological distribution of EKE at 200 hPa (EKE200) at synoptic scales (2 – 8 days) in the PAST experiment for DJF, MAM, JJA, and SON (from left to right), respectively. Second to seventh rows: future changes in EKE200 in +2 K ensembles forced by six different ΔSSTs (see Section 2). Contours al distribution of EKE at 200 hPa (EKE200) at synoptic scales (2 – 8 days) in the PAST experiment for DJF, MAM, JJA, and SON vely. Second to seventh rows: future changes in EKE200 in +2 K ensembles forced by six different ΔSSTs (see Section 2). Contours bl Fig. 3. Top row: climatological distribution of EKE at 200 hPa (EKE200) at synoptic scales (2 – 8 days) in the PAST experiment for DJF, MAM, JJA, and SON (from left to right), respectively. Second to seventh rows: future changes in EKE200 in +2 K ensembles forced by six different ΔSSTs (see Section 2). Contours show EKE200 in +2 K ensembles. Journal of the Meteorological Society of Japan 764 Vol. 97, No. 3 Fig. 4. Same as Fig. 3 but for 200 hPa horizontal wind speed. Fig. 4. Same as Fig. 3 but for 200 hPa horizontal wind speed. S. WATANABE et al. June 2019 765 . 5. 4.  Summary and discussion The climatological distribution and future changes of CAT over the North Pacific have been investigated using the PAST and +2 K ensembles in the d4PDF. The present-day climatology of the CAT distribution at 200 hPa and its seasonality derived from the PAST experiment in d4PDF agree with those for the JRA-55 data. The CAT frequency in the +2 K experiment decreases in the midlatitude central to western North Pacific along with the anticyclonic side of its present- day maximum, whereas it increases outside the present-day high-frequency band. This decrease is one of the key findings in the present study that has not been uncovered in previous studies based on different models and combinations of present and future sce- narios, as well as the selection of CAT indices (Storer et al. 2017). g p The inter-ΔSST variation of the projected change in the CAT frequency in MAM is smaller than that in DJF, but larger than that in JJA and SON. Three of the six ensemble members project a reduction of over 25 % for TI1 and Sv near Japan, and two of them project an increase in the frequency in the central North Pacific. An increase in TI1 of more than 25 – 50 % over Japan is projected only in JJA, whereas TI1 is projected to decrease (increase) in the northern (southern) part of Japan and further downstream in the jet stream in SON. Wider reductions (increases) are commonly seen in the six ΔSSTs for Sv (DEF and rNBE) in JJA and SON. Interestingly, despite the small inter-ΔSST variation for all CAT indices in these seasons, the future changes in the jet stream (represented by the 200 hPa wind speed |V |) and the activity of upper-level synoptic-scale disturbances (represented by the 200 hPa EKE with 2 – 8-day com- ponents) show a relatively large variation depending on ΔSST (Figs. 3, 4). The reason for this is unclear and is left for future studies. On the other hand, the inter-ΔSST variation of |V | and EKE sometimes coincides with that of the CAT indices. For example, the largest changes in the CAT indices in DJF for one ΔSST ensemble (+2 K_MI) might be attributable to the largest poleward shift of the jet stream and associ- ated enhancement of synoptic-scale disturbances over the North Pacific. 3.2  Changes in +2 K climate In the eastern Pacific, DEF and rNBE show a similar increase in DJF to that shown by Storer et al. (2017), except that their DEF shows a wider extension. Because the present result shows a large inter-ΔSST variation in DJF, the differences between the two studies may also be related to differences in SST change patterns. a broad increase in the CAT frequency near the Aleu- tian Low. Another interesting feature in DJF is that Sv and DEF, whose future changes are not positively correlated in the other three seasons, both decrease near Japan and further downstream in the jet stream. Indeed, future changes in these two indices are not as strongly correlated with each other in individual ΔSST ensembles, whereas their product, TI1, shows a robust reduction among all ΔSSTs. This future decrease in the CAT frequency in TI1 near Japan is not consistent with the results of Storer et al. (2017), which showed increases in all four indices (i.e., TI1, Sv , DEF, and rNBE). In the eastern Pacific, DEF and rNBE show a similar increase in DJF to that shown by Storer et al. (2017), except that their DEF shows a wider extension. Because the present result shows a large inter-ΔSST variation in DJF, the differences between the two studies may also be related to differences in SST change patterns. changes to changes in the climatological distribution of the jet stream and activity of upper-level synoptic- scale disturbances. 3.2  Changes in +2 K climate Top row: climatological distribution of CAT frequency at 200 hPa in the PAST experiment diagnosed by TI1 in DJF, MAM, JJA, and SON (from left to right), respectively. Second to seventh rows: future changes in +2 K ensembles forced by six different ΔSSTs (see Section 2), displayed as relative changes in percent: 100 × (+2 K − PAST)/PAST. The light- and dark-gray shading indicate regions where the CAT frequency in the 2 K ensembles is less than 0.1 % and 0.01 %, respectively. The black shading indicates grid boxes where no CAT is diagnosed throughout the analysis period (270 years) either in the PAST or in the +2 K experiment. Fig. 5. Top row: climatological distribution of CAT frequency at 200 hPa in the PAST experiment diagnosed by TI1 in DJF, MAM, JJA, and SON (from left to right), respectively. Second to seventh rows: future changes in +2 K ensembles forced by six different ΔSSTs (see Section 2), displayed as relative changes in percent: 100 × (+2 K − PAST)/PAST. The light- and dark-gray shading indicate regions where the CAT frequency in the 2 K ensembles is less than 0.1 % and 0.01 %, respectively. The black shading indicates grid boxes where no CAT is diagnosed throughout the analysis period (270 years) either in the PAST or in the +2 K experiment. Journal of the Meteorological Society of Japan 766 Vol. 97, No. 3 Fig. 6. Same as Fig. 5 but for Sv . 767 S. WATANABE et al. June 2019 Fig. 7. Same as Fig. 5 but for DEF. Journal of the Meteorological Society of Japan 768 Vol. 97, No. 3 Fig. 8. Same as Fig. 5 but for rNBE. S. WATANABE et al. June 2019 769 a broad increase in the CAT frequency near the Aleu- tian Low. Another interesting feature in DJF is that Sv and DEF, whose future changes are not positively correlated in the other three seasons, both decrease near Japan and further downstream in the jet stream. Indeed, future changes in these two indices are not as strongly correlated with each other in individual ΔSST ensembles, whereas their product, TI1, shows a robust reduction among all ΔSSTs. This future decrease in the CAT frequency in TI1 near Japan is not consistent with the results of Storer et al. (2017), which showed increases in all four indices (i.e., TI1, Sv , DEF, and rNBE). 2017). models. Geophys. Res. Lett., 46, 435–442. models. Geophys. Res. Lett., 46, 435–442. ) The present study focused on the climatological distribution of the CAT frequency and the projected changes for four seasons over the North Pacific. 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Japan Meteorological Agency, 2013: JRA-55 product users’ handbook: 1.25-degree latitude/longitude grid data. 22 pp. [Available at http://jra.kishou.go.jp/JRA-55/ index_en.html.] Acknowledgments The authors would like to thank two anonymous reviewers and journal editors for providing helpful comments and suggestions. The authors were support- ed by the Social Implementation Program on Climate Change Adaptation Technology (SI-CAT), MEXT, Japan. This study utilized the database for Policy Decision Making for Future Climate Change (d4PDF), which was produced using the Earth Simulator of JAMSTEC as a “Strategic Project with Special Sup- port” and with support from the Program for Risk Information on Climate Change (SOUSEI), the Social Implementation Program on Climate Change Adap- tation Technology (SI-CAT), the Integrated Research Program for Advancing Climate Models (TOUGOU) and the Data Integration and Analysis System (DIAS), all of which were sponsored by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. Kim, J.-H., W. N. Chan, B. Sridhar, R. D. Sharman, P. D. Williams, and M. Strahan, 2016: Impact of the North Atlantic Oscillation on transatlantic flight routes and clear-air turbulence. J. Appl. Meteor. Climatol., 55, 763–771. Kim, J.-H., R. Sharman, M. Strahan, J. W. Scheck, C. Bartholomew, J. C. H. Cheung, P. Buchanan, and N. Gait, 2018: Improvements in nonconvective aviation turbulence prediction for the world area forecast system. Bull. Amer. Meteor. Soc., 99, 2295–2311. Kobayashi, S., Y. Ota, Y. Harada, A. Ebita, M. Moriya, H. Onoda, K. Onogi, H. Kamahori, C. Kobayashi, H. Endo, K. Miyaoka, and K. Takahashi, 2015: The JRA- 55 Reanalysis: General specifications and basic char- acteristics. J. Meteor. Soc. Japan, 93, 5–48. Mizuta, R., H. Yoshimura, H. Murakami, M. Matsueda, H. Endo, T. Ose, K. Kamiguchi, M. Hosaka, M. Sugi, S. Yukimoto, S. Kusunoki, and A. Kitoh, 2012: Climate simulations using MRI-AGCM3.2 with 20-km grid. J. Meteor. Soc. Japan, 90A, 233–258. 4.  Summary and discussion A similar example is found in MAM for another ΔSST ensemble (+2 K_CC) that shows a unique large reduction in the activity of synoptic-scale disturbances, which leads to common reductions in all CAT indices. These examples demonstrate the possi- bilities and limitations in attributing CAT frequency The uncertainty in the projected CAT changes due to the ΔSST patterns from six selected CMIP5 climate models has been addressed for the first time. The un- certainty is maximized in the boreal winter and spring over the central North Pacific and is associated with uncertainties in future changes in the jet stream and the activity of upper-level synoptic-scale disturbances. Meanwhile, the inter-ΔSST variation of CAT changes is minimized in SON, and a robust reduction of the CAT frequency is projected in the midlatitude central to western North Pacific. The relative increase of the CAT frequency outside the present-day high-frequency envelope may also have implications for aircraft operations, because air- craft may experience CAT in different locations other than the ones at present. Two of the CAT indices, DEF and rNBE, show a remarkably broad increase over the eastern North Pacific, which may imply more frequent and spontaneous generation of small-scale gravity waves. The increase in the CAT frequency over the southern part of Japan and around the Bering Sea may also affect future aircraft operations. Future studies should investigate the model and scenario dependency of the findings in the present study. The High Reso- lution Model Intercomparison Project (HighResMIP) would provide the first opportunity to estimate these dependencies (Haarsma et al. 2016). The most serious limitation of the present study is the number of CAT indices considered, and these calculations should be repeated in future work using all 20 indices used in previous works (e.g. Williams 2017; Storer et al. Journal of the Meteorological Society of Japan Journal of the Meteorological Society of Japan 770 Vol. 97, No. 3 Vol. 97, No. 3 2017). References Mizuta, R., A. Murata, M. Ishii, H. Shiogama, K. Hibino, N. Mori, O. Arakawa, Y. Imada, K. Yoshida, T. Aoyagi, H. Kawase, M. Mori, Y. Okada, T. Shimura, T. Naga­ tomo, M. Ikeda, H. Endo, M. Nosaka, M. Arai, C. Takahashi, K. Tanaka, T. Takemi, Y. Tachikawa, K. Temur, Y. Kamae, M. Watanabe, H. Sasaki, A. Kitoh, I. Takayabu, E. Nakakita, and M. Kimoto, 2017: Over 5,000 years of ensemble future climate simulations by 60-km global and 20-km regional atmospheric models. Ellrod, G. P., and D. I. Knapp, 1992: An objective clear- air turbulence forecasting technique: Verification and operational use. Wea. Forecasting, 7, 150–165. Fujita, M., R. Mizuta, M. Ishii, H. Endo, T. Sato, Y. Okada, S. Kawazoe, S. Sugimoto, K. Ishihara, and S. Watanabe, 2019: Precipitation changes in a climate with 2-K surface warming from large ensemble simulations by 60-km global and 20-km regional atmospheric S. WATANABE et al. 771 June 2019 June 2019 Storer, L. N., P. D. Williams, and M. M. Joshi, 2017: Global response of clear-air turbulence to climate change. Geophys. Res. Lett., 44, 9976–9984. Bull. Amer. Meteor. Soc., 98, 1383–1398. Murata, A., H. Sasaki, M. Hanafusa, and K. Kurihara, 2013: Estimation of urban heat island intensity using biases in surface air temperature simulated by a nonhydro- static regional climate model. Theor. Appl. Climatol., 112, 351–361. Storer, L. N., P. D. Williams, and P. G. Gill, 2018: Aviation turbulence: Dynamics, forecasting, and response to climate change. Pure Appl. Geophys., doi:10.1007/ s00024-018-1822-0. Plougonven, R., and F. Zhang, 2014: Internal gravity waves from atmospheric jets and fronts. Rev. Geophys., 52, 33–76. Williams, P. D., 2017: Increased light, moderate, and severe clear-air turbulence in response to climate change. Adv. Atmos. Sci., 34, 576–586.i Sasaki, H., A. Murata, M. Hanafusa, M. Oh’izumi, and K. Kurihara, 2011: Reproducibility of present climate in a non-hydrostatic regional climate model nested within an atmosphere general circulation model. SOLA, 7, 173–176. Williams, P. D., and M. M. Joshi, 2013: Intensification of winter transatlantic aviation turbulence in response to climate change. Nat. Climate Change, 3, 644–648. Zhang, F., S. E. Koch, C. A. Davis, and M. L. Kaplan, 2000: A survey of unbalanced flow diagnostics and their applications. Adv. Atmos. Sci., 17, 165–183. Sharman, R., C. Tebaldi, G. Wiener, and J. Wolff, 2006: An integrated approach to mid- and upper-level turbu- lence forecasting. Wea. Forecasting, 21, 268–287.
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Microvascular Reactivity Measured by Dynamic Near-infrared Spectroscopy Following Induction of General Anesthesia in Healthy Patients: Observation of Age-related Change
International journal of medical sciences
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Abstract Background: The purpose of this study was to investigate the effect of general anesthesia on microvascular reactivity and tissue oxygen saturation (StO2) using near-infrared spectroscopy in conjunction with vascular occlusion tests (VOT). Age-related changes of microvascular reactivity, that is, the capacity of capillary recruitment, were examined. Methods: This prospective observational study was performed on 60 patients without comorbidities who underwent elective surgery under general anesthesia. Baseline StO2 on thenar eminence, hemodynamics, and laboratory profile were monitored before (T0) and 30 min after general anesthesia (T1). During VOT, occlusion slope representing oxygen consumption of muscle and recovery slope representing microvascular reactivity were also collected at T0 and T1. Results: Baseline StO2 and minimum / maximum StO2 during VOT increased under general anesthesia. Occlusion slope decreased while the recovery slope increased under general anesthesia. To observe aging effect, Receiver operating characteristic analysis was performed and age less than 65 years old showed a fair performance in predicting the increase of microvascular reactivity after the induction of anesthesia (AUC 0.733, 95% CI 0.594-0.845, P= 0.003). For age-related analyses, 27 patients of younger group (< 65 years) and 26 patients of older group (≥ 65 years) were divided. Recovery slope significantly increased under general anesthesia in younger group (2.44 [1.91-2.81] % ∙ sec-1 at T0 and 3.59 [2.58-3.51] % ∙ sec-1 at T1, P <0.001), but not in older group (2.61 [2.21-3.20] % ∙ sec-1 at T0, 2.63 [1.90-3.60] % ∙ sec-1 at T1, P = 0.949). Conclusions: General anesthesia could improve StO2 through increase of microvascular reactivity and decrease of tissue metabolism. However, microvascular reactivity to capillary recruitment under general anesthesia significantly improves in younger patients, not in older patients. Key words: Aging; cardiovascular physiology; anesthesia, inhalation; microcirculation; spectroscopy, near-infrared Microvascular Reactivity Measured by Dynamic Near-infrared Spectroscopy Following Induction of General Anesthesia in Healthy Patients: Observation of Age-related Change Ah-Reum Cho1,2, Hyeon-Jeong Lee1,2, Hyae-Jin Kim1, Wangseok Do1, Soeun Jeon1, Seung-Hoon Baek1,2, Eun-Soo Kim1,2, Jae-Young Kwon1,2, Hae-Kyu Kim1,2 1. Department of Anesthesia and Pain Medicine, Medical Research Institute, Pusan National University Hospital, Busan, Republic of Korea. 2. Department of Anesthesia and Pain Medicine, Pusan National University, School of Medicine, Yangsan, Republic of Korea  Corresponding author: Hyeon-Jeong Lee, Department of Anesthesia and Pain Medicine and Medical Research Institute, Pusan National University Hospital, Gudeok-ro 179, Seo-gu, Busan, 49241, Republic of Korea. Tel: 82-51-240-7399; Fax: 82-51-242-7466; E-Mail: lhjksk@pusan.ac.kr © The author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2020.08.26; Accepted: 2020.12.18; Published: 2021.01.01 Ivyspring International Publisher Ivyspring International Publisher International Journal of Medical Sciences 2021; 18(5): 1096-1103. doi: 10.7150/ijms.52433 1096 1096 Int. J. Med. Sci. 2021, Vol. 18 Ivyspring International Publisher General anesthesia In the operating room, standard monitoring including electrocardiography, non-invasive blood pressure (NIBP) monitors, and pulse oximetry were used. Skin temperature probes (400 series, GE Healthcare, Helsinki, Finland) were placed on the right palm. The operating room temperature was maintained at 22-24°C. Skin temperature was measured before and after induction of anesthesia. General anesthesia was induced with propofol 1.5 - 2 mg ∙ kg-1 and a continuous infusion of remifentanil 0.2 μg ∙ kg-1 ∙ min-1. After injection of rocuronium 0.8 mg ∙ kg-1, tracheal intubation was performed and mechanical ventilation was applied with an inspired oxygen fraction of 0.5, a tidal volume of 8 ml ∙ kg-1, and a respiratory rate adjusted to maintain end-tidal CO2 of 30-35 mmHg. General anesthesia was maintained with desflurane and remifentanil to maintain a bispectral index (BIS; Bispectral Index™, Aspect Medical System, Norwood, MA, USA) of 40-50 and hemodynamic parameters within 20% of the baseline values. Hartman’s solution was infused during the study period at the rate of 5 ml ∙ kg-1 ∙ h-1. Under general anesthesia, blood samples were collected to measure the serum lactate level. Owing to near-infrared spectroscopy (NIRS) technology, the detection of microcirculatory dysfunction has become easier and non-invasive. Many studies have shown that the dynamic NIRS parameters that can be measured with a brief ischemic challenge are clinically more useful than static tissue oxygen saturation (StO2) values [10,13-15]. A vascular occlusion test (VOT) is a method of observing the change in StO2 after applying a tourniquet with a higher pressure than the patient’s systolic blood pressure. The StO2 reduction rate (occlusion slope) during the ischemic period reflects oxygen extraction. The rate of StO2 increase (recovery slope) during reperfusion after the release of the vascular occlusion reflects microvascular reactivity [10,13,14]. The purpose of this study was to investigate the effect of anesthetics on microvascular reactivity and StO2 using near-infrared spectroscopy in conjunction with VOT. Age-related changes of microvascular reactivity, which means the capacity of capillary recruitment, were focused. Vascular occlusion test (VOT) VOT was performed twice for each patient, before (T0) and 30 min after the induction of general anesthesia (T1). Before induction, a NIRS sensor (INVOSTM 5100C Cerebral/Somatic Oximeter; Medtronic, Minneapolis, MN, USA) was placed on the thenar eminence and an automated tourniquet (A.T.S® 3000 Automatic Tourniquet System; Zimmer Inc., Warsaw, IL, USA) was placed around the ipsilateral upper arm. A NIBP was placed around the contralateral upper arm and the baseline blood pressure was measured. When the baseline StO2 was stabilized, the automatic tourniquet was inflated to 50 mmHg over the patient’s baseline systolic blood pressure and maintained for 5 min. After the 5 min ischemic period, the tourniquet was rapidly deflated to 0 mmHg. StO2 data were continuously recorded during the VOT procedure. Baseline StO2, minimum StO2 during the 5 min inflation of the tourniquet, time to minimum StO2, maximum StO2 during deflation of Introduction should identify therapeutic targets for functional microcirculatory restoration to prevent organ failure [3]. Microcirculatory function is impaired in a number of pathologies, including sepsis [4], diabetes mellitus Microcirculatory dysfunction and impaired tissue perfusion may persist even if systemic hemodynamic variables are optimized and within the therapeutic target [1,2]. This suggests that clinicians http://www.medsci.org 1097 Int. J. Med. Sci. 2021, Vol. 18 [5], shock [6,7], aging [8], and smoking [9]. However, research on the effects of anesthetics on microcirculatory function has begun only recently, and the results are still inconsistent [10,11]. One study reported that general anesthesia has a negative impact on reperfusion reserve [10]. Another study showed that general anesthesia increases the recovery slope, suggesting improvement of tissue microvascular reactivity and peripheral vasodilation [11]. As patients with microcirculatory dysfunction due to various underlying diseases were included in previous studies, inconsistent outcomes may have occurred. To accurately determine the effect of anesthetic agents on microvascular reactivity, patients without comorbidities must be studied. Moreover, age could also be an important consideration in studies on microcirculatory function, even in healthy subjects [12]. classification > II, age < 18 or > 80 years, body mass index > 30 kg m-2, disorders likely to influence microcirculation (uncontrolled hypertension, diabetes, peripheral vascular disease, or chronic venous insufficiency), pregnancy, smoking, sleep apnea, history of chronic obstructive and restrictive pulmonary disease, contraindications for anesthetic agents, or refusal to participate in the investigation. Results A total of 60 patients were enrolled in this study. Seven patients were excluded due to protocol violation. Demographic and intraoperative characteristics are summarized in Table 1. Statistical analysis Patient’s characteristics and hemodynamic variables of patients with and without the increase of recovery slope under general anesthesia are shown in Table 1. Patients whose recovery slope increased under general anesthesia were significantly younger than those whose recovery slope did not increase (P=0.013). The area under the ROC curve for age to predict the increase of recovery slope after the induction of anesthesia was 0.733 (Fig. 1, P = 0.003; 95% CI 0.594 - 0.845). If age was lower than 65 years old, the increase of recovery slope under general anesthesia was predicted with a sensitivity of 85.7% and a specificity of 61.1%. The primary outcome of this study was the difference of the recovery slope of the VOT after the induction of general anesthesia. According to our pilot study performed prior to this investigation, mean difference of recovery slope of 0.28 % ∙ sec-1 with SD of 0.72 % ∙ sec-1 was obtained. A sample size of 54 patients was necessary to gain a power of 80%, by using a Wilcoxon signed rank test with a two-sided significance level of five. Considering a drop-out rate of 10%, a total of 60 patients were required. Data are expressed as number (proportion), median [IQR], or mean (SD). All continuous variables were tested for normality assumption with a Q-Q plot and Kolmogorov-Smirnov test. StO2 values during VOT at T0 and T1 were compared with repeated measures ANOVA with a Bonferroni post hoc test. A paired t-test or Wilcoxon signed rank test was used to analyze differences in the hemodynamic variables and VOT-derived measurements between T0 and T1. Data collection Preoperative hemoglobin concentration was obtained. Mean blood pressure (MBP), heart rate (HR), pulsed oxygen saturation (SpO2), skin temperature, and VOT-derived measurements, including baseline StO2, occlusion slope, minimum StO2, time to minimum StO2, recovery slope, maximum StO2, and time to maximum StO2 were recorded at T0 and T1. Serum lactate level was measured at T1. Patients This study was approved by the Institutional Review Board of Pusan National University Hospital (IRB no. 1607-012-054, Busan, South Korea) and written informed consent was obtained from all subjects participating in the trial. The trial was registered prior to patient enrolment at clinicaltrials.gov (NCT03060798, Hyeon-Jeong Lee: February 19, 2017). This manuscript adheres to the applicable STROBE statements. pp Sixty adult patients who were referred for elective surgery under general anesthesia participated in this study. Exclusion criteria were an American Society of Anesthesiologists (ASA) physical status http://www.medsci.org Int. J. Med. Sci. 2021, Vol. 18 1098 analyses, patients were divided at 65 years old; 27 patients of younger group (< 65 years) and 26 patients of older group (≥ 65 years). An unpaired student t test or Mann-Whitney U test was used to analyze differences in the hemodynamic variables and VOT-derived measurements between the age groups. A P-value < 0.05 was considered significant. All statistical analyses were performed using PASW Statistics for Windows, Version 18.0 (SPSS Inc., Chicago, IL, USA) and MedCalc for Windows, version 13.2 (MedCalc Software, Ostend, Belgium). analyses, patients were divided at 65 years old; 27 patients of younger group (< 65 years) and 26 patients of older group (≥ 65 years). An unpaired student t test or Mann-Whitney U test was used to analyze differences in the hemodynamic variables and VOT-derived measurements between the age groups. the tourniquet, and time to maximum StO2 were obtained. The occlusion slope and recovery slope, which are VOT-derived dynamic parameters related to microcirculatory reactivity, were calculated based on the measured StO2 data. The occlusion slope was defined as the slope of StO2 descent to the lowest value. The recovery slope was calculated from deflation of the tourniquet until the recovery of StO2 to the highest value. A P-value < 0.05 was considered significant. All statistical analyses were performed using PASW Statistics for Windows, Version 18.0 (SPSS Inc., Chicago, IL, USA) and MedCalc for Windows, version 13.2 (MedCalc Software, Ostend, Belgium). Effects of general anesthesia on VOT-derived parameters and hemodynamic variables If age was lower than 65 years old, the increase of recovery slope under general anesthesia was predicted with a sensitivity of 85.7% and a specificity of 61.1%. Effects of general anesthesia on VOT-derived parameters and hemodynamic variables Younger (< 65 years) (n = 27) Older (≥ 65 years) (n = 26) P value Endoscopic sinus surgery 14 (51.9) 3 (11.5) Lactate; mg.l-1 0.87 [0.78-1.18] 1.18 [0.78-1.58] 0.296 Hemoglobin; g.dl-1 13.9 (1.6) 13.0 (1.2) 0.031 Fluid administration; ml 176.4 (31.2) 165.4 (27.8) 0.278 Data are number (proportion), mean (SD) or median [IQR]. Younger (< 65 years) (n = 27) Older (≥ 65 years) (n = 26) P value Endoscopic sinus surgery 14 (51.9) 3 (11.5) Lactate; mg.l-1 0.87 [0.78-1.18] 1.18 [0.78-1.58] 0.296 Hemoglobin; g.dl-1 13.9 (1.6) 13.0 (1.2) 0.031 Fluid administration; ml 176.4 (31.2) 165.4 (27.8) 0.278 Data are number (proportion), mean (SD) or median [IQR]. [2.58-3.51] % ∙ sec-1 in the younger group and 2.63 [1.90-3.60] % ∙ sec-1 in the older group, P = 0.047). MBP significantly increased and HR and skin temperature significantly decreased under general anesthesia in both groups. However, there were no differences in MBP, HR, SpO2, and skin temperatures between two age groups. surgery Lactate; mg.l-1 0.87 [0.78-1.18] 1.18 [0.78-1.58] 0.296 Hemoglobin; g.dl-1 13.9 (1.6) 13.0 (1.2) 0.031 Fluid administration; ml 176.4 (31.2) 165.4 (27.8) 0.278 Data are number (proportion), mean (SD) or median [IQR]. Figure 1. Receiver operating characteristic curve for age to predict the increase of recovery slope under general anesthesia. If age was lower than 65 years old, the increase of recovery slope under general anesthesia was predicted with a sensitivity of 85.7% and a specificity of 61.1%. Table 1. Effects of general anesthesia on VOT-derived parameters and hemodynamic variables Demographic and intraoperative characteristics of two age groups divided by age of 65 years old are shown in Table 2. The type of operation and hemoglobin showed significantly different between the groups. The changes in StO2 during VOT before and after the induction of anesthesia in two age groups are shown in Fig. 2. Repeated measures of ANOVA revealed significantly different StO2 values before and after the induction of anesthesia in both groups (all p < 0.001); the Bonferroni post hoc test revealed significant differences at all time points. The changes in microcirculatory and hemodynamic parameters during VOT at T0 and T1 depending on the age are shown in Table 3. At T0, baseline StO2 was significantly higher in the younger group compared to the older group (P = 0.025). After the induction of anesthesia, recovery slope were significantly higher in the younger group compared to the older group (3.59 Patients were divided by an increase of recovery slope under general anesthesia and an unpaired student t test or Mann-Whitney U test was used to analyze differences in the patient’s characteristics and hemodynamic variables between the groups. The significantly different variables were evaluated their ability to predict the increase of recovery slope of VOT under general anesthesia using a receiver operating characteristics (ROC) curves analysis with 95% confidence interval (CI). The optimal cut-off was selected to maximize the Youden index and age less than 65 years old showed a fair performance in predicting the increase of microvascular reactivity after the induction of anesthesia. For age-related http://www.medsci.org Int. J. Med. Sci. 2021, Vol. 18 1099 up and 2.63 0.047). MBP emperature nesthesia in fferences in etween two amic variables ecovery slope ith the recovery er esthesia P value 0.013 0.145 0.803 0.906 0.713 0.065 0.301 Younger (< 65 years) (n = 27) Older (≥ 65 years) (n = 26) P value Endoscopic sinus surgery 14 (51.9) 3 (11.5) Lactate; mg.l-1 0.87 [0.78-1.18] 1.18 [0.78-1.58] 0.296 Hemoglobin; g.dl-1 13.9 (1.6) 13.0 (1.2) 0.031 Fluid administration; ml 176.4 (31.2) 165.4 (27.8) 0.278 Data are number (proportion), mean (SD) or median [IQR]. Figure 1. Receiver operating characteristic curve for age to predict the increase of recovery slope under general anesthesia. If age was lower than 65 years old, the increase of recovery slope under general anesthesia was predicted with a sensitivity of 85.7% and a specificity of 61.1%. Effects of general anesthesia on VOT-derived parameters and hemodynamic variables Patient’s characteristics and hemodynamic variables between patients with or without the increase of recovery slope under general anesthesia All patients (n=53) Patients without the increase of recovery slope under general anesthesia (n=18) Patients with the increase of recovery slope under general anesthesia (n=35) P value Age; years 56.5 (14.5) 63.3 (14.4) 53.0 (13.5) 0.013 Sex 0.145 Male 24 (45.3) 10 (55.6) 14 (40.0) Female 29 (54.7) 8 (44.4) 21 (60.0) Body mass index; kg.m-2 24.0 (3.2) 23.8 (3.4) 24.1 (3.1) 0.803 Weight; kg 63.1 (12.0) 62.8 (10.5) 63.2 (12.9) 0.906 Height; cm 161.6 (9.1) 162.3 (8.8) 161.3 (9.3) 0.713 ASA class 0.065 I 26 (49.1) 10 (55.6) 8 (44.4)15 (55.5) 17 (48.6) II 27 (50.9) 8 (44.4) 18 (51.4) Type of operation 0.301 Laparoscopic cholecystectomy 18 (34.0) 8 (44.4) 10 (28.6) Thyroidectomy 18 (34.0) 5 (27.8) 13 (37.1) Endoscopic sinus surgery 17 (32.1) 5 (27.8) 12 (34.3) Lactate; mg.l-1 0.99 [0.78-1.48] 0.79 [0.65-1.62] 1.02 [0.84-1.34] 0.296 Hemoglobin; g.dl-1 13.5 (1.5) 13.6 (1.4) 13.5 (1.6) 0.837 Fluid administration; ml 170.7 (29.7) 163.3 (28.9) 174.6 (29.8) 0.194 Mean blood pressure; mmHg 96.0 [86.5-112.5] 95.0 [89.3-104.5] 0.954 SpO2; % 99.0 [97.0-100.0] 99.0 [97.0-100.0] 99.0 [96.0-100.0] 0.512 Heart rate; beats.min-1 74.0 [64.0-86.0] 71.0 [60.0-76.0] 76.0 [66.0-88.0] 0.292 Skin temperature; °C 32.3 (2.3) 31.7 (1.7) 32.9 (1.9) 0.245 Data are number (proportion), mean (SD) or median [IQR]. Table 2. Patients’ characteristics of the age groups Younger (< 65 years) (n = 27) Older (≥ 65 years) (n = 26) P value Age; years 45.1 (10.7) 68.3 (5.8) <0.001 Sex 0.502 Male 11 (40.7) 13 (50.0) Female 16 (59.2) 13 (50.0) Body mass index; kg.m-2 24.1 (3.3) 24.0 (3.1) 0.887 Weight; kg 64.2 (13.6) 62.0 (10.4) 0.521 Height; cm 162.7 (10.0) 160.5 (8.1) 0.389 Table 1. Patient’s characteristics and hemodynamic variables between patients with or without the increase of recovery slope under general anesthesia Table 1. Patient’s characteristics and hemodynamic variables between patients with or without the increase of recovery slope under general anesthesia Figure 1. Receiver operating characteristic curve for age to predict the increase of recovery slope under general anesthesia. If age was lower than 65 years old, the increase of recovery slope under general anesthesia was predicted with a sensitivity of 85.7% and a specificity of 61.1%. Figure 1. Receiver operating characteristic curve for age to predict the increase of recovery slope under general anesthesia. Discussion Changes in tissue oxygen saturation (StO2) during vascular occlusion test (VOT) before and after induction of general anesthesia in the younger and the older groups. A repeated measures ANOVA revealed significantly different StO2 values between before and after the induction of anesthesia, with a significant Bonferroni post hoc test for the differences at all the time points. Figure 2. Changes in tissue oxygen saturation (StO2) during vascular occlusion test (VOT) before and after induction of general anesthesia in the younger and the older groups. A repeated measures ANOVA revealed significantly different StO2 values between before and after the induction of anesthesia, with a significant Bonferroni post hoc test for the differences at all the time points. en saturation (StO2) during vascular occlusion test (VOT) before and after induction of general anesthesia in the younger and the older groups vealed significantly different StO2 values between before and after the induction of anesthesia, with a significant Bonferroni post hoc test for the Figure 2. Changes in tissue oxygen saturation (StO2) during vascular occlusion test (VOT) before and after induction of general anesthesia in the younger and the older groups. A repeated measures ANOVA revealed significantly different StO2 values between before and after the induction of anesthesia, with a significant Bonferroni post hoc test for the differences at all the time points. Table 3. Microcirculatory and hemodynamic parameters of the age groups. Table 3. Microcirculatory and hemodynamic parameters of the age groups. Discussion Our study showed that general anesthesia improves StO2 in healthy adult patients through an increase of microvascular reactivity and reduced metabolic demand. However, the important finding of our study was that the recovery slope significantly increased after the induction of general anesthesia only in the younger patients. This result suggests that general anesthesia may increase the microvascular reactivity and capillary recruitment only in the young, healthy patients [11,14]. Concordantly, age could predict the increase of recovery slope after the induction of anesthesia, showing an area under the ROC curve of 0.733. Table 2. Patients’ characteristics of the age groups Table 2. Patients’ characteristics of the age groups Younger (< 65 years) (n = 27) Older (≥ 65 years) (n = 26) P value Age; years 45.1 (10.7) 68.3 (5.8) <0.001 Sex 0.502 Male 11 (40.7) 13 (50.0) Female 16 (59.2) 13 (50.0) Body mass index; kg.m-2 24.1 (3.3) 24.0 (3.1) 0.887 Weight; kg 64.2 (13.6) 62.0 (10.4) 0.521 Height; cm 162.7 (10.0) 160.5 (8.1) 0.389 ASA class 0.339 I 15 (55.5) 11 (42.3) II 12 (44.4) 15 (57.7) Type of operation 0.004 Laparoscopic cholecystectomy 5 (18.5) 13 (50.0) Thyroidectomy 8 (29.6) 10 (38.5) The recovery slope during VOT reflects the capacity of microvascular reactivity to recruit the capillary network [16]. At rest, only 30% of capillaries are normally perfused, and 70% are not [17]. These blood vessels are reserves that can be opened under stress conditions through relaxation of the precapillary sphincter and arteriolar vasodilation [18]. Even in elderly patients without comorbidities in daily life, the limit of physiologic reserve can be seen during general anesthesia. This limited physiologic reserve is one of the causes of microcirculation changes during aging [19]. In aged organs, dynamic http://www.medsci.org 1100 Int. J. Med. Sci. 2021, Vol. 18 endothelial dysfunction, impaired vasodilatory and vasoconstrictive responses, increased vascular stiffness, and decreased vascular density and impaired vascular organization [8,22,23]. control of the precapillary sphincter to regulate blood flow does not work well, and reserved vessels are barely recruited [20,21]. A variety of mechanisms are involved, in which aging is associated with control of the precapillary sphincter to regulate blood flow does not work well, and reserved vessels are barely recruited [20,21]. A variety of mechanisms are involved, in which aging is associated with Figure 2. Int. J. Med. Sci. 2021, Vol. 18 First, VOT is not yet standardized, and the duration of peripheral ischemia is an area of strong debate. There are two methods to advocate peripheral ischemia: time-targeted and StO2-targeted VOT. We used 5-minute time-targeted VOT because a smaller minimum StO2 value after ischemia results in a more defined recovery slope [40,41]. Second, it is difficult to confirm that older participants are completely healthy as younger patients. Because we enrolled only the patients undergoing minor surgery, more advanced hemodynamic monitoring or tests related to cardiovascular disease could not be performed. However, in clinical practice, completely healthy elderly is rare and most of the elderly have the compensated comorbidities in their daily life and more severe microcirculatory dysfunction, which more prominent results might be seen in real world. Finally, the effects of FiO2 on microcirculation are in debate. Previous study showed that normobaric hyperoxia reduced capillary perfusion and oxygen consumption and increased heterogeneity of the perfusion, while there was no change in recovery slope of VOT in healthy subjects [42]. In the same line, high FiO2 had only a relatively small increase in mean (SD) StO2 of 5.3 (7.1) % and this effect reached a plateau when FiO2 was between 30% and 40% [43]. When previous studies that investigated the effect of anesthetics on StO2 in cardiac surgery, StO2 under general anesthesia seems more likely affected by anesthetic agents, rather than FiO2 [9,11,35]. In their studies, despite of increasing FiO2 to 0.5-0.6 under general anesthesia, only sevoflurane significantly increased StO2 and propofol did not significantly change StO2. Further research on the comparisons of y VOT parameters after the induction of anesthesia are not consistent among previous studies that showed a reduced or an increased recovery slope after the induction of anesthesia [10,11,35]. We assume that the reason for these differences is that the previous studies included patients with various comorbidities who required cardiac surgery; our study included only patients without comorbidities. Recent studies showed that reactive hyperemia is significantly decreased in elderly patients with heart failure with preserved ejection fraction or hypertension compared to healthy age-matched controls, indicating endothelial dysfunction in these patient groups [36,37]. Also, they demonstrated that vasodilation under loading condition, such as exercise, was blunted in these patients [36]. Considering these results, patients who required cardiac surgery in the previous studies would have significant microvascular dysfunction and decreased capacity of reactive vasodilation. Int. J. Med. Sci. 2021, Vol. 18 1101 Int. J. Med. Sci. 2021, Vol. 18 Int. J. Med. Sci. 2021, Vol. 18 Therefore, it is difficult to confirm that the improvement of StO2 at T1 was solely due to general anesthesia. However, other potential factors, such as body temperature, stress hormone caused by intubation, fluid administration, and decreased MBP are estimated to have little influence on our results. Body temperature within normal range does not seem to influence StO2 [38]. Previous study showed that stress hormones increased slightly in response to laryngoscopy and intubation, all returning to or below baseline 5 min later in normotensive patients [39]. Moreover, 161 ml of Hartman’s solution was infused in our study, which is not the amount that causes clinically significant hemodilution in people with normal hemoglobin. MBP was significantly decreased under general anesthesia where the lowest value was 66 mmHg which might provide enough perfusion pressure to allow peripheral autoregulation. Vasodilation occurs in a complex way through endothelium dependent vasodilation (EDV) mediated by endothelium or endothelium independent vasodilation (EIV) mediated by smooth muscle of the vessel wall [12]. EDV is known to decrease with age [12,24] and mechanisms include decreased NO sensitivity and bioavailability, and an increased oxidative stress [25,26]. On the contrary, EIV is maintained even in aged vessel [27]. Recovery slope of VOT has been known as a useful clinical tool for evaluating EDV [28,29]. In our study, the baseline StO2 is much lower in elderly patients, however, other VOT-derived parameters were not significantly different at T0. Assuming EIV is age independent, EDV may be also preserved during VOT in older patients under non-stress condition. Inhalational anesthetic agents inhibit EDV but promote EIV via reduction of intracellular Ca2+ availability and sensitivity to contractile proteins [30,31]. The net effect of these 2 opposing effects is generally vasodilation. Propofol and opioids decreases systemic vascular resistance in a predominantly EIV and partly mediated by EDV [32-34]. Considering VOT at T1 was performed 30 min after the injection of propofol and remifentanil, mainly desflurane affected the microcirculation. Our results showed opposite results that desflurane promoted EDV in younger patients. The reason of the contradictory results is not elucidative, but may not be consistent with the in vitro results because numerous factors affect the microvascular system in vivo. g There are some limitations to the interpretation of the results of our study. Discussion All patients (n=53) Younger (< 65 yrs) (n = 27) Older (≥ 65 yrs) (n = 26) T0 T1 P value T0 T1 P value T0 T1 P value Baseline StO2; % 60.0 [56.0-68.0] 70.0 [63.0-78.0] <0.001 66.0 [60.0-68.8] 71.0 [62.5-77.8] 0.002 58.0* [53.0-65.0] 70.0 [63.0-78.0] < 0.001 Occlusion slope; %.sec-1 0.19 [0.15-0.25] 0.15 [0.11-0.18] <0.001 0.19 [0.16-0.25] 0.15 [0.12-0.18] <0.001 0.21 [0.14-0.28] 0.12 [0.10-0.20] < 0.001 Minimum StO2; % 15.0 [15.0-30.0] 29.0 [15.0-47.0] <0.001 15.0 [15.0-31.5] 29.0 [15.0-46.0] <0.001 15.0 [15.0-28.0] 27.5 [15.0-50.0] <0.001 Time to minimum StO2; sec 271.0 [210.8-300.0] 300.0 [299.3-300.0] <0.001 270.0 [214.3-300.0] 300.0 [297.8-300.0] 0.004 285.5 [210.0-300.0] 300.0 [300-300.0] < 0.001 Recovery slope; %.sec-1 2.50 [1.99-2.97] 2.77 [2.24-3.98] 0.004 2.44 [1.91-2.81] 3.59 [2.58-3.51] <0.001 2.61 [2.21-3.20] 2.63* [1.90-3.60] 0.949 Maximum StO2; % 87.0 [80.8-95.0] 95.0 [89.8-95.0] <0.001 90.0 [82.5-95.0] 95.0 [90.5-95.0] 0.008 86.5 [79.0-91.0] 93.5 [89.0-95.0] <0.001 Time to maximum StO2; sec 27.0 [23.8-30.5] 22.0 [16.8-28.3] 0.202 26.0 [20.5-34.3] 24.0 [15.5-32.5] 0.559 28.0 [23.0-34.0] 22.0 [18.0-30.0] 0.264 Mean blood pressure; mmHg 95.5 [87.0-107.0] 89.0 [78.0-100.0] <0.001 94.5 [87.0-104.0] 88.0 [77.0-99.0] 0.003 97.5 [88.0-108.5] 89.0 [78.5-103.0] 0.003 SpO2; % 99.0 [97.0-100.0] 100.0 [98.0-100.0] 0.004 99.0 [97.0-100.0] 99.5 [98.0-100.0] 0.469 99.0 [96.0-100.0] 100.0 [98.0-100.0] 0.001 Heart rate; beats.min-1 74.0 [64.0-86.0] 82.0 [75.3-93.0] <0.001 78.0 [66.3-87.8] 85.5 [77.0-98.0] 0.029 72.0 [59.5-78.5] 82.0 [75.0-90.3] 0.013 Skin temperature; °C 32.3 (2.3) 33.5 (1.99) <0.001 31.9 (1.8) 33.4 (2.1) <0.001 32.3 (1.9) 33.6 (1.6) 0.041 Data are mean (SD) or median [IQR]. T0 = before the induction of anesthesia; T1 = after the induction of anesthesia; StO2 = tissue oxygen saturation. *p < 0.05 compared to the younger group. http://www.medsci.org helped data analysis and revising paper. helped data analysis and revising paper. effects of different types of general anesthetics on microcirculation of patients without underlying disease is needed. Ethics approval y gy 18. Levy BI, Schiffrin EL, Mourad JJ, Agostini D, Vicaut E, Safar ME, Struijker-Boudier HA. Impaired tissue perfusion: a pathology common to hypertension, obesity, and diabetes mellitus. Circulation 2008; 118: 968-76. This study was approved by the Institutional Review Board of Pusan National University Hospital (number H-1607-012-054) and registered at www.clinicaltrials.gov (NCT03060798). 19. Montagna W, Carlisle K. Structural changes in ageing skin. The British Journal of Dermatology 1990; 122 Suppl 35: 61-70. 20. Jackson DN, Moore AW, Segal SS. Blunting of rapid onset vasodilatation and blood flow restriction in arterioles of exercising skeletal muscle with ageing in male mice. The Journal of Physiology 2010; 588: 2269-82. References 1. De Backer D, Creteur J, Preiser JC, Dubois MJ, Vincent JL. Microvascular blood flow is altered in patients with sepsis. American Journal of Respiratory and Critical Care Medicine 2002; 166: 98-104. 2. Kara A, Akin S, Ince C. Monitoring microcirculation in critical illness. Current Opinion in Critical Care 2016; 22: 444-52. 2. Kara A, Akin S, Ince C. Monitoring microcirculation in critical illness. Current Opinion in Critical Care 2016; 22: 444-52. 3. Moore JP, Dyson A, Singer M, Fraser J. Microcirculatory dysfunction and resuscitation: why, when, and how. British Journal of Anaesthesia 2015; 115: 366-75. 4. Lush CW, Kvietys PR. Microvascular dysfunction in sepsis. Microcirculation (New York, N.Y.: 1994) 2000; 7: 83-101. 5. Muris DM, Houben AJ, Schram MT, Stehouwer CD. Microvascular dysfunction is associated with a higher incidence of type 2 diabetes mellitus: a systematic review and meta-analysis. Arteriosclerosis, Thrombosis, and Vascular Biology 2012; 32: 3082-94. 5. Muris DM, Houben AJ, Schram MT, Stehouwer CD. Microvascular dysfunction is associated with a higher incidence of type 2 diabetes mellitus: a 6. Fang X, Tang W, Sun S, Huang L, Chang YT, Castillo C, Weil MH. Comparison of buccal microcirculation between septic and hemorrhagic shock. Critical Care Medicine 2006; 34: S447-53. 7. Kirschenbaum LA, Astiz ME, Rackow EC, Saha DC, Lin R. Microvascular response in patients with cardiogenic shock. Critical Care Medicine 2000; 28: 1290-4. Abbreviations 8. Bentov I, Reed MJ. The effect of aging on the cutaneous microvasculature. Microvascular Research 2015; 100: 25-31. ASA: American Society of Anesthesiologists; BIS: Bispectral index; CI: Confidence interval; EDV: Endothelium dependent vasodilation; EIV: Endothelium independent vasodilation; HR: Heart rate; MBP: Mean blood pressure; NIRS: Near-infrared spectroscopy; SpO2: Pulsed oxygen saturation; ROC: Receiver operating characteristics; StO2: Tissue oxygen saturation; VOT: Vascular occlusion test. 9. Rossi M, Pistelli F, Pesce M, Aquilini F, Franzoni F, Santoro G, Carrozzi L. Impact of long-term exposure to cigarette smoking on skin microvascular function. Microvascular Research 2014; 93: 46-51. 10. Bernet C, Desebbe O, Bordon S et al. The impact of induction of general anesthesia and a vascular occlusion test on tissue oxygen saturation derived parameters in high-risk surgical patients. Journal of Clinical Monitoring and Computing 2011; 25: 237-44. p g 11. Kim TK, Cho YJ, Min JJ, Murkin JM, Bahk JH, Hong DM, Jeon Y. Tissue microcirculation measured by vascular occlusion test during anesthesia induction. Journal of Clinical Monitoring and Computing 2016; 30: 41-50. 12. Gerhard M, Roddy MA, Creager SJ, Creager MA. Aging progressively impairs endothelium-dependent vasodilation in forearm resistance vessels of humans. Hypertension (Dallas, Tex.: 1979) 1996; 27: 849-53. Competing Interests General anesthesia is known to reduce cardiovascular function, which would ultimately reduce organ perfusion. However, our study shows that general anesthesia would compensate tissue hypoperfusion by improving microvascular reactivity representing the ability to recruit capillaries and reducing metabolic demands. However, improved microvascular reactivity by general anesthesia was only apparent in the younger patients without accompanying diseases, not in the older patients, even those without comorbidities. These findings suggest that general anesthesia could have different effects on microvascular reactivity depending on the status of the microvasculature. Additional studies on the effects of general anesthesia on microvascular reactivity in certain diseases are necessary. The authors have declared that no competing interest exists. The authors have declared that no competing interest exists. Funding 14. Futier E, Christophe S, Robin E et al. Use of near-infrared spectroscopy during a vascular occlusion test to assess the microcirculatory response during fluid challenge. Critical Care (London, England) 2011; 15: R214. This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST) (No. NRF-2018R1C1 B5040928) and clinical research grant in 2020 from Pusan National University Hospital. challenge. Critical Care (London, England) 2011; 15: R214. 15. Shapiro NI, Arnold R, Sherwin R et al. The association of near-infrared spectroscopy-derived tissue oxygenation measurements with sepsis syndromes, organ dysfunction and mortality in emergency department patients with sepsis. Critical Care (London, England) 2011; 15: R223. p p ( g ) 16. Moens AL, Goovaerts I, Claeys MJ, Vrints CJ. Flow-mediated vasodilation: a diagnostic instrument, or an experimental tool? Chest 2005; 127: 2254-63. 17. Chade AR. Renal vascular structure and rarefaction. Comprehensive Physiology 2013; 3: 817-31. Acknowledgements yp ( ) 13. Butler E, Chin M, Aneman A. Peripheral Near-Infrared Spectroscopy: Methodologic Aspects and a Systematic Review in Post-Cardiac Surgical Patients. Journal of Cardiothoracic and Vascular Anesthesia. 2016. Int. J. Med. Sci. 2021, Vol. 18 And microvascular dysfunction appears to be more severe in the cardiac patients than in heathy elderly patients. There are numerous clinical variables that could contribute to regulate microcirculation in human. http://www.medsci.org 1102 Int. J. Med. Sci. 2021, Vol. 18 Int. J. Med. Sci. 2021, Vol. 18 Int. J. Med. Sci. 2021, Vol. 18 Int. J. Med. Sci. 2021, Vol. 18 26. Taddei S, Virdis A, Ghiadoni L, Salvetti G, Bernini G, Magagna A, Salvetti A. Age-related reduction of NO availability and oxidative stress in humans. Hypertension (Dallas, Tex.: 1979) 2001; 38: 274-9. yp ( ) 27. Sinkler SY, Segal SS. Aging alters reactivity of microvascular resistance networks in mouse gluteus maximus muscle. American Journal of Physiology.Heart and Circulatory Physiology 2014; 307: H830-9. y gy y y gy 28. Patel S, Celermajer DS. Assessment of vascular disease using arterial flow mediated dilatation. Pharmacological Reports : PR 2006; 58 Suppl: 3-7. 28. Patel S, Celermajer DS. Assessment of vascular disease using mediated dilatation. Pharmacological Reports : PR 2006; 58 Suppl: 29. Le Brocq M, Leslie SJ, Milliken P, Megson IL. Endothelial dysfunction: from molecular mechanisms to measurement, clinical implications, and therapeutic opportunities. Antioxidants & Redox Signaling 2008; 10: 1631-74. g g 30. Akata T. General anesthetics and vascular smooth muscle: direct actions of general anesthetics on cellular mechanisms regulating vascular tone. Anesthesiology 2007; 106: 365-91. gy 31. Villeneuve E, Blaise G, Sill JC, Guerard MJ, Buluran J, Girard D. Halothane 1.5 MAC, isoflurane 1.5 MAC, and the contractile responses of coronary arteries obtained from human hearts. Anesthesia and Analgesia 1991; 72: 454-61. g 32. Robinson BJ, Ebert TJ, O'Brien TJ, Colinco MD, Muzi M. Mechanisms whereby propofol mediates peripheral vasodilation in humans. Sympathoinhibition or direct vascular relaxation? Anesthesiology 1997; 86: 64-72. 33. Duman A, Saide Sahin A, Esra Atalik K, oZtin ogun C, Basri Ulusoy H, Durgut K, oKesli S. The in vitro effects of remifentanil and fentanyl on isolated human right atria and saphenous veins. Journal of Cardiothoracic and Vascular Anesthesia 2003; 17: 465-9. 34. Aguirre JA, Lucchinetti E, Clanachan AS, Plane F, Zaugg M. Unraveling Interactions Between Anesthetics and the Endothelium: Update and Novel Insights. Anesthesia and Analgesia 2016; 122: 330-48. g g 35. Vandenbulcke L, Lapage KG, Vanderstraeten KV, De Somer FM, De Hert SG, Moerman AT. Microvascular reactivity monitored with near-infrared spectroscopy is impaired after induction of anaesthesia in cardiac surgery patients: An observational study. European Journal of Anaesthesiology 2017; 34: 688-94. 36. Borlaug BA, Olson TP, Lam CS, Flood KS, Lerman A, Johnson BD, Redfield MM. Global cardiovascular reserve dysfunction in heart failure with preserved ejection fraction. Journal of the American College of Cardiology 2010; 56: 845-54. 37. Lee JF, Barrett-O'Keefe Z, Garten RS et al. Author Contributions y gy 21. Scheeren TW. Journal of Clinical Monitoring and Computing 2015 end of year summary: tissue oxygenation and microcirculation. Journal of Clinical Monitoring and Computing 2016; 30: 141-6. AC helped study design/planning, study conduct, data analysis, and writing and revising paper. HL helped study design/planning, study conduct, data analysis, and writing and revising paper. HjK helped study design/planning and revising paper. WD helped study conduct and revising paper. SJ helped study conduct and revising paper. SB helped study design/planning and revising paper. EK helped study conduct and revising paper. JK helped data analysis and revising paper. HkK 22. Muller-Delp JM. Aging-induced adaptations of microvascular reactivity. Microcirculation (New York, N.Y.: 1994) 2006; 13: 301-14. ( ) 23. Sweat RS, Sloas DC, Stewart SA et al. Aging is associated with impaired angiogenesis, but normal microvascular network structure, in the rat mesentery. American Journal of Physiology.Heart and Circulatory Physiology 2017; 312: H275-84. 24. DeSouza CA, Clevenger CM, Greiner JJ, Smith DT, Hoetzer GL, Shapiro LF, Stauffer BL. Evidence for agonist-specific endothelial vasodilator dysfunction with ageing in healthy humans. The Journal of Physiology 2002; 542: 255-62. g g y y gy 25. Muller-Delp JM, Spier SA, Ramsey MW, Delp MD. Aging impairs endothelium-dependent vasodilation in rat skeletal muscle arterioles. American Journal of Physiology.Heart and Circulatory Physiology 2002; 283: H1662-72. http://www.medsci.org 1103 Int. J. Med. Sci. 2021, Vol. 18 Evidence of microvascular dysfunction in heart failure with preserved ejection fraction. Heart (British Cardiac Society) 2016; 102: 278-84. y 38. Cho YJ, Lee SY, Kim TK, Hong DM, Jeon Y. Effect of Prewarming during Induction of Anesthesia on Microvascular Reactivity in Patients Undergoing Off-Pump Coronary Artery Bypass Surgery: A Randomized Clinical Trial. PloS One 2016; 11: e0159772. 39. Kayhan Z, Aldemir D, Mutlu H, Ogus E. Which is responsible for the haemodynamic response due to laryngoscopy and endotracheal intubation? Catecholamines, vasopressin or angiotensin? European Journal of Anaesthesiology 2005; 22: 780-5. 40. Lipcsey M, Eastwood GM, Woinarski NC, Bellomo R. Near-infrared spectroscopy of the thenar eminence: comparison of dynamic testing protocols. Critical Care and Resuscitation : Journal of the Australasian Academy of Critical Care Medicine 2012; 14: 142-7. 41. Iannetta D, Inglis EC, Soares RN, McLay KM, Pogliaghi S, Murias JM, CAPES scholarship holder. Reliability of microvascular responsiveness measures derived from near-infrared spectroscopy across a variety of ischemic periods in young and older individuals. Microvascular Research 2019; 122: 117-24. y g 42. Orbegozo Cortes D, Puflea F, Donadello K et al. Normobaric hyperoxia alters the microcirculation in healthy volunteers. Microvascular Research 2015; 98: 23-8. 43. Kyle B, Litton E, Ho KM. Effect of hyperoxia and vascular occlusion on tissue oxygenation measured by near infra-red spectroscopy (InSpectra): a volunteer study. Anaesthesia 2012; 67: 1237-41. http://www.medsci.org
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Long Noncoding RNAs: Emerging Players in Medulloblastoma
Frontiers in pediatrics
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Long Noncoding RNAs: Emerging Players in Medulloblastoma Pietro Laneve 1, Jessica Rea 2 and Elisa Caffarelli 1* 1 Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy, 2 Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy Central Nervous System tumors are the leading cause of cancer-related death in children, and medulloblastoma has the highest incidence rate. The current therapies achieve a 5- year survival rate of 50–80%, but often inflict severe secondary effects demanding the urgent development of novel, effective, and less toxic therapeutic strategies. Historically identified on a histopathological basis, medulloblastoma was later classified into four major subgroups—namely WNT, SHH, Group 3, and Group 4—each characterized by distinct transcriptional profiles, copy-number aberrations, somatic mutations, and clinical outcomes. Additional complexity was recently provided by integrating gene- and non- gene-based data, which indicates that each subclass can be further subdivided into specific subtypes. These deeper classifications, while getting over the typical tumor heterogeneity, indicate that different forms of medulloblastoma hold different molecular drivers that can be successfully exploited for a greater diagnostic accuracy and for the development of novel, targeted treatments. Long noncoding RNAs are transcripts that lack coding potential and play relevant roles as regulators of gene expression in mammalian differentiation and developmental processes. Their cell type- and tissue- specificity, higher than mRNAs, make them more informative about cell- type identity than protein-coding genes. Remarkably, about 40% of long noncoding RNAs are expressed in the brain and their aberrant expression has been linked to neuro-oncological disorders. However, while their involvement in gliomas and neuroblastomas has been extensively studied, their role in medulloblastoma is still poorly explored. Here, we present an overview of current knowledge regarding the function played by long noncoding RNAs in medulloblastoma biology. Edited by: Andrea Carai, Bambino Gesù Children Hospital (IRCCS), Italy Reviewed by: Anshu Malhotra, Emory University, United States Francesca Del Bufalo, Bambino Gesù Children Hospital (IRCCS), Italy *Correspondence: Elisa Caffarelli elisa.caffarelli@uniroma1.it Keywords: nervous system, pediatric tumor, medulloblastoma, long noncoding RNAs, oncogenes, tumor suppressors, diagnostic biomarkers, therapeutic targets Specialty section: This article was submitted to Pediatric Oncology, a section of the journal Frontiers in Pediatrics MINI REVIEW MINI REVIEW published: 14 March 2019 doi: 10.3389/fped.2019.00067 published: 14 March 2019 doi: 10.3389/fped.2019.00067 Keywords: nervous system, pediatric tumor, medulloblastoma, long noncoding RNAs, oncogenes, tumor suppressors, diagnostic biomarkers, therapeutic targets INTRODUCTION Medulloblastoma (MB), with an estimated 5000–8000 cases/year worldwide (1, 2), is an aggressive tumor arising in the cerebellum. It mainly affects children and is a major cause of mortality in pediatric oncology (3). While the previous classification of MB by the World Health Organization (WHO) was largely based on histological features (4), the new classification in 2016 exploited molecular parameters to catalog the large variety of tumors of the Central Nervous System (CNS) (5). Rational molecular-based classification was supported by the advancement of sequencing technologies allowing extensive genomic/transcriptomic studies. This classification benefits from the integration between histological and molecular parameters and led to no longer considering MB as a unique pathology. Received: 08 June 2018 Accepted: 18 February 2019 Published: 14 March 2019 Group 4 G4, the most common subtype, accounts for 35% of all MBs. These tumors are often metastatic at diagnosis and have intermediate prognosis. It is the most enigmatic subgroup, characterized by a neuronal gene expression signature, resembling that of glutamatergic neurons (7). Common alterations pertain to inactivating mutations in KDM6A gene, duplication of SNCAIP gene, and amplification of MYCN and CDK6 proto-oncogenes. G4 has been re-classified into G4α, characterized by MYCN and CDK6 amplifications, G4β, strongly enriched for SNCAIP duplications and putative PRDM6 overexpression, and G4γ enriched for focal CDK6 amplification (9). In this review, we highlight the link between MB tumors and the emerging class of regulatory long noncoding RNAs (lncRNAs), and their potential as promising cancer biomarkers and novel therapeutic agents. Citation: Citation: Laneve P, Rea J and Caffarelli E (2019) Long Noncoding RNAs: Emerging Players in Medulloblastoma. Front. Pediatr. 7:67. doi: 10.3389/fped.2019.00067 March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org Long Noncoding RNAs in Medulloblastoma Laneve et al. G3β with a more favorable prognosis compared to G3γ, which frequently harbors increased MYC copy number (9). Several subclasses of MB have been unveiled, each displaying dysregulated genes—the driver genes—altered by single nucleotide mutations, somatic copy-number aberrations, or by defects in transcriptional or post-transcriptional gene regulation. Mechanisms of Action LncRNAs may be engaged in fine-scale modulation of gene expression as well as in large-scale control of developmental programs. They may act through a variety of mechanisms, depending on their cellular localization. Some of them are exclusively localized in the nucleus, others in the cytoplasm, others change their localization during development or differentiation, and still others show both localizations. In the latter case, a single lncRNA might have multiple molecular functions. Medulloblastoma Recent genomic and transcriptomic analyses on a large cohort of primary tumors assigned MBs to four molecularly distinct subgroups (6, 7). They include the extensively characterized WNT and SHH subgroups, and the Group 3 (G3) and Group 4 (G4), whose pathogenesis and signaling pathways are poorly defined. Group 3 G3 is the most aggressive subgroup accounting for about 25% of all MBs, about half of them being metastatic at diagnosis (10). These tumors display a MYC signature, being characterized by amplification of the MYC proto-oncogene and exhibiting aberrant MYC expression in almost all cases (7). G3 shows intra- tumoral heterogeneity, including three further subtypes: G3α and SHH SHH MBs represent approximately 30% of all MB cases, characterized by an intermediate prognosis, with survival rates ranging from 60 to 80% (7). SHH tumors, mainly exhibiting desmoplastic histology, display an aberrant activation of the SHH signaling, due to mutations of negative regulators of SHH pathway, such as PTCH1 and SUFU, and copy number aberrations of SHH target genes, such as MYCN and GLI2 (7). TP53 mutations are found in about 30% of childhood SHH MBs and are associated with extremely poor outcomes. Recent analyses suggest that SHH subgroup consists of four distinct subtypes. It includes SHHα, enriched for MYCN and GLI2 amplifications, with the worst prognosis; SHHβ, harboring PTEN gene deletions and frequently metastatic; SHHγ displaying scarce copy number aberrations and SHHδ, that is enriched for TERT gene promoter mutations and has a favorable prognosis (9). LONG NONCODING RNAS Approximately 10% of all MB patients belong to this subgroup, characterized by the most favorable prognosis with 95% of survival (7, 8). WNT tumors, which exhibit classic histology, are recognizable by a WNT gene expression signature. Nuclear accumulation of β-catenin is considered a biomarker for WNT signaling pathway activation. This subgroup often carries heterozygous TP53 mutations, as well as mutations in the DEAD- box helicase gene DDX3X and in chromatin modifiers genes, such as SMARCA4 and CREBBP, indicating the implication of altered epigenome in the development of this disease. Integration of gene expression and DNA methylation profiles indicated that WNT subgroup comprises at least two subtypes, WNTα, mainly enriched for children and characterized by monosomy 6, and WNTβ, including mainly adults without monosomy 6 (9). RNA is considered as the most “rediscovered” biological macromolecule (11, 12) since, starting from the informational role assigned to mRNAs in 1961 (13, 14), novel unexpected functions have been attributed to RNA in the last three decades. In the 1980s, its capacity to catalyze biochemical reactions was associated with its ability to fold into complex tridimensional structures (15). In the early 1990s, regulatory functions were attributed to two long RNAs lacking protein- coding capacity, H19 (16, 17), and XIST (18, 19). Since then, a huge number of noncoding RNAs, both short and long in size, was discovered in parallel with the finding that more than half of the transcriptome encodes non-proteinogenic transcripts. Among them, the lncRNAs number in the tens of thousands and include also circular RNAs, covalently closed RNA circles derived from back-splicing of linear transcripts (20). LncRNAs are >200 nucleotides and represent very versatile molecules for their unique ability to specifically recognize both nucleic acids and protein partners via base-pairing and modular tridimensional structures, respectively. They are flexibly involved in important biological processes, such as development, cell differentiation and growth, thanks to their main functions of gene expression regulators and the genome structure architects. Frontiers in Pediatrics | www.frontiersin.org Nuclear lncRNAs Nuclear lncRNAs (Figure 1A) can be found in the nucleoplasm or associated with chromatin (21). Typically, these latter are supposed to control protein-coding gene expression at the March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org 2 Long Noncoding RNAs in Medulloblastoma Laneve et al. FIGURE 1 | Mechanisms of action of lncRNAs. (A) In the nucleus, lncRNAs can regulate gene expression by guiding epigenetic (1) or transcription (2) factors to specific loci, by acting as enhancers (3), by structuring the three-dimensional conformation of chromatin (4), or by recruiting splicing factors (5). (B) In the cytoplasm, they act by modulating mRNA stability (6) or translation (7), by sequestering miRNAs (8), or by coding small peptides (9). FIGURE 1 | Mechanisms of action of lncRNAs. (A) In the nucleus, lncRNAs can regulate gene expression by guiding epigenetic (1) or transcription (2) factors to specific loci, by acting as enhancers (3), by structuring the three-dimensional conformation of chromatin (4), or by recruiting splicing factors (5). (B) In the cytoplasm, they act by modulating mRNA stability (6) or translation (7), by sequestering miRNAs (8), or by coding small peptides (9). positively as BACE1-AS (37) and TINCR (38), and negatively as ½-sbsRNAs (39), or translation, as lincRNA p21 (40). Another role is that of decoys for microRNAs (miRNAs): in this case, the lncRNA functions as a competing endogenous RNA (ceRNA) that sequesters miRNAs from their mRNA targets, causing translational de-repression. This activity is based on regulatory crosstalk between multiple transcripts (41, 42). Notably, lncRNA- mediated ceRNA networks in cancer are continuously emerging (43, 44). However, only for a very limited number, such as Gas5 (45), linc-RoR (46, 47), NORAD (48), and linc-NeD125 (49), this function has been characterized: their aberrant enrichment or local increased concentration in pathological conditions can culminate in tumorigenesis. Finally, some lncRNAs may contain short open reading frames producing small, functional peptides (50). epigenetic level by recruiting chromatin modifiers to specific genomic loci. This is achieved through their scaffolding activity, by which they interact simultaneously with distinct protein complexes, and through their capability to act as “molecular guides,” that ensure the specificity of target recognition (21). This function can be carried out in cis or in trans. Nuclear lncRNAs The cis-acting RNAs are typically low-abundant, and regulated genes are located in the proximity of their transcription site; trans-acting RNAs are more abundant and can modulate the expression of genes at independent loci (21). Notably, perturbations of the epigenetic regulation were recognized as causative of malignancies (22), and some cancer-related lncRNAs, such as XIST (23), HOTAIR (24– 26), NBAT (27), and LINC-PINT (28), were reported to direct epigenetic modifications (29). Nuclear lncRNAs can also act as regulators of transcriptional programs, by recruiting transcription activators or repressors to specific loci (30, 31), as enhancer RNAs that exert enhancer-like functions (32, 33), as chromosome architects and nuclear organizers that contribute to the formation of specific sub-nuclear structures (21, 34, 35), or as regulators of alternative splicing (36). THE ROLE OF LNCRNAS IN CNS The CNS of mammals is a very sophisticated system in which neuronal and glial cells structurally and functionally interact to guarantee the proper brain activity. Numerous evidence correlates the evolutionary increase in human brain complexity with the expanding number of lncRNAs (51, 52). Accordingly, 40% of human annotated lncRNAs are expressed in the brain, where they display neuro-anatomical and/or cell-type specific expression, and about 30% of lncRNAs appears to be primate- specific (31, 53). Notably, compared to lncRNAs from other tissues, the brain-specific lncRNAs are: (i) the most evolutionarily Frontiers in Pediatrics | www.frontiersin.org Cytoplasmic lncRNAs In vitro studies revealed some lncRNAs, such as RMST (60), TUNA (61), DALI (62), and PAUPAR (63), that control complex gene expression programs underlying the neurogenic commitment of pluripotent embryonic stem cells. This is mainly achieved through their action of “guide” RNAs that convey transcriptional and/or epigenetic factors on the promoters of neuronal genes. In vivo analyses identified other species such as GOMAFU (56, 64, 65), EVF2 (66), PNKY (67), and linc-BRN1B (68) that, through the recruitment of epigenetic, transcriptional, or splicing factors, govern the balance between self-renewal and neuronal differentiation. LncRNAs also contribute to synaptogenesis and neuronal plasticity, which underlies learning, memory, and cognition, by regulating crucial proteins that control neurite elaboration (69), translation in synapses (70, 71), and ion channel subunits (72). Neuroblastoma (NB) is a pediatric tumor of the sympathetic NS, accounting for more than 7% of childhood malignancies (85). The molecular link between deregulated lncRNA expression and NB tumorigenic features is emerging (86), and several deregulated lncRNAs during NB pathogenesis have been uncovered (87–92). Our knowledge of lncRNA function in MB physiopathology is still fragmentary. Genome-wide association studies may help to understand how genetic polymorphisms in lncRNA loci contribute to MB predisposition (93). Furthermore, in spite of the numerous high-throughput expression studies carried out so far, lncRNAs have been largely disregarded. However, re-annotation of array-based data and integration of cancer phenotype associations allowed prioritizing disease-related lncRNAs in tumors, including MB (94), demonstrating the potential of data re-analyses. In another study, a de-novo genome-wide inspection of MB subgroup-specific chromosomal alterations identified the first G3 MB gene fusions (6). They involve the 5′-end of PVT1, a lncRNA hosting the putative MB oncogene miR-1024 (95, 96). In the PVT1-MYC fusion, the induction of miR-1024 and the associated malignant phenotype may be explained through an oncogenic positive feedback-loop, established by MYC on its response elements on PVT1 promoter (6). Other studies focused on the role played in MB by previously identified noncoding oncogenes. Among them, UCA1 (97) and CRNDE (98, 99) are upregulated in MB samples. UCA1 knockdown in MB cells results in the arrest of cell cycle progression, suppression of cell migration, and proliferation (100). Similarly, in vitro downregulation of CRNDE blocked cell cycle, inhibited proliferation and aggregation, while increasing apoptosis. Tumor growth was also reduced in MB mouse models silenced for CRNDE (101). Cytoplasmic lncRNAs Inversely, the lncRNA HOTAIR (102) is downregulated in MB samples, whereas its target genes HOXD8 and HOXD10 are upregulated (103). The misbalance of these crucial developmental genes may partially account for the embryonic origin and the pediatric onset of MB. However, their mechanisms of action are presently unknown. Cytoplasmic lncRNAs Cytoplasmic lncRNAs (Figure 1B) regulate gene expression at the post-transcriptional level, often exploiting their sequence complementarity with transcripts deriving from the same genomic locus or from independent loci. Upon specific target recognition, they are able to modulate mRNA stability, both March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org 3 Long Noncoding RNAs in Medulloblastoma Laneve et al. conserved species, (ii) predicted to retain conserved secondary structures, and (iii) preferentially adjacent to protein-coding genes involved in neuronal differentiation and function (54). Overall, these findings indicate that brain-specific lncRNAs likely possess conserved functions and are crucially implicated in higher-order cognitive abilities as well as in establishing neural cell-type diversity and function. This hypothesis is sustained by their spatiotemporal expression, which is exquisitely regulated during NS development (55) and in response to neuronal activity (56). So far, a growing body of literature shows that lncRNAs influence every step of neurodevelopment, from early stages of differentiation to synaptogenesis (57–59). In vitro studies revealed some lncRNAs, such as RMST (60), TUNA (61), DALI (62), and PAUPAR (63), that control complex gene expression programs underlying the neurogenic commitment of pluripotent embryonic stem cells. This is mainly achieved through their action of “guide” RNAs that convey transcriptional and/or epigenetic factors on the promoters of neuronal genes. In vivo analyses identified other species such as GOMAFU (56, 64, 65), EVF2 (66), PNKY (67), and linc-BRN1B (68) that, through the recruitment of epigenetic, transcriptional, or splicing factors, govern the balance between self-renewal and neuronal differentiation. LncRNAs also contribute to synaptogenesis and neuronal plasticity, which underlies learning, memory, and cognition, by regulating crucial proteins that control neurite elaboration (69), translation in synapses (70, 71), and ion channel subunits (72). conserved species, (ii) predicted to retain conserved secondary structures, and (iii) preferentially adjacent to protein-coding genes involved in neuronal differentiation and function (54). Overall, these findings indicate that brain-specific lncRNAs likely possess conserved functions and are crucially implicated in higher-order cognitive abilities as well as in establishing neural cell-type diversity and function. This hypothesis is sustained by their spatiotemporal expression, which is exquisitely regulated during NS development (55) and in response to neuronal activity (56). So far, a growing body of literature shows that lncRNAs influence every step of neurodevelopment, from early stages of differentiation to synaptogenesis (57–59). Frontiers in Pediatrics | www.frontiersin.org LNCRNAS IN NEURO-ONCOLOGICAL DISORDERS Based on their crucial role in NS development and function, lncRNA qualitative and/or quantitative alterations may profoundly impact on different neurological pathologies, including neurodevelopmental, neurodegenerative, neuro- immunological, and neuro-oncological disorders (73, 74). In the latter settings, lncRNAs have drawn extensive attention as molecules that may drive tumorigenesis. In addition, they can serve as predictors of cancer sub-types as well as potential therapeutic targets. Mechanistic insights into the role of lncRNAs in MB biology have been carried out only for a very few species, as discussed below. Mechanisms of Action of lncRNAs in Mb Mechanisms of Action of lncRNAs in Mb The colon cancer upregulated transcript CCAT1 (104) is a prototype of oncogenic lncRNA, associated with several carcinomas, where it promotes cell proliferation, invasion, migration, and chemoresistence (105–107). In MB, its expression is upregulated in 20 unstratified tumor samples and also in at least four MB cell lines (108). CCAT1 knockdown in MB cells causes the decrease of cell proliferation rate, (depending on CCNA and CDK2 gene repression), cell migration, and invasion. Its in vivo depletion reduces the volume of subcutaneous tumors of xenotransplanted mice (108). CCAT1 has been proposed to play its oncogenic role by altering the phosphorylated, active status of components of the tumorigenic MAPK pathway. In combination with previous reports indicating CCAT1 as a miRNA sponge (109–111), this study suggests that CCAT1 may control tumorigenesis through multiple activities. It is widely understood that mutations, epigenetic alterations or somatic copy number aberrations in the noncoding portion of the genome underlie cancer pathology (75). Accordingly, recent studies indicated that lncRNAs are highly deregulated in cancer, where they participate as tumor-suppressors or oncogenes in tumor initiation and progression. Notably, most lncRNAs displaying aberrant expression are cancer-type unique (76). However, despite the identification of a large number of lncRNAs in neurological cancers, only for a few of them mechanisms of action have been experimentally clarified. Extensive studies have been carried out in gliomas, the most prevalent types of primary intracranial carcinoma (77). Several lncRNAs associated with glioma stemness (78–80), proliferation, and migration (81–84) have been identified, and most of them function as miRNA decoys (81). March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org 4 Long Noncoding RNAs in Medulloblastoma Laneve et al. FIGURE 2 | Linc-NeD125-based network in MB. (A) MiR-19a-3p, miR-19b-3p, and miR-106a-5p pleiotropically control KDM6A, MYCN, CDK6, SNCAIP gene expression. (B) In G4 MB, linc-NeD125 is upregulated and, functioning as a decoy for the three miRNAs, causes translational derepression of the G4 MB driver genes KDM6A, MYCN, CDK6, SNCAIP. FIGURE 2 | Linc-NeD125-based network in MB. (A) MiR-19a-3p, miR-19b-3p, and miR-106a-5p pleiotropically control KDM6A, MYCN, CDK6, SNCAIP gene expression. (B) In G4 MB, linc-NeD125 is upregulated and, functioning as a decoy for the three miRNAs, causes translational derepression of the G4 MB driver genes KDM6A, MYCN, CDK6, SNCAIP. Mechanisms of Action of lncRNAs in Mb Another lncRNA implicated in MB is ANRIL (112), which plays a pivotal role in multiple cancers as an epigenetic regulator of its neighbor tumor-suppressors CDKN2A/B (113, 114). ANRIL expression is upregulated in MB cells, where its knockdown lowers cell viability and migration while increasing apoptosis, by deranging the expression of several apoptotic factors (115). ANRIL has been shown to act as a decoy for miR-323, a miRNA identified in neurons (116) and characterized as a glioma tumor-suppressor (117, 118). Consistently, miR-323 silencing counteracted the abovementioned ANRIL-dependent cell phenotypes. This regulative axis impinges on BRI3, a miR-323 target gene (119) encoding for a brain-expressed transmembrane factor (120). BRI3 activates MAPK, AKT and WNT signaling cascades, already associated with MB progression (121–123), through a double mechanism: BRI3 upregulation enhances the phosphorylation of p38, MAPK, ERK, and AKT kinases and stimulates the accumulation of Wnt3a, Wnt5a, and β- catenin. The dysregulation of such pathways may partially explain the apoptotic phenotypes observed upon imbalance of ANRIL/miR-323/BRI3 module (115). Recently, the ceRNA mechanism has emerged as a crucial pathogenic pathway in MB. Linc-NeD125 was the first ceRNA identified in MB and, generally, in tumors of the CNS (49). It was identified in NB cells as the precursor of miR-125-b1 (126), a neuronal-enriched miRNA (127) involved in neural cell differentiation (128), function (129) and NB and MB cell proliferation, and apoptosis (130, 131). Notably, linc-Ned125 is significantly and specifically upregulated in primary G4 MBs, compared to the other subgroups. In this context, it functions as a miRNA decoy. Linc-NeD125 interacts with miR-19a-3p, miR-19b-3p, and miR-106a-5p that pleiotropically control the expression of four G4 MB driver genes, namely KDM6A, MYCN, CDK6, and SNCAIP (7) (Figure 2). Through this mechanism, linc-NeD125 causes the driver gene translational de-repression, contributing to G4 MB tumorigenesis and/or to the maintenance of cancer cell identity. This study highlighted linc-NeD125 as a novel potential G4 driver gene, as well as a specific biomarker and a potential therapeutic target. Accordingly, its knockdown in G4- derived cells caused a significant reduction of cell proliferation, migration, and invasion (49). The second example of ceRNA in MB is the lncRNA Nkx2- 2as, that behaves as a tumor-suppressor in SHH MB subgroup. It is highly down-regulated in MB cells derived from a SHH mouse model and it suppresses the malignant phenotype of MB cells, functioning as a sponge for miR-103/107 and miR-548 m. Frontiers in Pediatrics | www.frontiersin.org REFERENCES 12. 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More recently, the lncRNA LOXL1-AS1, the antisense transcript to the LOXL1 genomic locus, whose variants are strongly associated with the exfoliation syndrome (124), was found to be overexpressed in MB tissues. In vitro and in vivo experiments revealed that it controls cell viability, proliferation, cell cycle, and metastasis by activating the PI3K- AKT pathway (125). March 2019 | Volume 7 | Article 67 Frontiers in Pediatrics | www.frontiersin.org 5 Long Noncoding RNAs in Medulloblastoma Laneve et al. FUTURE DIRECTIONS and cerebrospinal fluids, making the tumor diagnosis less invasive (75). Notably, lncRNAs are also considered new relevant targets for cancer therapy as highly tissue-specific drivers of cancer phenotypes. Finally, in this search for lncRNAs as novel molecules that distinguish clinically relevant cancer subtypes and predict tumor behavior, the circular RNAs are proving to be effective cancer biomarkers for their abundance, stability, and specificity (135). The main challenges in fighting cancer are the identification of specific biomarkers, for timely diagnosis and prognosis, and novel tumor-driver genes, which can be therapeutically targeted for suppressing tumor growth. The former function would help the choice of pre-operative treatments and facilitate the tumor follow-up examinations. Unfortunately, very few biomarkers are known for pediatric tumors (133) and in MB <20 protein-coding genes have been characterized as promising candidates. However, most of these biomarkers were identified from single studies and from heterogeneous tumor types, lacking tumor-specificity (133). The recent categorization of MB into at least four subtypes, with distinct features, led the scientists to consider them as distinct pathologies with likely different responses to therapy. This new perspective triggered the search for novel MB-subgroup specific biomarkers and therapeutic targets. For both issues lncRNAs are very challenging (75). 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Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis
Maǧallaẗ Diyālá al-ṭibbiyyaẗ/Maǧallaẗ diyālá al-ṭibbiyyaẗ
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Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Background: Leukemias are classified as lymphoid or myeloid, dependent on the type of stem cell that is affected. In addition, leukemia is classified as chronic or acute. Acute leukemia is a production of bone marrow-derived immature cells (blasts), include solid organs or peripheral blood. The FAB Cooperative Group original classification scheme proposed to divide1 ALL into three subtypes (L1 - L3). Currently, the world health organization (WHO), modify FAB classification depending on immunophenotype. Symptoms presence of anemia, splenomegaly, and thrombocytopenia, and those are naturally present at diagnosis, indicating the degree to which leukemic lymphoblasts have replaced the bone marrow and the first mark to an ALL diagnosis is typically an abnormal complete blood count result. Objective: To introduce causes of acute lymphocytic leukemia, recent classification methods, diagnosis, and symptoms and diagnosis. Conclusion: Acute lymphocytic leukemia occurs due to a defect in the bone marrow and is classified into several types. The most important classification by the World Health Organization is depending on immunophenotype. The main symptoms are the increase in white blood cells with anemia and thrombocytopenia. Fatimah Kadhim Ibrahim AL- Mahdawi Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Diyala Journal of Medicine Introduction ionizing radiation exposure, chromosomal abnormalities (Down syndrome), chemical compounds (benzene), or families with leukemic history/ members constitute the risk factors [2]. Abnormal production of blood cells in the bone marrow and blood-forming organs leads to a malignant disease usually referred to as leukemia, which can be categorized according to the rate progression [1]. Leukemia etiology is poorly described, with most authors finding it to be multifactorial. Thus, viral infections (Epstein Barr), 1 Medical Lab Technologies Department, Bilad Al-Rafidain University College -Diyala- Iraq 2 Baqubah Teaching Hospital- Diyala Health Directorate-Diyala-Iraq Acute Leukemia Acute leukemia is a production of bone marrow-derived immature cells (blasts), include solid organs or peripheral blood. Lymphoid leukemia is derived from the lymphoid stem cells, which normally give rise to the lymphocytes (T-cells, B-cells, dendric cells, natural killer cells, and plasma cells) [5]. For several forms of leukemia, the ratio of blast cells essential for acute leukemia diagnosis is greater than twenty percent, and don’t need any minimum percentage of blast cell when certain morphological and cytogenetic characteristics are present [6]. Lymphoblastic Acute lymphoblastic leukemia. “Acute” means leukemia will develop rapidly and will be lethal within a few months if untreated. "Lymphoblastic" means that it develops from early immature forms of lymphocytes, a type of leukocytes [8]. Classification Leukemia is a class of malignant hematologic disorder with mesenchymal Vol.19.Issue 2,December 2020 59 Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Fatimah Kadhim Ibrahim AL- Mahdawi Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis (lymphoid or myeloid) origin arising from the bone marrow, produces a high number of abnormal hematopoietic cells in terms of their proliferation, differentiation, and cell death programming (apoptosis) [3]. Leukemias are classified as lymphoid or myeloid, dependent on the type of stem cell that is affected. In addition, leukemia is classified as chronic or acute [4]. Types of Acute Leukemia Acute leukemia is divided into two main types acute lymphoblastic leukemia and acute myeloid leukemia dependent on the origin of whether the blasts are present to be lymphoblasts or myeloblasts [7]. Vol.19.Issue 2,December 2020 Diyala Journal of Medicine Classification of ALL The classification of ALL by French- American-British is based on morphology and cytochemical staining of blasts [9] Figure (1). The FAB Cooperative Group original classification scheme proposed to divide1 ALL into three subtypes (L1 - L3) [10]. Table 1 explains the characteristics of three subgroups of ALL as reported by Conter et al., 2004 [11]. Table (1): Characteristics of Acute Lymphoblastic Leukemia Subtypes of ALL Characteristics L1 lymphoblast  The small cells with a high nucleus-to-cytoplasm ratio.  Pale blue cytoplasm is rare, and confined to a tiny portion of the perimeter.  The cells have unclear nuclei and membranes of nuclei vary from round to cleft. L2 lymphoblast  Larger cells with a lower nucleus-to-cytoplasm ratio, particularly in a more heterogeneous population  Prominent nuclei (often with perinuclear chromatin condensation) and membranes of nuclear may be irregular or reniform. L3 lymphoblast  Heterogeneous group of cells similar to Burkitt’s-like leukemia, with deep basophilic cytoplasm and prominent cytoplasmic vacuolization Vol.19.Issue 2,December 2020 Diyala Journal of Medicine 60 c Leukemia, Classification, Clinical features and Diagnosis Fatimah Kadhim Ibrahim AL- Mahdawi A B C Figure (1): FAB morphological classification of lymphoblasts A: L1, B:L2, and C: L3 lymphoblasts [12] Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis A B C Figure (1): FAB morphological classification of lymphoblasts A: L1, B:L2, and C: L3 lymphoblasts [12] B A A B C Figure (1): FAB morphological classification of lymphoblasts A: L1, B:L2, and C: L3 lymphoblasts [12] B A C A A C Figure (1): FAB morphological classification of lymphoblasts A: L1, B:L2, and C: L3 lymphoblasts [12] Currently, the World Health Organization (WHO), modify FAB classification depending on immunophenotype as follows: [13]. of these advances, 2008 WHO classification incorporated the category of B-lymphoblastic leukemia/lymphoma with recurrent genetic abnormalities into the classification of precursor lymphoid neoplasms. Based on the knowledge available at the time, genetic lesions associated with distinct clinical features, immunophenotype, prognosis, or other unique biological characteristics were included in this category [14]. • Acute Lymphoblastic Leukemia in B-cell • Acute Lymphoblastic Leukemia in B-cell • Early pre-B Acute Lymphoblastic Leukemia (named pro B Acute Lymphoblastic Leukemia) - around 10% of cases. • Common Acute Lymphoblastic Leukemia - around 50% of cases. • Mature B-cell Acute Lymphoblastic Leukemia (Burkitt's leukemia) - around 4% of cases. Vol.19.Issue 2,December 2020 Diyala Journal of Medicine Diyala Journal of Medicine Classification of ALL Immunophenotyping is an important adjunct to diagnosis and is helpful in confirming the diagnosis as well as lineage allocation to leukemia. When interpreting the immunophenotype data, one should keep in mind that no single antigen is specific for any neoplasm and that combining morphologic features and a panel of antigenic markers is necessary to obtain a correct diagnosis Table (1). • Acute Lymphoblastic Leukemia in T-cell. • Pre-T Acute Lymphoblastic Leukemia - around 5-10% of cases. • Mature-T cell Acute Lymphoblastic Leukemia - around 15-20% of cases. Recent years have seen tremendous progress in uncovering genetic lesions that influence the biology of ALL. In recognition Vol.19.Issue 2,December 2020 Diyala Journal of Medicine 61 Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Fatimah Kadhim Ibrahim AL- Mahdawi Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Fatimah Kadhim Ibrahim AL- Mahdawi In addition, the combinations of markers expressed are to some extent reflective of the normal B- and T-cell development and can be used to determine the stage of development at which the leukemia transformation happened Table (2). In B-ALL this stage of maturation frequently correlates with the underlying cytogenetic abnormality. In T- ALL, the stage of maturation has been shown to correlate with survival in some studies. Finally, it must be pointed out that the expression of myeloid antigens is see frequently in B- and T-ALL and does no preclude the diagnosis of ALL. Similarly, B lineage antigens can be expressed in T-AL and vice versa. The criteria for making th diagnosis of acute leukemias of ambiguou lineage have been extensively revised in th 2008 World Health Organization (WHO classification. The requirements for assignin more than 1 lineage to given leukemia ar summarized in Table (3). In addition, the combinations of markers expressed are to some extent reflective of the normal B- and T-cell development and can be used to determine the stage of development at which the leukemia transformation happened Table (2). In B-ALL this stage of maturation frequently correlates with the underlying cytogenetic abnormality. In T- ALL, the stage of maturation has been shown to correlate with survival in some studies. Finally, it must be pointed out that the expression of myeloid antigens is seen frequently in B- and T-ALL and does not preclude the diagnosis of ALL. Similarly, B- lineage antigens can be expressed in T-ALL and vice versa. Diyala Journal of Medicine Vol.19.Issue 2,December 2020 Classification of ALL The criteria for making the diagnosis of acute leukemias of ambiguous lineage have been extensively revised in the 2008 World Health Organization (WHO) classification. The requirements for assigning more than 1 lineage to given leukemia are summarized in Table (3). ): Prevalence of migraine among obese versus non-obese individuals Table (2): Prevalence of migraine among obese versus non-obese individuals Commonly positive Variable expression B-ALL CD19* cCD22* cCD79a* PAX5† CD10 sCD22 CD24 TdT CD20 CD34 CD45 CD13 CD33 sIgM‡ T-ALL cCD3§ TdT CD7 CD1a CD2 sCD3 CD4¶ CD5 CD8¶ CD10 CD34 CD99 CD19 CD33 CD79a CD117 CD56 Antigens are listed approximately in order of frequency. Abbreviations: c, cytoplasmic; s, surface. *Almost always positive. †Most specific for B lineage, but can be positive in t(8;21) AML. ‡Rarely present. §Only marker considered lineage specific. ¶ Maybe co-expressed. Diyala Journal of Medicine Vol.19.Issue 2,December 2020 Diyala Journal of Medicine 62 Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Fatimah Kadhim Ibrahim AL- Mahdawi Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Fatimah Kadhim Ibrahim AL- Mahdawi Table (3): Immunophenotype of B and T lymphocyte progenitors B lineage CD10 CD19 CD22 CD79a Tdt Ig Early precursor (pro-B) Intermediate (common) Pre-B - + ± + + + + + + + + + + + + - - C-mu T lineage CD1a CD2 CD3 CD4 CD7 CD8 CD34 Pro-T Pre-T Cortical T Medullary T - - + - - + + + C C C C,S - - + * + + + - - + * ± ± - - Abbreviations: C, cytoplasmic; S, surface. *Medullary T lymphocytes are positive for either CD4 or CD8, but not both. Table (4): Criteria for Ambiguous Lineage Assignment Lineage Markers Myeloid Myeloperoxidase staining or At least 2 markers of monocytic differentiation ● NSE ● CD11c ● CD14 ● CD64 ● Lysozyme T lymphocyte Cytoplasmic CD3 demonstrated by flow cytometry using antibody specific to the epsilon chain ● Surface CD3 B lymphocyte Strong CD19 with at least 1 additional marker or Weak CD19 with at least 2 additional markers ● CD79a ● Cytoplasmic CD22 ● CD10 Clinical features of ALL indicating the degree to which leukemic lymphoblasts have replaced the bone marrow [16]. The first mark to an ALL diagnosis is typically an abnormal complete blood count result. Conclusions Acute lymphocytic leukemia occurs due to a defect in the bone marrow and is classified into several types. The most important classification by the World Health Classification of ALL A raised leukocyte (WBC count more than 10.000/mm3) [12]. Peripheral blood smears show blasts cells. Present thrombocytopenia (platelet count less than 100.000/mm3), and also anemia is present (hemoglobin less than 10g/dL), which is typically normocytic and normochromic with decrease reticulocytes number[17]. Conclusions Symptoms and signs of acute leukemia are caused by blasts cells infiltrating the bone marrow or extramedullary [10]. The signs are anemia, splenomegaly, and thrombocytopenia [1]. Others common symptoms and signs include fever, fatigue, weight loss, loss of appetite, malaise, palpitations, shortness of breath, dizziness, cold sensitivity, paleness, bleeding and easy bruising, sore throat, problems in vision, pain in joints, nausea, night sweats, heaabdominal abdominal discomfort, Feeling of fullness in the abdomen [15]. Diagnosis of ALL Abnormal leukocyte, thrombocytopenia and anemia are naturally present at diagnosis, Vol.19.Issue 2,December 2020 Diyala Journal of Medicine Diyala Journal of Medicine 63 Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis Organization is depending on immunophenotype. The main symptoms are the increase in white blood cells with anemia and thrombocytopenia. [9]N. L. Harris et al., “The World Health Organization classification of hematological malignancies report of the clinical advisory committee meeting, Airlie House, Virginia, November 1997,” Mod. Pathol., vol. 13, no. 2, p. 193, 2000. on Recommendations For classification of acute leukemia, it’s better to involve many parameters including morphology and immunophenotyping markers. [10] P. Mittal and K. R. Meehan, “The acute leukemias,” Hosp. Physician, vol. 5, pp. 37– 44, 2001. [11] V. Conter and C. Rizzari, “S Sala A,” Chiesa R, Citterio M ala Biondi A Ab Acute Lymphoblastic Leuk. Orphanet Encycl. Creat. date December, 2004. [11] V. Conter and C. Rizzari, “S Sala A,” Chiesa R, Citterio M ala Biondi A Ab Acute Lymphoblastic Leuk. Orphanet Encycl. Creat. date December, 2004. [12]J. Roganovic, “Acute lymphoblastic leukemia in children,” in Leukemia, IntechOpen, 2013. Vol.19.Issue 2,December 2020 Diyala Journal of Medicine References [1] M. Roy, A. Mukherjee, S. Mukherjee, and J. Biswas, “Leukemia Causes, Symptoms & Treatment. [1] M. Roy, A. Mukherjee, S. Mukherjee, and J. Biswas, “Leukemia Causes, Symptoms & Treatment. [12]J. Roganovic, “Acute lymphoblastic leukemia in children,” in Leukemia, IntechOpen, 2013. [2] P. Stana, G. Marina, and D. Anca, “Oral Manifestations in Acute Leukemia as the First Sign; The Interdisciplinary Approach of Diagnosis and Treatment,” J Mind Med. Sci 2015; 2(2):186–192. [13]S. Mostert, M. N. Sitaresmi, C. M. Gundy, and A. J. P. Veerman, “Influence of socioeconomic status on childhood acute lymphoblastic leukemia treatment in Indonesia,” Pediatrics, vol. 118, no. 6, pp. e1600–e1606, 2006. [3]P. Chandran et al., “Mesenchymal stromal cells from patients with acute myeloid leukemia have altered capacity to expand differentiated. hematopoietic progenitors,” Leuk. Res., vol. 39, no. 4, pp. 486–493, 2015. [4] W. Lockwood, “Leukemia: AML, CML, ALL and CLL.” 2015. [14]S. McGregor, J. McNeer, and S. Gurbuxani, “Beyond the 2008 World Health Organization classification: the role of the hematopathology laboratory in the diagnosis and management of acute lymphoblastic leukemia,” in Seminars in diagnostic pathology, 2012, vol. 29, no. 1, pp. 2–11. [5]N. J. Goulden and C. G. Steward, Pediatric Hematology: Methods and Protocols, vol. 91. Springer Science & Business Media, 2004. [5]N. J. Goulden and C. G. Steward, Pediatric Hematology: Methods and Protocols, vol. 91. Springer Science & Business Media, 2004. [15] E. A. Shephard, R. D. Neal, P. W. Rose, F. M. Walter, and W. Hamilton, “Symptoms of adult chronic and acute leukaemia before diagnosis: large primary care case-control studies using electronic records,” Br J Gen Pr., vol. 66, no. 644, pp. e182–e188, 2016. [16]G. Abdul-Hamid, “Classification of Acute Leukemia,” in Acute Leukemia-The Scientist’s Perspective and Challenge, IntechOpen, 2011. [6]M. Antica, Acute Leukemia: The Scientist’s Perspective and Challenge. BoD– Books on Demand, 2011. [6]M. Antica, Acute Leukemia: The Scientist’s Perspective and Challenge. BoD– Books on Demand, 2011. [7]A. V. Hoffbrand and D. P. Steensma, Hoffbrand’s essential haematology. John Wiley & Sons, 2019. [8]R. Hoffman, E. J. Benz Jr, L. E. Silberstein, H. Heslop, J. Anastasi, and J. Weitz, Hematology: basic principles and practice. Elsevier Health Sciences, 2013. Vol.19.Issue 2,December 2020 Diyala Journal of Medicine 64 Fatimah Kadhim Ibrahim AL- Mahdawi Acute Lymphoblastic Leukemia, Classification, Clinical features and Diagnosis [18]Stewart WF, Roy J, Lipton RB. Migraine prevalence, socioeconomic status, and social causation. Neurology. 2013;81(11):948-55. 65
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Digital Socio-Technical Innovation and Indigenous Knowledge
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Abstract Scientific research involving remote rural communities is often plagued by a lack of understanding of what constitutes indigenous knowledge. That is, indigenous perspectives, models of representation, and their ways of knowing. Through a long-standing community-university partnership in working with remote and rural communities in the Borneo Malaysian states of Sarawak and Sarawak and the Orang Asli communities in Peninsular Malaysia, we address this concern in presenting directions for shaping digital socio-technical innovation. We highlight the need to adopt a balanced indigenous worldview based on two case studies from past inter- actions with these indigenous communities to highlight how indigenous knowledge can now become contextualized within contemporary problem-solving scenarios. Keywords: indigenous knowledge management, indigenous worldview, sustainability oriented socio-technical innovation Poline Bala, Narayanan Kulathuramaiyer and Tan Chong Eng Poline Bala, Narayanan Kulathuramaiyer and Tan Chong En 1. Introduction Propelled by developments of industrial revolution 4.0, nations are gearing towards a knowledge-intensive economy. Therefore, optimism towards scientific knowledge and digital-based innovation to drive economic growth is on the rise. However, the roles of indigenous peoples’ place-based knowledge, skills, and experiences have largely been overlooked in the expansion of the digital-based framework of technological innovation. This is due to a lack of understanding of what constitutes indigenous knowledge - indigenous perspectives, models of representation, and their ways of knowing. In fact, because of the appearance of incommensurables between the two types of knowledge, in their encounters with each other, indigenous knowledge is often sidelined. This is despite for the untold number of years indigenous knowledge has helped indigenous communities around the globe to stay resilient in the face of complex challenges and diverse adversities. Drawing on two decades of community-university partnerships between Universiti Malaysia Sarawak and five different rural indigenous communities in the Malaysian states of Sarawak and Sabah on the island of Borneo and four remote Orang Asli communities in Peninsular Malaysia, this paper highlights the need to adopt a bal- anced indigenous worldview in order to ensure that traditional knowledge remains intact in their encounters with other knowledge systems. This paper addresses this concern through a socio-technical system framework, which is a balanced ecosys- tem whereby technology is embedded and woven, rather than externally imposed, into a social system for a balanced human-machine interaction and the integration of scientific exploratory models in solving complex problems. This requires a 1 Recent Advances in Knowledge Management careful co-envisioned and co-designed framework in a participatory manner that benefits the symbiosis between people, the ecosystem, and the environment. The next section of the chapter provides a brief overview of indigenous knowl- edge; that is its characteristics and its increased importance in the development agenda framework at different levels: international, national, and communities. It then highlights an emerging barrier between indigenous knowledge and scientific knowledge due to the appearance of incommensurables between the two types of knowledge. The chapter then offers case studies to highlight what are the pos- sibilities of the weaving of these two kinds of knowledge through a socio-technical innovation system. This is followed by a discussion and conclusion to the chapter. 2. Literature review Over the last decade, there is increased awareness that the vast collection of traditional knowledge of indigenous communities holds the key to solve many complex problems. Built over generations through close interaction with natural surroundings and a deep understanding of nature’s sociality, indigenous knowledge has helped communities to be resilient, live sustainably, and face global challenges such as climate change. Due to its significance as a tremendous resource, there have been attempts to include indigenous knowledge to deal with global causes and concerns. A robust example is an effort by James David Wolfensohn, who served as president of the World Bank (1995–2005). In 1998, the World Bank acknowledges that indigenous knowledge “represents an important component of global knowledge” (World Bank, 1998, as cited by [1]). With that, there was a deliberate attempt to shift the institution’s focus towards humanitarian efforts by drawing on indigenous knowl- edge as a resource to enhance development processes. Over the years, considerable progress has been made in promoting indigenous knowledge. In 2010, the World Bank’s [2] published its Indigenous knowledge for development: a framework for action. The framework explains the need for indig- enous knowledge to play strategic roles to expand the benefits of development assis- tance through the organization’s development activities. Henceforth, the framework for action to increase understanding on the significance of IK amongst its develop- ment associates and to provide suggestions on how best it can be integrated into development practices. What is obvious is indigenous knowledge is considered essential for maintaining global cultural diversity and biological diversity. The UN special rapporteur on indigenous issues has pointed out that indigenous communities around the world are the most effective custodians of millions of hectares of forest, which act as the world’s lungs. It was suggested that localized indigenous perceptions of ecosystems and natural habitats are able to provide solu- tions to many of the world’s problems from climate change to biological diversity. Today, the role of indigenous knowledge are increasingly becoming part of the development agenda; national initiatives and policies have emerged, with civil society forming a broad base of support and the number of development projects as well as programs integrating traditional and indigenous knowledge has doubled up. This includes movement by indigenous peoples themselves to build a capac- ity building to maintain and protect biodiversity while at the same time creating alternative sources of economic income. 1. Introduction It concludes that a socio-technical innovation model, which is a balanced ecosystem where technology is embedded into a social system as an integral knowledge weav- ing, provides a useful system framework to contextualize indigenous knowledge within contemporary problem-solving scenarios. 2. Literature review A good example by the indigenous 2 Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 communities themselves is the FORMADAT initiative. It was set up in 2015 as The Alliance of the Indigenous Peoples of the Highlands in the Heart of Borneo. According to Bala, et al. [3] the initiative is “to build on the shared historical and cultural bonds between the Lundayeh, Kelabit, Lun Bawang, and Sa’ban peoples living in the highlands of the heart of Borneo. The group aims to integrate conserva- tion and development at the landscape level and to generate benefits for local people by preserving the rich natural and cultural diversity of the region, an area that includes the largest surviving intact forested and traditionally farmed catchment area on the island of Borneo.” 4. Taking indigenous knowledge seriously However, despite increased global recognition of indigenous communities’ knowledge to maintain global cultural diversity and biological diversity, arguably indigenous knowledge is gradually disappearing. This is a result of worldwide rapid development and landscape changes and also as a result of increased encounters between the paradigms of indigenous knowledge and scientific knowledge. p g g g g There is little doubt that UNESCO [10] has highlighted a recent shift in the rela- tionship between science and other systems of knowledge, reflected in the explicit recognition of indigenous knowledge in many global environmental governances described above. Nonetheless, there are still conflicting ideas about what it means to take indigenous knowledge seriously. There is still widespread assumption that science is superior to other knowledge systems. This stems mainly from the incom- mensurable between scientific and indigenous conceptual models, their ontologies, and their systems [11–14], which continue to create barriers to meaningful collabo- ration and the integration of indigenous and scientific knowledge. g g g As aptly described by Simeone ([15], pg. 1–2). He says, “Unlike the western custom of disseminating knowledge through publication, traditional knowledge systems exist principally in the form of songs, proverbs, stories, folklore, com- munity laws, common or collective property and inventions, practices, and rituals. The knowledge is transmitted through specific cultural mechanisms such as those just listed, and often through designated community knowledge hold- ers, such as elders. The knowledge is considered collective to the community, not private to one individual or small group.” He went to say that, “While Western science tends to be written and compartmentalize, IK are more holistic and are communicated orally. As orally based knowledge, IK are transmitted through observations and experiences while scientific knowledge are passed on through lectures and theories. Often times than not scientific knowledge are value-free and theoretical, whilst indigenous knowledge is more spiritual and embedded in social values.” The differences can be demonstrated by the following two diagrams, which illustrate the framing of the two types of knowledge. Diagram 1(a) is an illustration of indigenous knowledge, which was co-created with remote community leaders. Diagram 1(b) on the other hand represents the prescriptive modeling of knowledge by researchers structuring and creation of scientific knowledge (Figure 1). y g g g Due to the differences, some observers express concern that western science creates conflicts for indigenous knowledge and may even destroy it. • Context-embedded artifacts The characteristics listed above, highlights the knowledge gaps in current literature, calling for a deepening of understanding of what indigenous knowledge is, and how balance and fairness can be the basis for its assimilation. This paper explores these defining characteristics through the case studies explored, to shed some light towards a more balanced worldview. 3. Defining indigenous knowledge But what is indigenous knowledge? UNESCO provides a general portrayal to local and indigenous knowledge as the understandings, skills, and philosophies developed by societies with long histories of interaction with their natural sur- roundings. For rural and indigenous peoples, local knowledge informs decision- making about fundamental aspects of day-to-day life. g p y y Others are more descriptive in their definitions of indigenous knowledge. For instance, Warren ([4], p. 127) argues, indigenous knowledge is a profound, detailed and shared beliefs and rules with regards to the physical resource, social norms, health, ecosystem, culture, livelihood of the people who interact with environment both in rural and urban settings. It has been the basis for local level decision making in agriculture, health care, food preparation, education, natural resource manage- ment, and a host of other activities. Meanwhile, [5] highlights that “Indigenous people have had their own ways of looking at and relating to the world, the universe, and to each other. Their tradi- tional education processes were carefully constructed around observing natural processes, adapting modes of survival, obtaining sustenance from the plant and animal world, and using natural materials to make their tools and implements” (as cited by [6], p. 10). y p Gorjestani [7] observed that “Indigenous knowledge (IK) is used at the local level by communities as the basis for decisions pertaining to food security, human and animal health, education, natural resources management, and other vital activities. IK is a key element of the social capital of the poor and constitutes their main asset in their efforts to gain control of their own lives.” Masango [8] defined indigenous knowledge as “The totality of all knowledge and practices established on past experiences and observations that are held and used by people”. Gope et al. [9] characterized “Indigenous knowledge” as community-centric by nature, which reflects community practices and usually possesses a deep connection with land, locale, and community. Indigenous knowledge is highly tactic and hence it is quite difficult to codify and document Indigenous knowledge. Apart, indig- enous knowledge is usually disseminating across generations through content and by virtue of observing the various community practices. 3. Defining indigenous knowledge y g y From the extensive definitions above, some common characteristics attribute to indigenous knowledge include the following: • Multi-layered, multi-dimensional, based on a holistic worldview • Connections between all living things • Understanding for fair distribution of resource 3 Recent Advances in Knowledge Management • Integrated lifestyles (knowledge embedded in life) • Integrated lifestyles (knowledge embedded in life) • Modeled & exchanged implicitly • Context-embedded artifacts 4. Taking indigenous knowledge seriously This has led to calls for a shift in understanding indigenous knowledge to dismantle the barriers between indigenous traditional knowledge and scientific knowledge [16]. It is this call which inspires this chapter for it encapsulates the experiences we have gained 4 Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 Figure 1. (a), (b): The framing of indigenous and scientific knowledge. Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 Figure 1. (a), (b): The framing of indigenous and scientific knowledge. over two decades of research in rural digital inclusion efforts by introducing infor- mation communication technologies (ICTs), especially the internet as new tools for social and economic transformations amongst indigenous communities in Malaysia. This is within a challenging context: terrain with extreme variations in elevation, long distances, and sparce populations located in widespread locations. Moreover, with communities with diverse ethnic backgrounds and with different levels of socioeconomic status, and at times zero digital literacy. g y The diverse and dispersed communities require a careful context-specific for the deployment of the information communication technologies and their designs. Not only the team encounter differences in terms of experiences and standard of living but lifestyle, cultural practices, and worldviews, which are constitutive of their indigenous knowledge. 5. Background context In 1999 an interdisciplinary team of researchers based at Universiti Malaysia Sarawak (UNIMAS) has embarked on the e-Bario project in the Kelabit Highlands of Sarawak [17]. This was to explore how indigenous communities in remote and rural areas can be “integrated” in Malaysia’s race towards a Knowledge based-society by 2010. The knowledge society framework was deemed to inculcate the values and culture of life-long learning and the creation of knowledge-based products and services amongst its population. Exploring the use of telephones, computers, Very Small Aperture Terminals (VSATs), and the Internet, e-Bario was implemented as a pilot project to explore the economic, social, and cultural potentials of ICTs through community-based Telecentre model for rural development in Sarawak. This is especially because ICTs are predicted to promote new social, economic, and cultural opportunities in rural areas [18]. pp Due to its success e-Bario became a catalyst to explore the roles that telecentre can play in advancing community-based development amongst other indigenous communities in Sarawak, Sabah, and Peninsular Malaysia. As a consequence, the University has formed long-standing community-university partnerships with diverse and dispersed indigenous communities who live in remote and rural areas in Sarawak, Sabah, and Peninsular Malaysia. The out-of-the-way locations of these indigenous communities create immense distance both in time and space and therefore exemplify the disconnected portion of the digital divide in Malaysia. They are often are without network access, lack of 5 Recent Advances in Knowledge Management adjacent infrastructure (e.g., grid electricity), lack of digital and language literacy, low income and affordability, lack of relevant content and services as well as lack of cultural and social relevance and therefore acceptance [19]. See Table 1 for a complete list of the indigenous communities involved. p g There is no doubt that because of the lack of digital and language literacy, it was easy to assume that these indigenous communities are knowledge-poor and incom- petent in a global world. This is in spite of their capacities to manage the fragility of their own cultural heritage from human and non-human threats such as climate change. Their inherent indigenous wisdom are orally based and more embedded, therefore it was easy to overlook in the process of research and developmental efforts. Moreover, digital innovation framework has been torn between a western- scientific idea and a more indigenous, community-based concept. 5. Background context Little attention is given to indigenous place-based knowledge, skills, and experiences within the No Communities (Ethnic Group) Location Geographical terrain Economic activities Language 1 Kelabit Bario, Sarawak Upland plateau Wet Rice farming, hunting Process Timber Entrepreneurs Kelabit 2. Penan Long Lamai, Sarawak Mountain/riverine Hill rice farming, hunting and gathering Penan 3 Lun Bawang Ba Kelalan Highland/Valley Wet rice farming, border trading Lun Bawang 4 Bajau Pulau Larapan, Sabah Island Fishing Bajau 5 Dusun Kampung Buayan, Sabah Mountain range Farming, hunting, gathering Dusun 6 Temiar Pos Balar Mountain/riverine Farming, hunting, gathering Temiar 7 Temiar Pos Gob Mountain/ headwaters Farming, hunting, gathering Temiar 8 Semai Pos Lenjang Mountain/riverine Farming, hunting, gathering Semai 9 Semai Pos Sinderut Mountain/ headwaters/valley Farming, hunting, gathering, rubber tapping Semai Table 1. List of diverse and dispersed indigenous communities and bridging digital divide initiative by the Universiti Table 1. List of diverse and dispersed indigenous communities and bridging digital divide initiative by the Universiti Malaysia Sarawak (UNIMAS). 6 Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 expanding digital-based framework for knowledge management. These unique ways of knowing are important facets of the world’s cultural diversity and provide a foundation for locally appropriate sustainable development. It is made up of a rich understanding of the plant, crop, and tree species, medicines, animal breeds, and local ecological and biological resources. This includes their useful and adaptive techniques to respond to changes in the physical and social environment. Raise the question of whether is it possible to introduce and transfer academic knowledge about the new digital technologies without displacing the position or disintegrating the integrity of existing local indigenous knowledge. 7. Case study 1: community-led massive open online courses (MOOCs) for life long learning The Massive Open Online Courses is an outcome of the emerging knowl- edge society to empower everyone to contribute to knowledge exchange at the global level; leading to making higher education accessible to everyone. (see for instance Anant, [22]). Nonetheless, MOOCs model and framework is a challenge to blend in with the indigenous rural community way of life to sustain lifelong learning. Single mothers Association community members in Bario made the ill- fitting very clear to us when we first mooted the idea at a focus group discussion meeting. g In response, the spokesperson said: “Thank you for introducing this new system to us. We look at it and admire how it works for instance to provide means to receive and learn new ideas and things. That is very admirable. However, I don’t think we need any more ideas from outside to make us better farmers. In fact, over the years we have developed our own farming system and we are very good at it. Ilah let ngen tetepuh [knowledge from our ancestors]. And this is evident from the sufficient rice and food we provide for our families and our community. We would like to ask, why not use the platform for us to teach our skills and our languages to others especially our grandchildren. Currently, most of us are far removed from our grandchildren since most of them are living in town and are going to national schools where they learn other languages such as Bahasa Malaysia and English. As a result, many do not know to speak their mother tongue. We are not really able to communicate and teach them at the moment because of the distance and language barrier. Can we redesign your platform for us to teach them our way of life - for instance how to prepare our own traditional food and to introduce our traditional adornment which are important as markers of identity.” Another person went on to say, “With your platform [videos] you are able to capture what we do and keep them to show them. For we teach our younger genera- tion by showing them how it is done. They learn from observing and trying it out for themselves. We don’t teach them by giving them instructions, because for us when they try and do it for themselves after seeing us doing it, that knowledge will last longer in their minds. 6.1 Socio-technical systems innovation and case studies Models of socio-technical technical innovation such as the telecentre as a driver for socio-economic impact need to be carefully co-envisioned and co-designed in a participatory manner. The context of the innovation has to adopt a knowledge- based inquiry and as a value-creation activity that benefits the people, the ecosys- tem, and the environment. The design of such an Indigenous Innovation model has to be aligned to cul- tural protocols and norm and social practices to cultivate symbiotic relationships with people, the environment and nature (see [20]). This process-oriented model illustrated in Figure 2, will then drive balanced human-machine interactions and integrate with scientific exploratory models in solving complex problems [21]. 6. Methodological framing The method and approach employed have been largely guided by principles of participative, interdisciplinary, and transcultural interactions. First, it has been par- ticipative whereby indigenous local communities have been engaged in the design, planning, and implementation of the project. Second, the initiatives involved by an interdisciplinary team of researchers from different academic fields: anthropology, archaeology, geographer/geographic information system, computer science, and knowledge engineering sciences. Thirdly, it was transcultural in nature. It involved transcultural interactions between the scientists and community scholars, between members of the indigenous communities, and members of the multidisciplinary team. In short, it was a collaborative effort to ensure serious dialog and partnerships between knowledge experts and the local communities as collaborators. The latter are not merely recipients or objects of the technologies being introduced, but their worldviews and knowledge systems are taken seriously. Raise questions in what ways can the team develop models, protocols, and frameworks, which not only support the unique structure of indigenous knowledge but also facilitate efforts to weave the two knowledge towards a better understand- ing of indigenous knowledge systems. Is it possible to formulate knowledge portals or protocols in order to assimilate two knowledge paradigms, for instance, to digitally integrate the knowledge of the past through a digital based framework to increase local awareness, interest, and understanding about the significance and value of their world to others who matter to them. Two case studies of socio- technical innovation below aim to answer these concerns. Figure 2. Socio-technical innovation model. g Socio-technical innovation model. 7 7 Recent Advances in Knowledge Management 7. Case study 1: community-led massive open online courses (MOOCs) for life long learning I want to teach my grandchildren how to make this orna- ment using beads. There are many techniques that they should know, and they can only learn from us. Nobody else knows how to do this; they cannot learn it on their own. They have to learn from us.” y Invited as collaborators, the single mothers’ community members reshaped the current model of MOOC by fitting it into specific roles in the community. First, they have made it clear that they did not need any more information 8 Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 to upgrade their standard of living as farmers. Second, they would like to ensure that the knowledge – skills, expertise that they have accumulated over the years, not only be documented but to be passed on to their descendants (grandchildren). More importantly, by turning the project into a community-driven activity, the single mothers are transformed into knowledge creators and co-designers and not merely consumers of technological-based frameworks. They have redesigned the MOOC channel into community sustainability channels. Their stories suggest that for it to be fully appreciated, MOOCs has to deliver value as an integrated socio- technical system to enable life-long learning for indigenous rural communities. 8. eToro: innovation ecosystem This research began in 2007 amongst the indigenous Penan community in Long Lamai, Sarawak. Nomadic in the recent past, they still depend on the for- est for their livelihood. Through a trans-disciplinary, participatory approach, a long-standing partnership has evolved to closely mirror indigenous practices in knowledge sharing [23–25]. g g The socio-technical model approach as a knowledge-sharing networks started with the acknowledgment of the tremendous knowledge repository possessed by the community elders and which are implicitly locked in traditional practices. In order to understand their traditional knowledge system, the team adopted a visual charting approach to map the close link between the community laws, nature, the rainforest, social practices, language, culture and heritage, and customary practices and rituals. The deep connection between the land, locale, and community began to unravel through a family-based activity known as the Toro journey. As an intimate joint activity of a Penan family, Toro is an activity-based knowledge sharing and men- toring journey, which is usually undertaken within a period of a week solely for hunting, to collect forest resources, and also to groom future guardians of the forest (Figure 3). This is where plant knowledge related to social beliefs and for daily use is shared and transmitted. This includes knowledge of medicinal plant use and the meanings of different landscapes in their environment. As a forest-journey interac- tions and knowledge exchanges, the Toro journey provided snapshots on models of multidimensional layers of inherent indigenous wisdom. Figure 3. Penan elder: If you do not know your origin [Forest], you are not a Penan. Figure 3. Penan elder: If you do not know your origin [Forest], you are not a Penan. Figure 3. Figure 3. Penan elder: If you do not know your origin [Forest], you are not a Penan. 9 9 Recent Advances in Knowledge Management There is a concern that with the intervention of modern technology through the telecentre, the knowledge related to this symbiotic relationship might erode. But, the blended socio-technical model approach has enabled the rural community’s ‘knowledge-rich scholars’ to co-create technological solutions and involves the community to decide on the design of the system thereby allowing a snaturalized participation and involvement in collaboratively recording indigenous knowledge. A botanical indigenous knowledge base was thereby developed via a coordinated co-creation method where the elders worked closely with rural youths in document- ing local knowledge. 8. eToro: innovation ecosystem The knowledge elicitation activities benefitted fully from the community’s integral knowledge management capability without over-looking implicitly indigenous values. What is clear is that compared to a purely systemic approach in modeling community sustainability, the approach has revealed directions for unlocking intangible benefits by truly harnessing the previously untapped cultural heritage and implicitly held knowledge resources. Moreover, through the approach a multi- level decision-making process involving the community players in a variety of roles such as knowledge extraction system and systems interface co-designers, a co-constructed socio-technical innovation in an ecosystem of the equal partnership was produced (Figure 2). The drive of the spirited community that believed in the utmost need to conserve a symbiotic relationship with nature and the forest has been the impetus in empowering a values-based socio-technical innovation. 9. Findings and discussion The cases above suggest that any scientific knowledge and technological innova- tion as drivers either to promote knowledge-based products and services or to create values and culture of life-long learning amongst indigenous communities require careful co-envisioned and co-designed in a participatory manner. The context of the innovation has to adopt a knowledge-based inquiry and a value-creation activity that benefits the symbiosis between people, ecosystem, and environment. It is imperative to ensure that the intervention of modern technology must not erode knowledge processes related to this symbiotic relationship. This is important to bear in mind as indigenous communities are under increas- ing pressure to adapt to global knowledge. In their encounter with scientific knowledge, the values of their indigenous cultural knowledge are often in a disad- vantageous position and being undermined. This is in spite of the increased global recognition of indigenous communities’ knowledge not only to help indigenous communities to be resilient, live sustainably in the face of challenges such as climate change, but also to maintain global cultural diversity and biological diversity. g g y g y For the interdiscplinarian team from UNIMAS, who values sound methodological research, reframing the methodology towards participative, transcultural dialogs provide a framework to adopt a balanced indigenous worldview leading to proto- cols that inculcate the recognition of the coexistence of multiple worldviews and knowledge systems. Compare to a purely systemic approach in modeling community sustainability, the groundbreaking methodological model led to the development of a socio-technical technical systems innovation. As illustrated in Figures 4 and 5 this can lead to the harnessing of indigenous knowledge and worldviews to design indigenous innovation models. It involved the repurposing of technologies by align- ing them to cultural protocols and norms and social practices to cultivate symbiotic relationships with people, the environment, and nature. The process-oriented model (Figure 2) allows for a balanced human-machine interaction and the integration of scientific exploratory models in solving complex problems. 10 Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 Figure 4. eToro – Innovation ecosystem. Source: Adapted from [26, 27]. Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 Harnessing their oral-based indigenous knowledge expressions, the indigenous single mothers of the Kelabit community participated in producing MOOC modules with the reshaped model. 9. Findings and discussion This is to enable life-long learning for the indigenous women and their grandchildren through their community sustainability channels (Figure 5). Meanwhile, the e-Toro innovation system highlights indigenous place-based structured knowledge. Through the Toro journey as an activity-based knowledge sharing and mentoring journey, tacit indigenous knowledge is demonstrated and observed through carefully selected oral stories in which instruction and values are embedded In Figure 3 the designated community knowledge holder a Penan elder Figure 4. eToro – Innovation ecosystem. Source: Adapted from [26, 27]. Figure 5. MOOCs for community sustainability channels. Figure 4. Figure 4. eToro – Innovation ecosystem. Source: Adapted from [26, 27]. Figure 5 Figure 5. MOOCs for community sustainability channels. Figure 5. MOOCs for community sustainability channels. Figure 5. MOOCs for community sustainability channels. Harnessing their oral-based indigenous knowledge expressions, the indigenous single mothers of the Kelabit community participated in producing MOOC modules with the reshaped model. This is to enable life-long learning for the indigenous women and their grandchildren through their community sustainability channels (Figure 5). Meanwhile, the e-Toro innovation system highlights indigenous place-based structured knowledge. Through the Toro journey as an activity-based knowledge sharing and mentoring journey, tacit indigenous knowledge is demonstrated and observed through carefully selected oral stories in which instruction and values are embedded. In Figure 3, the designated community knowledge holder, a Penan elder transmits the value of knowing the forest: If you do not know your origin [Forest], you are not a Penan. Harnessing their oral-based indigenous knowledge expressions, the indigenous single mothers of the Kelabit community participated in producing MOOC modules with the reshaped model. This is to enable life-long learning for the indigenous women and their grandchildren through their community sustainability channels (Figure 5). Meanwhile, the e-Toro innovation system highlights indigenous place-based structured knowledge. Through the Toro journey as an activity-based knowledge sharing and mentoring journey, tacit indigenous knowledge is demonstrated and observed through carefully selected oral stories in which instruction and values are embedded. In Figure 3, the designated community knowledge holder, a Penan elder transmits the value of knowing the forest: If you do not know your origin [Forest], you are not a Penan. Meanwhile, the e-Toro innovation system highlights indigenous place-based structured knowledge. Through the Toro journey as an activity-based knowledge sharing and mentoring journey, tacit indigenous knowledge is demonstrated and observed through carefully selected oral stories in which instruction and values are embedded. In Figure 3, the designated community knowledge holder, a Penan elder transmits the value of knowing the forest: If you do not know your origin [Forest], you are not a Penan. 11 Recent Advances in Knowledge Management As depicted in case studies, the inherent layers and dimensions of societal struc- ture have to be preserved in the co-design efforts, to integrate within an encompass- ing framework that stakeholders can relate to and contribute to in a meaningful way. Figure 4. Connections between all living things relates to an over-arching principle of “unity in diversity” that has captured (as in both case studies) in the simplistic modeling terms through life-illustrations and analogical models of co-creation. 10. Conclusion Clearly, indigenous knowledge is integral to a cultural complex that also encom- passes language, systems of classification, resource use practices, social interac- tions, ritual, and spirituality. The recognition that local and indigenous people have their own ecological understandings, conservation practices, and resource manage- ment goals has important implications as indigenous people are now recognized as essential partners in environmental management. p g The paper has revealed directions, protocols, and framework for collaborative engagement between two different paradigms with regards to intangible benefits of previously untapped cultural heritage and implicitly held knowledge resources amongst indigenous communities. It has shed insights into how the socio-technical innovation model, which is a balanced ecosystem where technology is embedded into a social system as an integral knowledge weaving, provides a useful system framework to contextualize indigenous knowledge within contemporary problem- solving scenarios. As highlighted in this paper, the need to create a playground for the exchange of implicitly held knowledge, in co-created models that preserve the local context and scenario, and yet at the same time not separated from life-learning situations holds the key to the symbiotic blending of knowledge. Author details Poline Bala1*, Narayanan Kulathuramaiyer2 and Tan Chong Eng3 1 Institute of Borneo Studies, Universiti Malaysia Sarawak, Kuching, Malaysia 2 Institute of Social Informatics and Technological Innovation, Universiti Malaysia Sarawak, Kuching, Malaysia 3 Faculty of Computer Science and Information Technology, Universiti Malaysia Sarawak, Kuching, Malaysia *Address all correspondence to: bpoline@unimas.my © 2022 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Author details 12 Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 Digital Socio-Technical Innovation and Indigenous Knowledge DOI: http://dx.doi.org/10.5772/intechopen.101861 [12] Cruikshank J. Do glaciers Listen? Local Knowledge, Colonial Encounters, and Social Imagination. Vancouver, British Columbia, Canada: University of British Columbia Press; 2005 [6] Barnhardt R, Kawagley AO. Indigenous knowledge systems and alaska native ways of knowing. Anthropology & Education Quarterly. 2005;36(1):8-23. DOI: 10.1525/aeq.2005.36.1.008 References [8] Masango CA. Indigenous knowledge protection: Prospects in South Africa’s intellectual property framework. 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Biochar improves the nutrient cycle in sandy-textured soils and increases crop yield: a systematic review
Environmental evidence
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Bekchanova et al. Environmental Evidence (2024) 13:3 https://doi.org/10.1186/s13750-024-00326-5 Bekchanova et al. Environmental Evidence (2024) 13:3 https://doi.org/10.1186/s13750-024-00326-5 Environmental Evidence Open Access Open Access © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. 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Biochar improves the nutrient cycle in sandy‑textured soils and increases crop yield: a systematic review Madina Bekchanova1,2*   , Luca Campion1, Stephan Bruns1, Tom Kuppens1,3, Johannes Lehmann4, Marijke Jozefczak2, Ann Cuypers2 and Robert Malina1 Abstract Background  Biochar is a relatively new development in sustainable agricultural management that can be applied to ameliorate degraded and less fertile soils, especially sandy-textured ones, to improve their productivity with respect to crop production through improved nutrient availability. However, as the literature has shown, the response of sandy-textured soils to biochar varies in terms of effect size and direction. Therefore, the present study systemati- cally reviewed the available evidence to synthesize the impact of biochar amendments on aspects of the nutrient cycle of sandy-textured soils. Methods  Both peer-reviewed and gray literature were searched in English in bibliographic databases, organizational web pages, and Internet search engines. Articles underwent a two-stage screening (title and abstract, and full-text) based on predefined criteria, with consistency checks. Validity assessments were conducted, utilizing specifically designed tools for study validity. Data extraction involved categorizing the various properties of the nutrient cycle into nine main Soil and Plant Properties (SPPs), each of which was studied independently. Nine meta-analyses were performed using a total of 1609 observations derived from 92 articles. Comparing meta-averages with and without correction for publication bias suggests that publication bias plays a minor role in the literature, while some indication for publication bias is found when accounting for heterogeneity by means of meta-regressions. Review findings  According to the results, soil total and available nitrogen [N], phosphorous [P] and potassium [K], plant nutrient level, and potential cation exchange capacity (CEC) increased by 36% (CI [23%, 50%]), 34% (CI [15%, 57%]), 15% (CI [1%, 31%]), and 18% (CI [3%, 36%), respectively, and ­N2O emission and mineral nutrient leaching decreased by 29% (CI [− 48%, − 3%]) and 38% (CI [− 56%, − 13%). On average, however, biochar had no effect on soil mineral nitrogen and nutrient use efficiency. Publication bias was identified in the response of effective CEC. After corrections for publication bias, the response shifted from 36% to a negative value of − 34% (CI [− 50%, − 14%]). Meta- regression found that the effect modifiers experimental continent, biochar application rate, and soil pH, explain result heterogeneity. Stronger responses came from the continent of South America, higher application rates, and higher pH soils. Overall, biochar is found useful for many SPPs of nutrient cycling of sandy-textured soils, thereby contributing to increased crop yields in such soils. Abstract Keywords  Soil properties, Soil ecosystem services, Soil amendment, Soil fertility, Sustainable agriculture, Food crop yield, Biomass production, Meta-analysis *Correspondence: Madina Bekchanova madina.bekchanova@uhasselt.be Full list of author information is available at the end of the article *Correspondence: Madina Bekchanova madina.bekchanova@uhasselt.be Full list of author information is available at the end of the article Background Sandy-textured soils are marginal soil types for crop pro- duction [1] due to their poor fertility resulting from low organic matter and nutrient contents [2, 3], poor aggre- gate stability, and low water-holding capacity [4]. How- ever, for certain crops, such as onions or asparagus, sandy soils are considered fertile soils [5]. These soils cover 6% of the Earth’s surface [2], and some are being intensively cultivated in many countries to meet the high demand for food [6]. Sandy soils rely heavily on external inputs such as organic and inorganic fertilizers to restore soil produc- tivity by increasing their nutrient level and consequently engaging in agriculture [7]. However, the use of inorganic fertilizer can cause environmental pollution by releasing ­N2O into the atmosphere, increasing ­NH3 volatilization and N leaching [8]. This situation increases the need for environmentally sound technologies that can improve soil nutrient management and fertility. The existing heterogeneity in results in the litera- ture on the size and magnitude of biochar’s impact on nutrient cycling in sandy-textured soils highlights the need for a systematic review to synthesize and better comprehend the underlying causes. Although three previous studies [8, 38, 39] have investigated similar aspects, our study brings forward new contributions both in content and methodology, complementing existing studies. For example, these reviews focused on biochar’s impact on the soil nutrient cycle, provid- ing state-of-the-art insights. In contrast, our research is grounded in a systematic review, strictly following Col- laboration for Environmental Evidence (CEE) guide- lines at every stage [40]. The review study conducted by Zhang, Jing [38] mainly addressed the biochar effect on soil microbial activity and nutrient uptake in field studies, while our study includes different experimen- tal designs such as field, greenhouse, and laboratory. Studies conducted by Biederman and Harpole [39] and Liu, Zhang [8] concentrated primarily on soil nutrient cycling (in general) following biochar application, in contrast, ours exclusively investigates changes in sandy- textured soils, covering a broad spectrum of nutrient cycling components in such soils. Methodologically, we introduce an in-depth analysis of publication bias, which is often overlooked in ecological reviews [41]. Since CEE guidelines recommend updates every 5 years [40], our study could serve as a valuable update to previously published two review studies [8, 39]. This review helps to reduce uncertainty and enhances clarity for policymakers about the effect of biochar on the soil nutrient cycle. © The Author(s) 2024. 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The Creative Commons Public Domain Dedication waiver (http://​creat​iveco​ mmons.​org/​publi​cdoma​in/​zero/1.​0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Page 2 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Introduction [31, 32], resulting in increased nutrient availability, extractable P, microbial biomass N, and reduced ­NO3 − leaching of sandy-textured soils [28, 33]. However, some other studies have shown that the same biochar types have no effect on nutrient availability [36, 41]. Review studies have highlighted that a higher biochar application rate might increase soil ­NH3 volatilization and the magnitude of soil ­N2O emissions [8, 30]. In contrast, Shakoor, Shahzad [34] found that the biochar application rate had no effect on ­N2O emissions. Varia- tions in the effect of biochar on soil nutrients can also be caused by pyrolysis temperature [35–37].h Stakeholder engagement measured by comparing the treatment (with biochar) to the control (without biochar). To fully understand the potential heterogeneity in the impact of biochar on SPPs, we also examined potential effect modifiers as explained in sub-section Potential Effect Modifiers and Reasons for Heterogeneity. A systematic review of biochar’s effect on soil ecosys- tem services was first brought forward in a meeting of the BASTA project, funded by the Research Foundation Flanders, in December 2019 (BASTA stands for “Bio- char’s added value in sustainable land use with targeted applications”) [42]. The main aim of that project was the production of biochar from various residual biomasses and their application in different agricultural settings (composting, anaerobic digestion, manure storage, grow- ing media, and open field). Stakeholders of the project (academia, biochar producers, research institutes, agen- cies, policymakers) are aware of the lack of synthesis on biochar’s soil ecosystem services and they support the systematic review. In this review, we defined sandy-textured soils as soils consisting of at least 50 percent sand, using the soil tex- ture categorization by the United States Department of Agriculture (Table  1) [43]. Sandy-textured soils were chosen as the BASTA project will conduct experiments on this type of soil and fill the current research gap. Fur- thermore, our analysis focused exclusively on biochar experiments conducted on the topsoil layer (0–0.3 m soil depth) to examine the impact on this uppermost layer of soil. Hence, the scope of this study is limited to review- ing the changes in the topsoil nutrient cycle following biochar application. The results of this review clarify the interaction between biochar and sandy-textured soils and its effect on the nutrient cycle, which can be beneficial for further analysis of soil nutrients. The advisory committee, which was set up during the development of the protocol, was interested in various soil ecosystem services such as the water cycle, the nutri- ent cycle, climate regulation, and biomass/crop produc- tion. The advisory committee also contributed to the creation of search terms and search databases. Because the search terms and databases were comprehensive, the number of results retrieved became too vast to fit within the applicable time and money constraints. Hence, in the full-text screening phase, the advisory committee pro- posed focusing only on the nutrient cycle. This choice was based on its importance for the BASTA project. Background They can use the results of this review as a roadmap to facilitate policy recommendations for biochar applications as a soil amendment. The results could be valuable to biochar producers, farmers, and other stakeholders that are interested in improving soil conditions through biochar application. Our review also discerned research gaps in current studies and pro- vides a roadmap for further research. Biochar, a recent development in agricultural manage- ment [9], has attracted attention as an environmentally sound and sustainable soil management method to reg- ulate soil nutrient cycles, reduce nitrogen effluents [10], and increase the fertility of agricultural land [11, 12]. Biochar is usually obtained by pyrolysis of various bio- mass materials (such as wood and wood-related residues, manure and litter, peat, organic waste, and agricultural waste) [13] at different production conditions [14]. As a soil amendment, biochar can mitigate soil ­N2O emissions [15], reduce ­NH3 volatilization in soil [16], and increase soil N retention by reducing the need for fertilizer [17– 19]. Furthermore, recent studies have revealed that bio- char can enhance the uptake of N, P, and K by plants [20, 21]. However, other studies have also reported negative effects of biochar associated with increased N leach- ing due to soil structure deterioration [22, 23], acceler- ated soil ­NH3 volatilization due to raised soil pH, and increased soil ­N2O emissions through enhanced nitri- fication [24]. These contradictory results show that the effects of biochar are still ambiguous. f Not all soil types can benefit from biochar appli- cation to the same extent [25]. For example, sandy- textured soils are more likely to benefit from biochar amendments in the long run than other textured soils [25–28]. Even for sandy-textured soils, the effects of biochar addition can differ based on the interaction between biochar characteristics and the properties of sandy-textured soils [29]. Soil nutrient availability after biochar application essentially depends on the biochar characteristics and biochar application rate [30]. Some primary studies reported higher levels of nutrients in biochars obtained from manure and biosolids than those derived from straw- and wood-based feedstocks Page 3 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Stakeholder engagement All deviations from the protocol are explained explicitly in each subsection where the deviations occurred. Methods Based on our prior protocol [44], the guidelines of the Collaboration for Environmental Evidence [40], and the ROSES reporting standards (Additional file  1) [45], we used a systematic review, including meta-analyses, to synthesize the existing evidence base on the effects of biochar characteristics on sandy-textured soils’ nutri- ent cycle. We also identify the factors that influence the effect of biochar on the nutrient cycle of sandy-textured soils (such as experimental design, geographic location, climate type, duration of the experiment, soil type, soil depth, and soil treatment before biochar). Review objectiveh The primary focus of this review was to systematically review and synthesize studies of the effect of biochar on the nutrient cycle of sandy-textured soils. To this end, we formulated the following research question: What is the direction and magnitude of biochar’s impact on nutrient cycling provided by sandy-textured soils? The research question components were structured based on the PICO model: population, intervention, comparator, and out- come. The population in this study consists of sandy-tex- tured soil types. The intervention is the soil amendment using biochar, where the control of no biochar amend- ment serves as the comparator. Finally, the outcome is a change in sandy-textured soils’ nutrient cycle, which was Bibliographic databasesh The following bibliographic databases were used to col- lect publications: Deviation from protocol As mentioned in the Stakeholder Engagement section, we focused only on one ecosystem service—that is, the nutrient cycle—instead of four. Considering the large number of articles (> 2,500) to be screened during the full-text screening (Fig. 1), it was decided—after consul- tation with the co-authors and advisory committee—to reduce the number of papers by focusing only on the Table 1  Soil types chosen for the study Common names of soils Sand (%) Silt (%) Clay (%) Textural class Sandy soils (coarse-textured) 86–100 0–14 0–10 Sand 70–86 0–30 0–15 Loamy sand Loamy soils (moderately coarse-textured) 50–70 0–50 0–20 Sandy loam Loamy soils (moderately fine-textured) 45–80 0–28 20–35 Sandy clay loam Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 4 of 34 search strings as outlined in the previously published protocol [44]. Search strings used in each source were stored and are provided in Additional file 2. nutrient cycle instead of four ecosystem services. Text- mining made this possible (see Screening for more infor- mation). The research question was changed accordingly. Since these adjustments were made after the first phase of the screening process, we did not make any changes to the search strings. Instead, we restricted the second screening stage to keywords related to the nutrient cycle based on the relevant search strings. Deviations from the protocol are explicitly elaborated under the specific sections (see “Searching for Articles”, “Screening”, “Eligi- bility”, “Study validity assessment”, and “Data Synthesis and”). Searching for articles Search string T i h • Web of Science “Core collection”: https://​www.​webof​ knowl​edge.​com Topic searches were used that searched by title— abstract—keywords (TITLE—ABS- KEY). Three of the four PICO components (population, intervention, and outcome) were combined to build search terms. Within each component, search terms were combined using ‘OR’ operators. To combine the three PICO components, ‘AND’ operators were used. Truncation characters (* and $) were used to make the search more expansive. To con- struct the search string (Table 2), an initial scoping exer- cise was carried out on the Web of Science (WoS) ‘Core collection’ database, which was complemented with related synonyms by the advisory committee. The insti- tutional subscription of UHasselt was used to collect the search results.h • Scopus: https://​www.​scopus.​com/ • AGRICOLA: https://​www.​agric​ola.​nal.​usda.​gov/ • AGRIS: https://​www.​agris.​fao.​org/ • ProQuest Environmental Sciences and Pollution Management: https://​search.​proqu​est.​com/​advan​ced • EBSCO Open Dissertations: https://​bibli​oboard.​ com/​opend​isser​tatio​ns/h • Networked Digital Library of Theses and Disserta- tions: http://​www.​ndltd.​org/ • Open access theses and dissertations: https://​oatd.​ org/ The search terms were designed to retrieve all publi- cations on biochar’s effect on the nutrient cycle, water cycle, climate regulation, and crop/biomass yield of sandy-textured and contaminated sandy soils. No changes were made to the search terms, as the restric- tion to the scope of the nutrient cycle occurred after the first screening of the records retrieved using those terms. Both peer-reviewed publications and gray lit- erature (not submitted to peer-reviewed journals) were retrieved to minimize publication bias [46]. The following sources were searched: bibliographic databases (for peer- reviewed publications), organizational/institutional web- sites, and web-based searches (for gray literature, which can include publications, organizational reports, theses, etc.). The search terms displayed in Table  2 are mostly applicable to bibliographic databases as they have more advanced search functions. When the search terms were applied to organizational websites and Internet-based searches, the search formula and Boolean operators were simplified because some had limited search interfaces. During the protocol development, the comprehensive- ness of the search was tested against 15 benchmark arti- cles, and the results demonstrated the adequacy of our Search languageh The search was conducted in English and search results in other languages were not considered for this review. As English is the common language within the review team, it provided dual consistency checking in screening, full-text screening, quality appraisal, and data extraction. Organizational websitesh The following organizational websites were searched to obtain potential additional studies that were not cov- ered by the bibliographic databases. As mentioned above, some organizational websites did not have a very advanced search function. Thus, some manual searches were executed using the search terms defined in Table 2. Furthermore, six of these organization websites returned no results or no related results (Additional file 2). • International Biochar Initiative: https://​bioch​ar-​inter​ natio​nal.​org/​bioch​ar/ • UK Biochar Research Center: https://​www.​bioch​ar.​ ac.​uk/​resea​rch.​php?​id=​10&r=a • US Biochar Initiative: https://​bioch​ar-​us.​org/​bioch​ar-​ intro​ducti​oni • European Biochar Certificate: https://​www.​europ​ ean-​bioch​ar.​org/​en/​home • Sonoma Biochar Initiative: https://​sonom​abioc​harin​ itiat​ive.​org/ • Israel Biochar Research Network: https://​sites.​google.​ com/​site/​ibrni​srael​bioch​arnet​work/​home Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 5 of 34 Fig. 1  ROSES flow diagram [73], showing the search results, screening processes, critical appraisal, and the final number of articles included in the systematic review. Blue indicates that articles have gone to the next stage; red dotted lines imply that articles/studies have been removed at that stage Fig. 1  ROSES flow diagram [73], showing the search results, screening processes, critical appraisal, and the final number of articles included in the systematic review. Blue indicates that articles have gone to the next stage; red dotted lines imply that articles/studies have been removed at that stage Page 6 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Search record database • Research Institute for Agriculture, Fisheries and Food (ILVO, Belgium, Flanders): https://​www.​ilvo.​vlaan​ deren.​be/​EN/​Home Endnote X9 was used to import the search results. When it was not possible to import a certain document into the software, a record was generated manually. After final- izing all searches, the reference files were merged and checked for duplicates. Before removing any of the dupli- cates, they were rechecked and compared with regard to title, abstract, and year of publication. Once all duplicates were removed, the final version was checked with End- note’s deduplication tool. • Netherlands Organisation for Applied Scientific Research (TNO, The Netherlands): https://​www.​tno.​ nl/​en/ • Wageningen University & Research (The Nether- lands): https://​www.​wur.​nl/​en/​wagen​ingen-​unive​ rsity.​htm • Julius Kühn Institute—Federal Research Centre for Cultivated Plants (Germany): https://​www.​julius-​ kuehn.​de/​en/ Organizational websitesh Environmental Evidence Table 2  Search terms (formatted in Web of Science) Intervention Population Outcome (TS = (biochar* OR "biochar amendment$" OR agrichar OR "black carbon$" OR "biochar-mediated" OR charcoal OR "biochar field study")) (TS = ("hydrological control*" OR "hydraulic properties*" OR "hydrologic* cycle" OR “water retention” OR “clean water” OR “hydrological control” OR “water leak*” OR “water leach*” OR "water availabl*" OR "soil water availability" OR "readily available water" OR evaporation OR "water runoff" OR "plant available water" OR "WHC" OR "soil humidity" OR "field capac- ity" OR "nutrient loss" OR "soil moisture" OR "water holding capacity" OR "water content" OR "water infiltration" OR "water cycle" OR "nutrient availabl*" OR "available nutrient$" OR nutri- ent$ OR "nutrient cycle" OR "nitrogen availabil*" OR "nutrient exchange capacit*" OR "available nitrogen" OR NPK OR "nutri- ent leak*" OR "nutrient leach*" OR "soil nutrients" OR "available phosphorus" OR "phosphorus availabil*" OR "available potas- sium" OR "potassium availabil*" OR "climate regula*" OR "climate mitigation" OR "climate change mitigation" OR "climate chang*" OR "global warming" OR “carbon sequestration” OR "soil carbon sequestration" OR “carbon capture and storage” OR "emission$" OR "CCS" OR “ammonia emission$*” OR “methane emission$*” OR "nitrate emission$" OR "nitrous-oxide emission$" OR " NH4 " OR " NO3 " OR " CH4 " OR " N2O " OR " CO2 " OR "greenhouse gas emission$" OR "crop growth" OR "crop yield" OR "crop produc- tion" OR "biomass growth" OR "biomass yield" OR "biomass production" OR "raw material" OR "plant growth" OR "field" OR yield OR "increase" OR "improve*" OR "decrease" OR "mitiga*" OR "growth" OR "alleviat*" OR "effect$" OR "impact")) (TS = ("sand* soil$" OR "sandy soil" OR “sand* loamy soil$” OR “loamy sandy soil” OR “contaminated* soil$” OR "heavy metal* soil$" OR "sandy loam soil" OR "sandy loam" OR ultisol OR "agri- cultural soil" OR "loamy sand" OR "sandy clay loam" OR "cropping system" OR “sandy calcareous soil”)) Search formula = Intervention + Population + Outcome Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 7 of 34 • Biochar for sustainable soils: https://​bioch​ar.​inter​ natio​nal/ Subsequently, we chose 100 lowest-ranking results that were randomly selected. Google Scholar returned many results that were related and unrelated to the review objective; therefore, following [46] and [47], we only downloaded the first 1000 relevant results using Publish or Perish software, as stated in the protocol. Organizational websitesh The software assisted in retrieving relevant articles and adding them to the reference list in Endnote. Citations or patents were not considered in Google Scholar. Finally, we did not include the reference lists of relevant articles for the addi- tional searches due to the large number of hits retrieved from all sources. • Ithaka Institute: http://​www.​ithaka-​insti​tut.​org/​en/​ home • New Zealand Biochar Research Centre: https://​www.​ massey.​ac.​nz/​massey/​learn​ing/​colle​ges/​colle​ge-​of-​ scien​ces/​resea​rch/​agric​ulture-​envir​onment-​resea​rch/​ bioch​ar-​resea​rch-​centre/​bioch​ar-​resea​rch-​centre_​ home.​cfm • Environmental Protection Agency [18]: https://​www.​ epa.​gov/ • Research Institute for Organic Agriculture: https://​ knowl​edge4​policy.​ec.​europa.​eu/​organ​isati​on/​resea​ rch-​insti​tute-​organ​ic-​agric​ulture_​en Article screening and study eligibility criteria Screening processh • Mercator Research Institute on Global Commons and Climate Change (Germany): https://​www.​mcc-​ berlin.​net/​en/​index.​htmlh The screening processes involved two steps, both of which were performed by two reviewers independently. In the first step, the results were filtered by title and abstract. All titles and abstracts were double-screened. Before the actual screening began, both reviewers screened 100 randomly selected articles from the search results to ensure consistency. If a reviewer had any doubts about excluding a paper, it was marked and later discussed with the other reviewer to come to an agree- ment. The involvement of an adjudicating reviewer was not needed, since the reviewers could reach a consensus. The level of agreement with respect to consistency was verified using the Kappa statistic [47]. All disagreements were discussed in detail between reviewers prior to start- ing the actual screening.h • Thünen Institute—Federal Research Institute for Rural Areas, Forestry and Fisheries (Germany): https://​www.​thuen​en.​de/​en/​about-​us/​the-​insti​tute/ • Agroscope (Switzerland): https://​www.​agros​cope.​ admin.​ch/​agros​cope/​en/​home • James Hutton Institute (United Kingdom): https://​ www.​hutton.​ac.​uk/ • Rothamsted Research (United Kingdom): https://​ www.​rotha​msted.​ac.​uk/ • UK Centre for Ecology & Hydrology (United King- dom): https://​www.​ceh.​ac.​uk/ The second step involved a review of the full text of the remaining articles. This is the stage at which we deviated from the protocol, as the vast number of results conflicted with our time and budget constraints. Instead of reviewing all results remaining after the first stage, we only screened results that were related to the nutrient cycle of sandy–textured soils. To implement this, we employed a text-mining method with the key- words related to the nutrient cycle (Additional file  3) using tidyverse, magrittr, and pdftools packages of R ver- sion 3.3.0 [48]. Before applying text-mining, we deter- mined the cut-off level of eight counts of nutrient cycle Study validity assessment Eligibility criteria The eligibility criteria were based on the PICO model and are summarized in Table 3. All studies included after the full-text screening were critically appraised to assess their internal and external validity and to evaluate their suitability for the data syn- thesis. Studies were appraised for the different types of biases by being categorized as ‘low,’ ‘moderate,’ and ‘high’ risk of bias. Population  To establish eligible populations, we excluded studies that conducted experiments on soils not classified as sandy-textured soils (Table 1) and studies that did not focus on the topsoil layer (0–0.3 m). Contrary to the protocol [44], if the soil type upon which an experi- ment was performed was not defined, it was excluded from this review. Due to the vast number of articles, we were unable to contact every author when the soil type was not specified. The criteria were created based on the critical appraisal tool of v0.3 developed by CEE [51], and previously pub- lished systematic review studies in the journal Environ- mental Evidence [52] to assess the internal validity of the studies and consider many possible biases: selection bias, performance bias, attrition bias, and reporting bias. In this study, we adapted these frameworks to the research question of our review and deviated from the protocol by making some minor changes to the criteria in Addi- tional file 5: Table S5.1. For example, studies that lacked randomized experiments were classified as a ’high’ risk of bias. This classification was made because such stud- ies have the potential to introduce confounding factors into the analysis. This decision was taken after consulta- tion with experts in the field. Studies were summarized as a ‘moderate’ or ‘high’ risk of bias if they were evaluated as ‘moderate’ or ‘high’ risk of bias for at least one of the critical appraisal criteria. Our main reason for excluding studies with a ‘moderate’ risk of bias from the data syn- thesis was that they would increase the amount of miss- ing data related to effect modifiers, and this might cause sampling bias, limiting the generalizability of the results [53]. Thus, contrary to the protocol, only studies with a ‘low’ risk of bias were used to extract the necessary data for data synthesis [44]. All information related to the critical appraisal (e.g., excluded studies) was recorded in Excel and presented in Additional file 6. Web‑based searches In addition to the bibliographic database and organiza- tional website searches, web-based searches were also conducted. Contrary to what is stated in the protocol, we only used Google Scholar, mainly because it yielded very similar results to Google. We performed this test by randomly selecting 100 results from each dataset and comparing them against each other. To achieve this, we initially exported the search results to an Excel sheet. We used the Excel randomization function, assigning a 9-digit random number between 0 and 1 to each cell. Bekchanova et al. Environmental Evidence (2024) 13:3 Page 8 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence plots received the same amount of fertilizers, manure, or compost. keywords by manually screening 150 randomly selected papers that remained after the first stage of screening and then comparing them to the text-mining results for con- sistency. After the text-mining, papers that did not yield eight counts of nutrient cycle keywords were excluded, reducing the number of articles by 1014 (Fig. 1). The manual full-text screening of the remaining articles was based on the eligibility criteria provided in the following section, which was slightly different from the previously published protocol [44], as stated in detail in the sub-sec- tion of Eligibility Criteria. Articles (co-)authored by one of the reviewers were assigned to another reviewer so that no reviewer had to assess their own work. As in the first phase of screening, consistency checking was per- formed before screening using 10 percent of the remain- ing articles. All articles left out at the manual full-text screening stage were recorded, together with an explana- tion for their omission (Additional file 4). Outcomes  The outcomes considered were: positive, neg- ative, or no changes in different components of the nutri- ent cycle of sandy-textured soils. Changes in major soil nutrients were considered for this study, such as nitrogen (N), phosphorus (P), potassium (K), and other soil min- eral processes. Following discussion with the advisory committee, it was decided that the various components of the nutrient cycle should be referred to as soil and plant properties (SPPs) relevant to the nutrient cycle. Study designs  Experimental primary studies, especially laboratory experiments, greenhouse experiments, and field experiments using control and treatment groups, were included in the review. Earlier review studies were accounted for by screening their reference lists. Study validity assessment Intervention  The eligible intervention was biochar, produced from biomass and used in agriculture as a soil amendment. Some studies have used terms such as char- coal and black carbon as synonyms for biochar; however, in production and application, black carbon and charcoal can differ from biochar. For instance, black carbon can be made by burning fossil fuels as well as biomass [49], while charcoal is mainly produced to provide affordable energy to rural areas [50]. However, we included the terms ‘black carbon’ and ‘charcoal’ in the search terms and checked, at the full-text screening stage, whether they were made from organic feedstocks with the intended application as a soil amendment. We also included the term Agrichar, as it is used in some organizational websites and is closely related to biochar. Comparator  Control sites or plots without any interven- tion—that is, no biochar added—were used as a compara- tor. Control sites or plots that were treated with fertilizers, manure, or compost were also included if the intervention Page 9 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Table 3  Overview of eligibility criteria Screening stage I means screening of the title and abstract, Screening stage II means screening of the full text Criterion Included Excluded Screening stage I Screening stage II Justification Population Sandy-textured soils with 50% or more sand in the soil composition Other soil textures or soil types not given X X Marginal soils, such as sandy-textured soils, are widely used in agricultural processes and seem to benefit from biochar. Data coding and extraction strategy Data were extracted from studies assessed as having a ‘low’ risk of bias. When each study reported estimates for different SPPs or multiple estimates for the same SPPs, all estimates were placed in individual rows with the mean value of the given result. Essential data were extracted based on the data coding table provided in the protocol [44], which was complemented with further soil and biochar data during the data extraction (for exam- ple, soil and biochar bulk density, pH, and dry weight) (Additional file  7: Table  S7.1). This additional data was necessary to conduct the meta-regression analysis and subsequent calculations, including the conversion of measurement units. Each study’s full text was read, and data were manually extracted and entered into a spread- sheet. If the data were only presented in tables or graphs, they were extracted using WebPlotDigitizer (WPD) [54]. We excluded studies for which the data was impossible to decipher using WPD. As mentioned in the protocol, data extraction was managed by one reviewer (the first author) instead of two. However, prior to conducting the meta-analysis, a third co-author, an expert in the field, rigorously reviewed the extracted data. To guarantee data accuracy and reliability, five random articles were chosen for detailed cross-checking. Study validity assessment The heterogeneity in the results of primary studies is the reason why this review focuses on these soils Intervention Biochar obtained by pyrolysis and/or gasification of various biomass materials Biochar made from materials other than biomass or technologies other than pyrolysis and/or gasification X X In accordance with the definition of biochar adopted for this review, the included biochar samples were specifically derived from biomass through pyrolysis and/or gasification processes Comparator Control sites or plots without biochar that corre- spond to intervention sites or plots Control sites or plots that do not corre- spond to intervention sites or plots X To ensure comparability between comparator and intervention Outcome Positive, negative, or no changes in different soil ecosystem processes of the nutrient cycle of sandy-textured soils Other soil ecosystem processes of sandy- textured soil X These soil ecosystem processes of the nutrient cycle were identified as relevant by the advisory committee of this review, being also the partners in the project funding this review (BASTA, Research Foundation – Flanders, grant S000119N) Study design Lab (incubation), greenhouse, and field experi- ments Review studies X Primary study designs provide observations for qualitative and quantitative synthesis Publication type Research articles, research reports, dissertations, etc Review studies X X In order to consistently account for primary data only, review studies were excluded Language English Other languages X X English was the common language within the review team, so it provided dual consist- ency at all stages of the screening Page 10 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence (2024) 13:3 Table 4  Potential effect modifiers Existing modifiers New modifiers Experimental country Soil pH Experimental design (i.e., greenhouse, lab, field) Biochar pH Experimental condition Biochar application with manure Climate type Biochar with compost Duration of experiment Feedstock for biochar Biochar carbon content Pyrolysis temperature Biochar application rate Type of soil Table 4  Potential effect modifiers As with screening, consistency checking was also car- ried out for the critical appraisal. Again, all studies were independently evaluated by the same two appointed reviewers. In case of disagreements regarding any of the criteria, it was discussed between reviewers until a con- sensus was reached. Data synthesis and presentation Data preparation Since nutrient cycling in the soil is a complex system, we tried to extract all related measurements and, after dis- cussion with experts, grouped them into nine major SPPs based on the data availability, as shown in Table 5. This decision was taken at the data extraction stage after the protocol was published. We believe that the combination of these nine SPPs provides a reasonable representation of nutrient cycling. However, before combining them, we checked the divergence of the outcomes of different measurement methods. For example, there are different soil phosphorus measurement methods, such as Olsen P and Mehlich 1, 3 extraction, which means that the results can differ greatly, in which case the grouping would lead to inaccurate results. Thus, we analyzed the statistical difference among these methods (Additional file 8) and found that the difference was not statistically significant. Potential effect modifiers and reasons for heterogeneity f y gi Soil total NPK is the total content of NPK nutrients, while soil NPK availability is the nutrients in the soil that are readily available to plants. Soil mineral nitrogen includes processes such as nitrification, ammonifica- tion, as well as ammonium and nitrate, which are forms of plant-available nitrogen if they are exchangeable or in soil solution. The nutrients (NPK) absorbed by a plant and the nutrient content in the roots and shoots of the plant are considered as plant nutrient level. The differ- ence between the two types of CEC is their measurement methods. For example, effective CEC can be measured at soil pH, whereas potential CEC is usually measured at a pH of 7 by very different methods. Thus, it is not rec- ommended to merge them into one CEC. NUE can be defined as the crop yield or biomass per input unit (that is, fertilizer or biochar), while mineral N leaching is the leaching of ammonium or nitrate to groundwater.f Potential effect modifiers and reasons for heterogeneity To better understand possible heterogeneity in the effects found by different studies, possible effect modifi- ers were retrieved and recorded in the spreadsheet. The list of effect modifiers shown in Table 4 was compiled in consultation with the advisory committee. These effect modifiers were published in the peer-reviewed protocol of this review [44]. We made minor updates on the effect modifiers listed in the protocol with some new modera- tors (Table 4). During the data extraction processes, we realized that these new modifiers can have an effect on response varia- tion, so we included them in the list of possible modifiers as well. The effect of these effect modifiers on the varia- tion in the outcome is investigated by means of the meta- regression analysis. In addition, the results in different units were converted to the same units for each SPP for analysis purposes. Bekchanova et al. Environmental Evidence (2024) 13:3 Page 11 of 34 Bekchanova et al. Potential effect modifiers and reasons for heterogeneity Environmental Evidence Table 5  Grouped major SPPs relevant to the nutrient cycle Grouped (SPPs) Soil and plant properties (SPPs) Soil total NPK K concentration, K content, N concentration, N content, P concentration, P content, total K, total N, total P Soil mineral nitrogen Ammonification rate, available ammonium, available nitrate nitrogen, exchangeable ammonium, extract- able ammonium, N mineralization, nitrate nitrogen rate, nitrification, soil ammonium, soil ammonium concentration, soil ammonium content, soil nitrate nitrogen, soil nitric nitrogen Plant nutrient level Shoot N, Shoot P, Shoot K, K uptake, P uptake, N uptake, plant N N2O emission Nitrous oxide emission Soil NPK availability Available N, available P, available K, dissolved K, dissolved P, exchangeable K, extractable K, extractable P Potential CEC Potential CEC Effective CEC Effective CEC Nutrient use efficiency Nutrient use efficiency Mineral N leaching Cumulative ammonium leaching, cumulative nitrate nitrogen leaching, leached ammonium, leached nitrate nitrogen, nitrate leaching Table 5  Grouped major SPPs relevant to the nutrient cycle K concentration, K content, N concentration, N content, P concentration, P content, total K, total N, total P K concentration, K content, N concentration, N content, P concentration, P content, total K, total N, total P Ammonification rate, available ammonium, available nitrate nitrogen, exchangeable ammonium, extract- able ammonium, N mineralization, nitrate nitrogen rate, nitrification, soil ammonium, soil ammonium concentration, soil ammonium content, soil nitrate nitrogen, soil nitric nitrogen where Xb is the mean value of the soil nutrient cycle with the biochar treatment and Xnb is the mean value of the soil nutrient cycle with the control of no biochar. We use the natural logarithmic transformation, LnRR = ln(RR) , to normalize the data [57]. The biochar treatment is considered to have no effect when the lnRR = 1 , a posi- tive effect when lnRR > 1 , and a negative effect when lnRR < 1 . The variance of LnRR was calculated as follows: Furthermore, some studies have reported biochar appli- cation rates in different measurement units (such as kg/ ha, kg/pot, or g/kg or in percentage). All were converted into t/ha in order to standardize measurement units. The data were cleaned up before analysis using the tidyverse package of R version 3.3.0 [48]. Descriptive statistics and narrative synthesis Data from the ‘low’ risk of bias studies were also used for the narrative synthesis and descriptive statistics of evidence. We have made tables and figures to show the number of publications per year and per experimen- tal country, experimental designs, types of experiments (control, treatment), and duration of experiments. (2) v = SD2 b (nb ∗X2 b) + SD2 nb (nnb ∗X2 nb) (2) where SDb and SDnb are the standard deviations (SD) of treatment and control, respectively, and nb is the sample size of the treatment and nnb is the control sample size [57]. Where it was not possible to extract SD, the stand- ard error (SE) was used to calculate SD [41]. According to Lajeunesse [58], Eqs. 1 and 2 are biased when deal- ing with small to medium sample sizes. Consequently, the following equations, grounded in the second-order Taylor expansion, have been proposed to mitigate these biases [59]. where SDb and SDnb are the standard deviations (SD) of treatment and control, respectively, and nb is the sample size of the treatment and nnb is the control sample size [57]. Where it was not possible to extract SD, the stand- ard error (SE) was used to calculate SD [41]. According to Lajeunesse [58], Eqs. 1 and 2 are biased when deal- ing with small to medium sample sizes. Consequently, the following equations, grounded in the second-order Taylor expansion, have been proposed to mitigate these biases [59]. Effect size and its variance The square root of the inverse of the effective sample size is given by (7) yi = β0 + s(2)ij + u(3)j + ǫij (7) where β0 is the overall estimate (or meta-analytic mean), yij is the effect size i nested in study j , s(2)ij accounts for within-study heterogeneity (level 2), u(3)j accounts for between-study heterogeneity on (level 3), and ǫij is the corresponding sampling error (level 1). We compared a three-level model with a two-level model using the anova function in R, where the results showed that the three-level model is a better fit for our data. The model is estimated with multilevel model with random effects (ML-REML), as it provides unbiased estimates of the var- iance parameters [55]. We further account for depend- ence due to multiple observations from the same study by clustering standard errors at the level of primary studies [64, 65]. We used inverse variance weighting to assign a greater weight to more precisely estimated studies [57].f where β0 is the overall estimate (or meta-analytic mean), yij is the effect size i nested in study j , s(2)ij accounts for within-study heterogeneity (level 2), u(3)j accounts for between-study heterogeneity on (level 3), and ǫij is the corresponding sampling error (level 1). We compared a three-level model with a two-level model using the anova function in R, where the results showed that the three-level model is a better fit for our data. The model is estimated with multilevel model with random effects (ML-REML), as it provides unbiased estimates of the var- iance parameters [55]. We further account for depend- ence due to multiple observations from the same study by clustering standard errors at the level of primary studies [64, 65]. We used inverse variance weighting to assign a greater weight to more precisely estimated studies [57].f (9)  1/ni =  n1i+n2i/n1in2i (9) where n1i is the sample size of the control, while n2i is the sample size of the treatment. When the true effect size is zero [64], the PET method works best. PEESE is also regressed in a similar way as PET. The difference is that, instead of SE (in our case (   1/ni) ), the squared SE— that is, the variance (in our case ( 1/ni ) [41])—is used as the predictor [64]. If no evidence for publication bias is found, a ML-REML model can be applied [64]. Effect size and its variance In addition to narrative synthesis, a quantitative synthe- sis—that is, a meta-analysis—was performed to assess the effects of biochar on the nutrient cycle of sandy-textured soils. Studies with incomplete or missing information that could not be retrieved were excluded from the meta- analysis. For each SPP (Table 5), we studied the effect of biochar (treatment) compared to no biochar (control). In total, nine meta-analyses were performed. All calcula- tions were carried out using the metafor package in R ver- sion 3.3.0 [48, 55]. For each comparison between biochar and no biochar, we calculated the response ratio (RR), which is the favored method for calculating the effect size in ecological studies [39, 56]: (3) LnRR2 = ln  Xb Xnb  + 1 2(CV2 b nb −CV2 nb nnb ) (4) v(LnRR)2 = CV2 b nb + CV2 nb nnb + CV4 b 2n2 b + CV4 nb 2n2 nb (3) (4) where CV (sd/m) is the coefficient of variation. If the SDs were reported then we used Eq. 3 and 4 to calculate effect sizes and variances. However, most studies did not include data on SD and SE. To address this, we used a method known as "missing cases," following the sugges- tion of Nakagawa, Noble [60], and employed Eqs. 5 and (1) RR = Xb Xnb RR = Xb Xnb (1) Bekchanova et al. Environmental Evidence (2024) 13:3 Page 12 of 34 6. In this approach, we imputed the pooled CV using data from studies that did report SDs. presence of publication bias, the funnel plot would be asymmetrical, with smaller studies showing large effect 6. In this approach, we imputed the pooled CV using data from studies that did report SDs. presence of publication bias, the funnel plot would be asymmetrical, with smaller studies showing large effect 6. In this approach, we imputed the pooled CV using data from studies that did report SDs. 6. In this approach, we imputed the pooled CV using data from studies that did report SDs. Effect size and its variance presence of publication bias, the funnel plot would be asymmetrical, with smaller studies showing large effect (5) LnRR3 = ln  Xb Xnb  + 1 2    k i=1(nbiCV bi  /k i=1nbi] 2 nb − k i=1(nnbiCV nbi  /k i=1nnbi] 2 nnb    (6) v(LnRR3) = k i=1(nbiCV bi  /k i=1nbi] 2 nb + k i=1(nnbiCV nbi  /k i=1nnbi] 2 nnb + k i=1(nbiCV bi  /k i=1nbi] 4 2n2 b − k i=1(nnbiCV nbi  /k i=1nnbi] 4 2n2 nb (5) (6) sizes being more likely to be published, while smaller studies without significant or large effects may be miss- ing [64]. Each study may report multiple effect sizes for the same SPP [61], violating the traditional independency assumption [62]. We applied a multilevel model using the rma.mv function in the metafor R package to account for the dependency of effect sizes Specifically, we use a three-level model that accounts for the sampling variance of individual effect sizes (level 1), the variance between effect sizes from the same study (level 2), and the vari- ance between studies (level 3) [63] using the following formula: PET-PEESE deals with small study effects that are the potential indicators of publication bias. The PET method is based on a regression model where the SE of the study’s effect size is used to correct for publication bias: (8) yi = β0 + β1SEi + s(2)ij + u(3)j + ǫij (8) Unlike stated in the formula, we used the square root of the inverse of effective sample size (   1/ni) instead of SE because it is recommended for the studies where the effect size is calculated based on response rate [41]. LnRR includes both treatment and control means in its point estimate, leading to a correlation between these estimates and their sampling standard errors [41], which causes a funnel asymmetry [68]. Therefore, when the effect size is computed in the form of LnRR, it has been proposed to use ‘effective sample size’ as a moderator instead of SE [41] and it also accounts for unbalanced sampling [69]. Review findings Review descriptive statistics Literature searches and screening Searches were carried out in bibliographic databases in April 2021, which returned 12,191 records.h The majority of records from bibliographic databases resulted from the EBSCO Open Dissertations, Web of Science core collection, Scopus, and AGRICOLA, with 4407, 2410, 2458, and 1612 results, respectively (Fig. 1). Other sources, such as organizational websites sug- gested by the advisory committee and Google Scholar, were searched in May 2021 and provided 300 and 2600 recordings, respectively (Additional file  2). We used Endnote X9 to check for duplicates, which resulted in 3371 recordings. Afterward, we conducted a manual duplicate check and found 2036 extra duplicates. After all duplicates were removed, 9684 unique records remained. Once the title and abstract screening had been implemented, 2738 studies remained. Because the amount for the full-text screening was very large, we decided to focus on one ecosystem service, namely the nutrient cycle, instead of four by applying text-min- ing, as we described in the section ‘screening process.’ After the text-mining, we were able to reduce the num- ber to 1724 articles, of which the full text was screened. Full-text screening reduced the number of articles by 1142 for the reasons listed in Fig. 1. Subsequently, 582 remaining articles were critically appraised, of which 109 articles were eligible for qualitative and quantita- tive synthesis (see Additional file 6). Of these, 17 were not suitable for the quantitative synthesis, which meant that 92 studies were used for the data extraction and meta-analysis. yif We used funnel plots with 1/SE (precision) for lnRR as measures of uncertainty to visualize outliers in the data- set (Additional file 11), as suggested by Nakagawa, Lag- isz [41]. Outliers that seemed to contribute to excessive noise were further investigated. Subsequently, we used a conventional boxplot method to remove these outli- ers from the dataset. The removal process was guided by the calculation of the first quartile, the third quartile, and the interquartile range (IQR) of 1/SE. Data points falling below the first quartile or above the third quartile by a factor of 10 times the IQR were considered outliers and removed from the analysis. A sensitivity analysis was performed to assess the presence and absence of outliers on the direction and magnitude of the effect sizes (Addi- tional file 11). Effect size and its variance We used funnel plots and PET (the precision-effect test) and PEESE (the precision-effect estimate with standard error) tests to check for publication bias, as this method is suggested for ecological studies [41, 66]. Publication bias happens when studies with non-signif- icant or minimal effect sizes (small studies) are unpub- lished, resulting in a non-normal distribution of LnRR [41, 67]. In the absence of publication bias, all studies would be symmetrically distributed around the pooled effect size within the funnel plot [64]. However, in the We employed state-of-the-art model selection, namely randomized LASSO (least absolute shrinkage and selec- tion operator) to examine the impact of effect modifiers on the overall effect. LASSO is a statistical technique Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence (2024) 13:3 Page 13 of 34 Page 13 of 34 Page 13 of 34 Bekchanova et al. Environmental Evidence used for variable selection and regularization in regres- sion analysis. It is specifically designed to handle high- dimensional data where the number of predictors is larger than the number of observations. By applying a penalty to the regression coefficients, LASSO encour- ages some coefficients to be shrunk to zero, effectively identifying the most significant predictors [70]. This method plays a crucial role in preventing overfitting and enhancing the interpretability of the regression model. The randomized LASSO model solves the variable selec- tion problems by resampling the data and computing a LASSO on each resampling [70, 71]. We quantified vari- able importance by running the LASSO model for five different model sizes (1–5 regressors) per SPP (except for NUE due to a limited number of unique papers) and generating selection probabilities for each predictor (effect modifiers). For the variables selected, we calcu- lated the coefficient sign through ordinary least squares; the results are visualized in Additional file  12. When the selected variable had a higher probability, the model variable was found to have a stronger explanation for the biochar effect on SPPs, while the weaker effect was seen when the probability sign had a lower percentage. Consistently high probabilities indicate that the underly- ing variable is a robust predictor of the effect size for the respective SPP. The variables with zero-percent probabil- ity were read as unimportant predictors. We addressed publication bias in LASSO models by incorporating the square root of the effective sample size in the LASSO model. Review findings Review descriptive statistics Lit t h d Review findings Review descriptive statistics Literature searches and screening Searches were carried out in bibliographic databases in April 2021, which returned 12,191 records.h Effect size and its variance If the measure of precision is not a robust pre- dictor, there is additional evidence that publication bias might not be present, and vice versa if the precision is robust. We implemented LASSO in glmnet package in R, and it is only based on fixed effects models [72]. used for variable selection and regularization in regres- sion analysis. It is specifically designed to handle high- dimensional data where the number of predictors is larger than the number of observations. By applying a penalty to the regression coefficients, LASSO encour- ages some coefficients to be shrunk to zero, effectively identifying the most significant predictors [70]. This method plays a crucial role in preventing overfitting and enhancing the interpretability of the regression model. The randomized LASSO model solves the variable selec- tion problems by resampling the data and computing a LASSO on each resampling [70, 71]. We quantified vari- able importance by running the LASSO model for five different model sizes (1–5 regressors) per SPP (except for NUE due to a limited number of unique papers) and generating selection probabilities for each predictor (effect modifiers). For the variables selected, we calcu- lated the coefficient sign through ordinary least squares; the results are visualized in Additional file  12. When the selected variable had a higher probability, the model variable was found to have a stronger explanation for the biochar effect on SPPs, while the weaker effect was seen when the probability sign had a lower percentage. Consistently high probabilities indicate that the underly- ing variable is a robust predictor of the effect size for the respective SPP. The variables with zero-percent probabil- ity were read as unimportant predictors. We addressed publication bias in LASSO models by incorporating the square root of the effective sample size in the LASSO model. If the measure of precision is not a robust pre- dictor, there is additional evidence that publication bias might not be present, and vice versa if the precision is robust. We implemented LASSO in glmnet package in R, and it is only based on fixed effects models [72]. Study validity assessment f h d Most of the studies were assigned low validity due to a high risk of bias (303 articles; 52.1%). The second- largest group of studies was given moderate validity due to a moderate risk of bias (170 articles; 29.2%). The remaining studies were of high validity with a low risk of bias (109 articles; 18.7%). Of the studies that had a high risk of bias, most suf- fered from performance bias (27.8%) with confounding factors being present, or it was hard to judge whether confounders exist (Fig. 2). Because the study design was not based on proper experiments (that is, control vs. treatment), a further 25% of the studies were at high risk of bias. Another 21% of high risk of bias were due to the fact that the sampling method of the stud- ies was not appropriate to collect data on the popula- tion in question. The remaining studies lacked clear statistical analyses (5%), mismatch of intervention and Page 14 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence 2 9 17 19 20 28 28 29 128 153 167 375 15 77 20 36 84 49 7 11 1 0 Heterogeneity/ effect modifiers Objecves & Hypothesis External Validity Intervenon Adequate data availability Selecon bias Stascal analysis Degree of replicaon Sampling Study design Performance bias Excluded (High risk of bias) Excluded (Medium risk of bias) Number of papers Fig. 2  Excluded studies with high and moderate risk of bias (in percentage) and isk ge- een and ula- ils) mal ons ar- dity sis, 20 28 28 29 128 153 167 36 84 49 7 11 1 0 vailability Selecon bias Stascal analysis Degree of replicaon Sampling Study design Performance bias f bias) Excluded (Medium risk of bias) entage) Fig. 3  Number of publications by years Excluded (High risk of bias) Fig. 2  Excluded studies with high and moderate risk of bias (in percentage) Excluded (Medium risk of bias) Excluded (Medium risk of bias) Excluded (High risk of bias) Fig. 2  Excluded studies with high and moderate risk of bias (in percentage) Fig. 3  Number of publications by years Fig. 3  Number of publications by years comparator (5%), inadequate data availability (3%), and intervention description (3%). Study location Included articles were published from 2008 to 2021. Over time, the number of publications increased—that were more than 10 times as many publications in recent years as at the beginning of this decade (Fig. 3). Included studies were conducted across 28 coun- tries. Asia is the continent where the highest number of studies were conducted (37.6%; Additional file  10: Table 10.1), most of which were in China (22 studies; 23.6%). A small number of contributions came from other Asian countries (such as Iran and India, which had three publications each). The second-most pub- lications came from the European continent (20.4%), where many countries made small contributions, although Finland stands out with five studies (Fig. 4). Africa accounted for 17.2% of studies, 11 of which were conducted in Nigeria. Furthermore, 9.7% of studies were carried out in South America, all of which came from Brazil (nine studies). Finally, 8.6% of studies were Study validity assessment f h d One hundred and seventy articles had a moderate risk of bias, mainly due to a lack of consideration of heteroge- neity/effect modifiers (55.6%), the discrepancy between intervention and comparator (selection bias) (12.4%), and a lack of external validity (for example, the study popula- tion, in particular, cannot be generalized to sandy soils) (11.4%). Insufficient data availability (5.3%) and minimal description of statistical analysis (7.3%) were also reasons for a moderate risk of bias (Fig. 2). As mentioned ear- lier, only studies with a low risk of bias and high validity were used for both qualitative and quantitative analysis, thereby deviating from the protocol. Fig. 3  Number of publications by years Study design and population of interest Of the 92 articles retained after critical appraisal, 56 were based on field experiments (60.9%), making it the most frequent study design, often performed in sandy loam (32%) and sandy soil (16%). The remaining field experiments were conducted in sandy clay loam (6.5%), loamy sand (5.4%) and, to a lesser extent, in coarse sand and loamy soil. Greenhouse experiments were the sec- ond-most applied study design with 25 articles (27.2%), mainly used for sandy loam (13.9%) followed by sandy soil (10.8%). The remaining 11 articles (11.9%) were lab- based studies, for which sandy loam (7.5%) and sandy soil (3.2%) were the most studied. Given that the largest num- ber of studies were carried out in sandy loam and sandy soils, their proportion in each experimental design is much higher than for other types of soils (Fig. 5). Outcome In total, there were 49 soil properties that were grouped by their relevance into nine SPPs: mineral N leaching, effective CEC, potential CEC, ­N2O emission, NUE, plant nutrient level, soil mineral nitrogen, soil NPK availabil- ity, and soil total NPK. Soil total NPK was studied most (28.9%), followed by soil NPK availability (23.7%) and soil mineral nitrogen (16.6%; Fig. 7). There were as many arti- cles on plant nutrient level as on ­N2O emissions (7.1%), while there were 13 articles on effective CEC and 12 on conducted in North America (mostly the USA) and 6.5% in Oceania. conducted in North America (mostly the USA) and 6.5% in Oceania. with no amendment means that the control site has not been treated with any other treatments and biochar only means that only biochar is applied to untreated soils (Fig. 6). The second-most common type of comparator and treatment was control with fertilizer (23.2%), treated with fertilizer only and no biochar, and biochar with fer- tilizer, followed by control with manure without biochar and biochar with manure (8.5%). There were also experi- mental studies (4.7%) where the control was treated with compost and biochar with compost being its interven- tion. The remaining studies (2.4%) applied control with fertilizer and manure, and control with fertilizer and compost, and their associated treatments. The effect of these treatments varies across different SPPs. Narrative synthesish The narrative synthesis was based on 92 articles with a low risk of bias. These included articles yielded 1609 data observations. A database of these studies with qualitative and quantitative data is available in Additional file 9. In the narrative synthesis, we cover the following aspects: study location, study design and population of interest, intervention and comparator, outcome, potential effect modifiers, and sources of heterogeneity. Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 15 of 34 Fig. 4  Number of publications by experimental country Fig. 4  Number of publications by experimental country Intervention and comparatorh There were six types of controls, with corresponding treatments. Ninety-two unique articles yielded a total of 129 counts for types of controls and treatments. Controls with no amendment and treatment alone were the most applied comparator and treatment (61.2%). A control Bekchanova et al. Environmental Evidence (2024) 13:3 Page 16 of 34 Bekchanova et al. Environmental Evidence Fig. 5  Proportion of population of interest in different study designs Fig. 6  Type of treatments with their corresponding controls Fig. 5  Proportion of population of interest in different study designs Fig. 5  Proportion of population of interest in different study designs Fig. 5  Proportion of population of interest in different study designs Fig. 6  Type of treatments with their corresponding controls Fig. 6  Type of treatments with their corresponding controls Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 17 of 34 Fig. 7  Number of articles for each SPP Fig. 7  Number of articles for each SPP (231), and Oceania (153). The fewest observations were supplied from North America [86]. potential CEC. Less studied SPPs were NUE and mineral N leaching (both representing 2.4% of articles). Various types of feedstocks were used for the produc- tion of biochar, which were classified into three catego- ries: agricultural residue, manure/digestate, and woody biomass [74]. Among these, agricultural residues domi- nated both in the number of articles [52] and in the num- ber of data sets (844, after aggregation). Woody biomass was also often studied, with 585 observations aggregated from 42 articles (Table 6). On the contrary, only 14 arti- cles considered manure/digestate, with 180 observations. Articles were also categorized with regard to pyrolysis temperature: ‘low’ when the pyrolysis temperature is less than or equal to 400 ℃, ‘medium’ when the temperature is between 400 and 600 ℃, and ‘high’ when the tempera- ture is equal to or greater than 600 ℃ [38]. In total, 52 articles were conducted on medium pyrolysis tempera- ture, with 823 observations; low pyrolysis temperature was studied in 30 articles, yielding 549 aggregated data sets, and high pyrolysis temperature was not applied in many experimental studies, with 173 data sets from 14 articles. There were four articles with 64 missing data sets (Table 6). Altogether, this represents more than 92 unique articles, because several unique articles have not studied just one type of pyrolysis temperature or type of feedstock, but several. Effect modifiers and sources of heterogeneityf According to the data, some effect modifiers were reported in almost every paper, such as geographic location, experimental design, types of feedstock, and pyrolysis temperature. Annual temperature and biochar application rate were overlooked a few times. The least reported effect modifiers were the type of climate and annual precipitation. Soil pH, biochar pH, soil bulk den- sity and soil dry weight were barely reported. Hence, to provide consistency in the analysis, if there were more than 50% missing values for any of the effect modifiers, they were no longer considered effect modifiers in the analysis (Additional file 9). Description of the data from primary studies included in the meta‑analysis Most observations (1341) were retrieved from 83 peer- reviewed while 268 observations from nine articles were grey literature, comprised of five dissertations (120 observations), three master’s theses (132 observations), and one university repository (16 observations). A sig- nificant number of observations came from Asia (467 observations), followed by Africa (412). The remaining observations came from Europe (259), South America For analysis purposes, the biochar application rate is also divided into four groups based on data availability, Bekchanova et al. Environmental Evidence (2024) 13:3 Page 18 of 34 Bekchanova et al. Description of the data from primary studies included in the meta‑analysis Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 19 of 34 changes from 38% (CI [6%, 78%]) to −  34% (CI [−  50%, − 14%]). such as ‘ < 10’, ‘10–30’, ‘30–50’ and ‘ > 50’ t/ha. Biochar application rates ‘ < 10’ and ‘10–30’ were the most com- monly applied rates, the former being applied in 51 arti- cles with 664 observations and the latter in 49 articles with 536 aggregated observations. The remaining two other categories, ‘30–50’ and ‘ > 50’, generated 194 obser- vations from 17 articles and 215 observations from 19 articles, respectively (Table 6). Given that the duration of the experiment varied in each study, we classified them into five groups as follows: ‘ < 60,’ ‘60–160,’ ‘160–402,’ ‘402–730,’ and ‘ > 730’ days. The most common experi- ment duration was ‘60–160’ days, studied in 28 articles (503 data sets). Subsequent experiments of ‘160–402’ and ‘402–730’ days were with data sets of 388 and 319, respectively (Table  6). Observations 246 and 152 were assigned to the shortest and longest experimental periods of ‘ < 60’ and ‘ > 730’days, respectively. Other SPPs of sandy-textured soils had an effect after biochar amendment before and after the publication bias correction. When the CI of the effect size did not over- lap with zero, it was deemed significantly different from zero. For example, the soil total NPK of sandy-textured soils increased by 36% (CI [23%, 50%]) after being treated with biochar. Soil mineral nitrogen was also augmented after biochar application by 5%; however, it was not sig- nificantly different from a null (CI [− 8%, 19%]). This is followed by plant nutrient levels, which had an increase of 15% (CI [1%, 31%]) in sandy-textured soils induced with biochar. ­N2O emissions were reduced significantly by 29% (CI [−  48%, −  3%]) after biochar, resulting in decreased emissions into the atmosphere. Soil NPK availability was the second highest responded SPP of sandy-textured soils following biochar application (34%, CI [15%, 57%]), followed by potential CEC (18%, CI [3%, 36%]). Since no publication bias was detected in the response of these SPPs, the responses with correction for publication bias support the findings without correction for publication bias (Figs. 8a and b). There were 42 articles with 556 observations that applied irrigation before and after biochar application, while 51 articles reported no irrigation application. The effect of biochar on SPPs related to nutrient cycleh The effect of biochar on SPPs related to nutrient cycle The results of nine meta-analyses are shown in Fig. 8 (one meta-analysis for each of the nine SPPs). Of the total observations used in the meta-analysis, 4% were detected as outliers based on the criterion set in the method sec- tion of “Effect Size and its Variance” (Additional file 11). When we removed outliers to analyze the sensitivity of the results, the mean effect sizes did not vary from positive to negative, from significant to non-significant, or vice versa, for any of the SPPs reported here. There- fore, we consider the results to be robust to the outlier removal and we only provide the results without outliers. Figure 8 presents the estimated meta-averages for the nine SPP without correction for publication bias (Fig. 8a) and with correction for publication bias (Fig. 8b). Visual inspection of funnel plots and the PET-PEESE models suggest that publication bias is of minor importance in the literature (Additional file 13). This is also consistent with the observation that the estimated meta-average and confidence intervals are similar for the models with and without correction for publication bias (Fig. 8). An exception applies for Effective CEC, where the estimate The effect of biochar on SPPs related to nutrient cycle The results of nine meta-analyses are shown in Fig. 8 (one meta-analysis for each of the nine SPPs). Of the total observations used in the meta-analysis, 4% were detected as outliers based on the criterion set in the method sec- tion of “Effect Size and its Variance” (Additional file 11). When we removed outliers to analyze the sensitivity of the results, the mean effect sizes did not vary from positive to negative, from significant to non-significant, or vice versa, for any of the SPPs reported here. There- fore, we consider the results to be robust to the outlier removal and we only provide the results without outliers. In addition to SPPs, we also performed a supplemen- tary analysis to assess the effect of biochar on food crop yield and biomass production based on the observations from the same papers. Description of the data from primary studies included in the meta‑analysis Environmental Evidence Table 6  Description of the observations included in the meta-analysis Variables Categories Subcategories Unique papers (number of observations) Paper type Peer-reviewed Peer-reviewed 83 (1,341) Gray literature Dissertations 5 (120) Master’s theses 3 (132) University repository 1 (16) Experimental design Field experiment Field 53 (893) Controlled experiments Greenhouse 19 (505) Laboratory 11 (211) Experimental continents Africa – 16 (412) Asia – 35 (468) Europe – 19 (254) North America – 8 (85) Oceania – 6 (149) South America – 9 (231) Feedstock type Agricultural residue – 52 (844) Manure/digestate – 14 (180) Wood-based – 42 (585) Pyrolysis group (°C)  ≤ 400 Low 30 (549) 400 < ; > 600 Medium 52 (823)  ≥ 600 High 14 (173) Biochar application rate (t/ha)  < 10 – 51 (664) 10–30 – 49 (536) 30–50 – 17 (194) 50 <  – 19 (215) Experiment duration (days)  < 60 – 14 (246) 60–160 – 28 (503) 160–402 – 23 (384) 402–730 – 20 (318) 730 <  – 9 (152) Types of treatments Biochar alone – 79 (1,020) Biochar with compost – 6 (33) Biochar with manure – 11 (127) Biochar with fertilizer – 30 (401) Biochar with fertilizer & compost – 1 (6) Biochar with fertilizer & manure – 2 (12) Tillage application Not tilled – 64 (1,047) Tilled – 29 (552) Irrigation application Not irrigated – 51 (1,053) Irrigated – 42 (556) Base fertilizer application before and after biochar Fertilizer applied – 42 (589) Fertilizer not applied – 51 (1,010) SPPs Soil total NPK – 61 (506) Soil mineral nitrogen – 35 (247) Plant nutrient level – 15 (106) N2O emission – 15 (53) Soil NPK availability – 50 (468) Potential CEC – 12 (37) Effective CEC – 13 (49) Table 6  Description of the observations included in the meta-analysis Variables Categories Paper type Peer-reviewed Gray literature Experimental design Field experiment Controlled experiments Experimental continents Africa Asia Europe North America Oceania South America Feedstock type Agricultural residue Manure/digestate Wood-based Pyrolysis group (°C)  ≤ 400 400 < ; > 600  ≥ 600 Biochar application rate (t/ha)  < 10 10–30 30–50 50 <  Experiment duration (days)  < 60 60–160 160–402 402–730 730 <  Types of treatments Biochar alone Biochar with compost Biochar with manure Biochar with fertilizer Biochar with fertilizer & compost Biochar with fertilizer & manure Tillage application Not tilled Tilled Irrigation application Not irrigated Irrigated Base fertilizer application before and after biochar Fertilizer applied Fertilizer not applied SPPs Soil total NPK Soil mineral nitrogen Plant nutrient level N2O emission Soil NPK availability Potential CEC Effective CEC NUE Mineral N leaching Table 6  Description of the observations included in the meta-analysis Subcategories Unique pape of observatio Peer-reviewed 83 (1,341) Dissertations 5 (120) Master’s theses 3 (132) University repository 1 (16) Field 53 (893) Greenhouse 19 (505) Laboratory 11 (211) – 16 (412) – 35 (468) – 19 (254) – 8 (85) – 6 (149) – 9 (231) – 52 (844) – 14 (180) – 42 (585) Low 30 (549) Medium 52 (823) High 14 (173) – 51 (664) – 49 (536) – 17 (194) – 19 (215) – 14 (246) – 28 (503) – 23 (384) – 20 (318) – 9 (152) – 79 (1,020) – 6 (33) – 11 (127) – 30 (401) – 1 (6) – 2 (12) – 64 (1,047) – 29 (552) – 51 (1,053) – 42 (556) – 42 (589) – 51 (1,010) – 61 (506) – 35 (247) – 15 (106) – 15 (53) – 50 (468) – 12 (37) – 13 (49) – 5 (23) – 5 (44) Bekchanova et al. Description of the data from primary studies included in the meta‑analysis Some studies also mentioned the use of tillage, which was only applied in field experiments, and 29 articles reported the use of tillage during the experiment with 552 observa- tions (Table  6). Several control soils were treated with inorganic or organic fertilizer before being used in the experiment. Specifically, 42 articles (589 observations) indicated fertilizer as a base treatment. These effect mod- ifiers, in turn, can affect the overall effect of biochar on SPPs, which we discuss in the following sections. No significant difference was found between control and biochar treatments for NUE (− 3%, CI [− 17%, 14%]). Finally, mineral N leaching from sandy-textured soils was reduced by 38% (CI [− 56%, − 13%]), contributing to less groundwater contamination. The results were practically the same before and after correction for publication bias. It should be noted that meta-analyses of some SPPs— such as NUE and mineral N leaching—are based only on a few primary studies, so the corresponding results should be read with caution. The effect of biochar on SPPs related to nutrient cycleh 8  The response of SPPs to biochar application, n means the number of observations: a estimated meta-averages without correction for publication bias; b estimated meta-averages corrected for publication bias (PET & PEESE model). An effect is significant (P < 0.05) if its 95% confidence interval (CI) does not include 1. The biochar treatment is considered to have no effect when the lnRR = 1 , a positive effect when lnRR > 1 , and a negative effect when lnRR < 1 . Confidence intervals are not symmetrical around the effect sizes because they were back-transformed from the log response ratio Fig. 8  The response of SPPs to biochar application, n means the number of observations: a estimated meta-averages without correction for publication bias; b estimated meta-averages corrected for publication bias (PET & PEESE model). An effect is significant (P < 0.05) if its 95% confidence interval (CI) does not include 1. The biochar treatment is considered to have no effect when the lnRR = 1 , a positive effect when lnRR > 1 , and a negative effect when lnRR < 1 . Confidence intervals are not symmetrical around the effect sizes because they were back-transformed from the log response ratio The effect of biochar on SPPs related to nutrient cycleh Food crop yields are annual food crops such as cereals, maize, wheat, and rice, as well as fruits and vegetables, while biomass production is defined here as the shoot of a plant and all types of plants that are produced as above-ground biomass and do not include the harvested portion of food crops. As shown in Fig. 9, food crop yield increased by 20% (CI [6%, 36%]) in sandy-textured soils treated with biochar, but biomass production showed no effect (− 8%, CI [− 16%, 1%]). No publication bias effect was detected. Figure 8 presents the estimated meta-averages for the nine SPP without correction for publication bias (Fig. 8a) and with correction for publication bias (Fig. 8b). Visual inspection of funnel plots and the PET-PEESE models suggest that publication bias is of minor importance in the literature (Additional file 13). This is also consistent with the observation that the estimated meta-average and confidence intervals are similar for the models with and without correction for publication bias (Fig. 8). An exception applies for Effective CEC, where the estimate f Provided that 60% of the included studies did not report SD or SE to calculate the variations of the total effect sizes, they were imputed with the pooled CV using data from studies that did report SDs as described in the methods section of ‘Effect size and its variation calcula- tion.’ A sensitivity analysis was conducted by removing all observations with variations determined based on pooled Page 20 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence ich changed some of the average treatment effects Explaining heterogeneity: meta‑regression analysis o The response of SPPs to biochar application, n means the number of observations: a estimated meta-averages without correction ication bias; b estimated meta-averages corrected for publication bias (PET & PEESE model). An effect is significant (P < 0.05) if its nfidence interval (CI) does not include 1. The biochar treatment is considered to have no effect when the lnRR = 1 , a positive effect RR > 1 , and a negative effect when lnRR < 1 . Confidence intervals are not symmetrical around the effect sizes because they were nsformed from the log response ratio 8  The response of SPPs to biochar application, n means the number of observations: a estimated meta-averages without correction Fig. Explaining heterogeneity: meta‑regression analysis of each SPP CV, which changed some of the average treatment effects to non-significant (Additional file 11: Fig. S11.11). This is because fewer observations result in less power, and the loss of significance is not surprising. If the variations had not been determined (based on the pooled CV) when SD or SE was absent, huge amounts of important data would have been missed in the analysis, and we would have been limited to drawing a conclusion based on a few datasets. We analyzed the reasons for variations in the response of each SPP to biochar application using the effect modifiers mentioned in the sub Sect. "Potential Effect Modifiers and Reasons for Heterogeneity". We pre- sent the results of the LASSO analysis if the variables selected in a minimum of one out of five LASSO mod- els as explained in the sub-section of Effect Size and its Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence (2024) 13:3 Page 21 of 34 Page 21 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Variance. The visualization of the full variable selection is given in Additional file 12. Based on our analysis, the following moderators were the main predictors explain- ing the heterogeneity in the responses of SPPs to biochar application: experimental continent, duration, biochar application rate, fertilizer application rate, soil pH, and publication year. In the sections below, we discuss the key predictors for the response of each SPP based on Table 7, and the results are visualized. LASSO analysis also underlined the significance of medium-level fertilizer application with biochar as a predictor, demonstrating its negative impact on the response of soil total NPK (Fig. 10). This could be attrib- uted to the relatively lower fertilizer application rate as some studies have demonstrated significant benefit of higher fertilizer application rates in combination with biochar for soil NPK content [77, 78]. Publication year was also highlighted as an influential predictor, indicat- ing a positive trend in soil total NPK response to biochar application over time. Soil total NPK  According to the LASSO analysis, the most important predictors affecting the response of total soil NPK were biochar experimental continent, biochar application rate, fertilizer application rate, and publication year (Table 7). Specifically, the experimental continent, such as South America, stood out as the most important and key predictor, positively influencing the response. Explaining heterogeneity: meta‑regression analysis of each SPP In contrast, the response of soil total NPK was negative in Oceania. This variation can be attributed to the region’s specific climate and environmental factors, notably rainfall patterns and temperature fluctuations. South America’s climate has appeared to enhance total NPK in sandy-textured soils following biochar applica- tion. Biochar application rate, particularly the highest application rate, was the second important predictor for the response of soil total NPK (Fig. 10), with a positive impact on the response. Several studies showed that higher biochar application rates led to an increase in total NPK content in sandy-textured soils [8], contrib- uting to their improved quality and fertility. A higher application rate of biochar enriches soil nutrient con- tent through mechanisms such as increased soil pH, increased organic matter, and improved CEC [75, 76]. Soil mineral nitrogen  The significant predictors of soil mineral nitrogen response to biochar application were soil pH, biochar application rate, soil texture, and experi- mental duration (Table 7). A positive response in soil min- eral nitrogen to biochar application was observed when the soil pH ranged from 5.6 to 6.5. This finding aligns with the results reported by [80, 81]. In sandy-textured soils, higher pH levels contribute to reducing soil acidity, creat- ing a favorable environment for processes like mineraliza- tion and nitrification, ultimately leading to increased soil mineral nitrogen. According to LASSO, a higher biochar application rate increased soil mineral nitrogen, likely due to enhanced microorganism activity promoting greater N mineralization and biochar components with a high C:N ratio stimulating N immobilization [80, 82]. Loamy sand had a negative impact on the response (Fig. 11), which could be a result of limited improvement in soil temperature, moisture, and aeration, which, in turn, failed to stimulate soil mineral nitrogen with bio- char application [83–85]. Furthermore, the influence of biochar on soil mineral nitrogen appears to diminish over Fig. 9  The response of food crop yield and biomass production to biochar application, n means the number of observations. An effect is significant (P < 0.05) if its 95% confidence interval (CI) does not include 1. The biochar treatment is considered to have no effect when the lnRR = 1, a positive effect when lnRR > 1 , and a negative effect when lnRR < 1 . The reason why confidence intervals are not symmetrical around the effect sizes is that they were transformed back from the log response ratio Fig. Page 22 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Table 7  Coefficient signs following Randomized LASSO selection for each SPPs Soil total NPK Soil mineral nitrogen Plant nutrient level N2O emission NPK availability Potential CEC Effective CEC NUE Mineral N leaching Study location and Climate C ti t ± ± Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence (2024) 13:3 Page 22 of 34 Table 7  Coefficient signs following Randomized LASSO selection for each SPPs The direction of effect: “−” means that the effect of the predictor was negative in all selected models; “ + ” means the predictor was positive in all selected models. The effect direction was consistent in the LASSO analysis; that is, the effect of the predictor was always positive or always negative. To determine the coefficient sign for the selected variables, we employed ordinary least squares (79) regression. However, we could not perform LASSO analyses due to a scarcity of available papers on NUE and mineral N leaching Soil total NPK Soil mineral nitrogen Plant nutrient level N2O emission NPK availability Potential CEC Effective CEC NUE Mineral N leaching Study location and Climate  Continent  ±   ±   +   +   +   Annual temperature  Annual precipitation Experimental condition  Experimental design –  Experimental duration –  ±   +   Biochar application rate  +   +   +  -  ±   +  –  Biochar with fertilizer  Fertilizer application rate – –  ±   Biochar with manure  Manure application rate Biochar properties  Feedstock types  Pyrolysis temperature  +  – Soil status  Soil texture –  +   Soil pH  +  – – –  Soil minimum depth  Soil maximum depth  +   Fertilizer before biochar  Manure before biochar  Irrigation application  Tillage application Publication status and bias  Publication year  +  –  +  -  Square root of effective sample size  +   +   +   +   +   + Table 7  Coefficient signs following Randomized LASSO selection for each SPPs The direction of effect: “−” means that the effect of the predictor was negative in all selected models; “ + ” means the predictor was positive in all selected models. The effect direction was consistent in the LASSO analysis; that is, the effect of the predictor was always positive or always negative. To determine the coefficient sign for the selected variables, we employed ordinary least squares (79) regression. However, we could not perform LASSO analyses due to a scarcity of available papers on NUE and mineral N leaching an extended duration (Fig. 11). As explained by Singh and Cowie [86], this diminishing effect can be attributed to the depletion of labile soil organic carbon [87]. We addressed publication bias with the square root of the effective sample size in the LASSO model, and according to the analysis, publication bias was also detected. Explaining heterogeneity: meta‑regression analysis of each SPP 9  The response of food crop yield and biomass production to biochar application, n means the number of observations. An effect is significant (P < 0.05) if its 95% confidence interval (CI) does not include 1. The biochar treatment is considered to have no effect when the lnRR = 1, a positive effect when lnRR > 1 , and a negative effect when lnRR < 1 . The reason why confidence intervals are not symmetrical around the effect sizes is that they were transformed back from the log response ratio Fig. 9  The response of food crop yield and biomass production to biochar application, n means the number of observations. An effect is significant (P < 0.05) if its 95% confidence interval (CI) does not include 1. The biochar treatment is considered to have no effect when the lnRR = 1, a positive effect when lnRR > 1 , and a negative effect when lnRR < 1 . The reason why confidence intervals are not symmetrical around the effect sizes is that they were transformed back from the log response ratio Page 22 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Table 7  Coefficient signs following Randomized LASSO selection for each SPPs Soil total NPK Soil mineral nitrogen Plant nutrient level N2O emission NPK availability Potential CEC Effective CEC NUE Mineral N leaching Study location and Climate C ti t ± ± ditions (Fig. 12). Biochar application rates, mainly higher rates, had a positive effect on the response of plant nutri- ent levels (Fig. 12). In contrast, some studies found that higher application rates may significantly reduce nutri- ent uptake [88, 89]. However, Liu, Zhang [90] highlighted biochar’s ability to maximize N uptake in soils with poor structure, such as sandy soils. The benefit of biochar application to plant nutrient levels in sandy soils can be explained by biochar’s ability to improve soil structure and water-holding capacity [91]. LASSO analysis also identified low pyrolysis temperature as having a positive impact on the response (Fig. 12). Biochar produced at low temperatures can lead to biochar with higher nutrient Plant nutrient level  The key predictors influencing the response of plant nutrient levels were the experimental continent, biochar application rate, and pyrolysis tem- perature (Table 7). The negative influence of biochar on plant nutrient uptake in Oceania and its positive response in Asia can be attributed to regional environmental con- Page 23 of 34 Page 23 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Fig. 10  The results of randomized LASSO on the key predictors in soil total NPK response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models Fig. 10  The results of randomized LASSO on the key predictors in soil total NPK response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models from the meta-analysis conducted by Liu, Zhang [90]. Biochar reduces ­N2O emissions in high-pH soils by pro- moting nitrification, converting NH+ 4 to NO− 3 , as elevated pH levels improve aeration and microbial activity [94]. The results also indicated a slightly positive effect of pub- lication bias on response (Fig. 13). content that can support nutrient release over time [92], making it beneficial for plant nutrient uptake. The results also indicate the presence of publication bias that is posi- tively impacting on the response. N2O emission  Experiment duration, biochar applica- tion, and soil pH were selected as influential predictors by LASSO (Table 7) for the ­N2O emission response. Page 22 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Table 7  Coefficient signs following Randomized LASSO selection for each SPPs Soil total NPK Soil mineral nitrogen Plant nutrient level N2O emission NPK availability Potential CEC Effective CEC NUE Mineral N leaching Study location and Climate C ti t ± ± 11  The results of randomized LASSO on the key predictors in soil mineral nitrogen response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models properties of the biochar, as they can vary in compo- sition, surface area, and charge characteristics [100]. Some biochars may have a higher affinity for retaining certain cations, while others may not be as effective. The experimental continent, especially South America, was a crucial predictor and positively influenced the response. As can be seen in Fig. 15, the response of potential CEC was negative at lower soil pH “5.6–6.5” after biochar application. This is mainly because soil pH is strongly associated with soil CEC [100]. As soil pH decreases, it becomes acidic, and the number of negative charges on the colloids decreases [101], thereby decreasing poten- tial CEC. LASSO also identified publication year as a predictor with a negative impact on the response. tion, which may allow biochar to adsorb and hold more nutrients [97], making them available in the soil. LASSO analysis also identified a positive response of NPK avail- ability to biochar application in South America (Fig. 14). Additionally, LASSO revealed the square root of the effec- tive sample size as an influential predictor with a positive effect, signifying the impact of publication bias on the response. Potential CEC  According to LASSO, fertilizer appli- cation rate with biochar, experimental continent, bio- char application rate, and soil pH were among the most important and robust predictors for potential CEC response (Table 7). Higher rates of fertilizer application with biochar had an adverse impact on the response of potential CEC (Fig. 15). A reduction in potential CEC may result from declines in calcium ( Ca+ 2 ) and magne- sium ( Mg+ 2 ) after higher fertilizer application rates [98], or disruption in the balance of base cations in the sorp- tion composite [99]. Additionally, a higher application rate of fertilizer with biochar may cause a dilution effect that may further diminish potential CEC [100]. On the other hand, only biochar application at a higher rate was favorable for the response of potential CEC in sandy- textured soils (Fig. Page 22 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Table 7  Coefficient signs following Randomized LASSO selection for each SPPs Soil total NPK Soil mineral nitrogen Plant nutrient level N2O emission NPK availability Potential CEC Effective CEC NUE Mineral N leaching Study location and Climate C ti t ± ± Bio- char had a negative effect on the short-term response of ­N2O emissions but showed a positive effect in the long term (Fig. 13). This pattern could be related to the vola- tile content of biochar, which could potentially explain the short-term ­N2O emissions in sandy soils amended with biochar [93]. The application of biochar at a medium rate (30–50 t/ha) resulted in a decrease in the response of ­N2O emissions (Fig. 13). This outcome can be explained by the influence of biochar on various soil N transformation pro- cesses in sandy soils, namely enhanced mineralization and nitrification and a reduction in denitrification [94, 95]. The ­N2O emissions in soil occur mainly as a microbial process, involving nitrifiers that oxidize NH+ 4 under aer- obic conditions and denitrifiers that reduce NO− 3 under anaerobic conditions [90]. As it can be seen in Fig. 13, a decrease in ­N2O emission following biochar is observed in soils with higher pH (6.5–7.5), consistent with findings Soil NPK availability  Soil texture, biochar applica- tion rate, and the experimental continent were the most influential and robust predictors of soil NPK availability response (Table  7). Soil texture, namely coarse loamy, was one of the most important predictors with a posi- tive impact on the response of NPK availability following biochar (Fig. 14). The porous nature of coarse loamy soils may allow biochar to be integrated into the soil structure effectively, promoting nutrient retention and reducing nutrient leaching [89]. A low biochar application rate negatively impacted the NPK availability response, while a high application rate had a positive effect (Fig. 14). Sandy- textured soils have lower nutrient retention capacity [96], leading nutrients to leach more easily. High biochar appli- cation rates may increase the nutrient-holding capacity of sandy soils, preventing leaching and making them avail- able to plants [89]. Furthermore, higher application rates might provide a greater surface area for nutrient adsorp- Bekchanova et al. Environmental Evidence (2024) 13:3 Page 24 of 34 Page 24 of 34 Bekchanova et al. Environmental Evidence Fig. 11  The results of randomized LASSO on the key predictors in soil mineral nitrogen response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models Fig. Page 22 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Table 7  Coefficient signs following Randomized LASSO selection for each SPPs Soil total NPK Soil mineral nitrogen Plant nutrient level N2O emission NPK availability Potential CEC Effective CEC NUE Mineral N leaching Study location and Climate C ti t ± ± 15) This can be linked to different Effective CEC  Randomized LASSO models selected different predictors as important, such as experimen- tal country, duration, soil pH, and publication year (Table  7). The square root of effective sample size emerged as the most influential, with a positive effect on the response of effective CEC (Fig. 16), suggesting a like- lihood of publication bias. The results show that effec- tive CEC is positively affected at longer experimental durations (Fig. 16). This can be attributed to the aging processes that biochar undergoes over time, which Page 25 of 34 Page 25 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Fig. 12  The results of randomized LASSO on the key predictors in plant nutrient level response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models Fig. 12  The results of randomized LASSO on the key predictors in plant nutrient level response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models Fig. 12  The results of randomized LASSO on the key predictors in plant nutrient level response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models may increase its ability to retain and exchange cations [102]. Furthermore, microbial activity plays a crucial role in altering the surface chemistry of biochar [103], improving its ability to retain cations and consequently increasing CEC. The response of effective CEC yielded an intriguing result by showing a negative trend in soils with higher pH levels (7.5–8.5). This outcome may be attributed to variations in biochar properties and appli- cation rates. In Africa, the effect of biochar on effective CEC has yielded inconclusive results, with both positive and negative outcomes. Further research is required to clarify the impact of biochar on effective CEC in sandy soils in this region. Furthermore, the selection of pub- lication year as an important predictor with a positive effect suggests a positive shift in the response over time. Page 22 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Table 7  Coefficient signs following Randomized LASSO selection for each SPPs Soil total NPK Soil mineral nitrogen Plant nutrient level N2O emission NPK availability Potential CEC Effective CEC NUE Mineral N leaching Study location and Climate C ti t ± ± influence of higher fertilization rates on nutrient leaching depends on the balance between nutrient uptake by plants and nutrient losses due to leaching. At high fertilizer lev- els, plants may not be able to utilize all of the nutrients applied, resulting in a surplus that may leach into ground- water. Our analysis indicated that low biochar applica- tion rates reduced mineral N leaching (Fig. 17), although other meta-analyses have demonstrated the benefits of higher biochar application rates [89]. This discrepancy may be attributed to the surface properties of biochar, which enable it to adsorb ions in the soil solution [89]. The electrostatic and capillary forces on the biochar surface contribute to reducing nutrient leaching from soils. Soils amended with biochar can adsorb NO− 3 through its anion exchange sites, thus decreasing nitrogen losses. Addition- ally, biochar may increase soil water-holding capacity due to its large specific surface area and high porosity, reduc- ing soil water percolation and the nitrogen contained in it [104] [105]. As per the analysis, biochar produced at high temperatures reduced the response to mineral N leaching, which may be due to the ability of biochar at high temper- atures to retain NO− 3-N effectively, preventing its leaching into groundwater [30]. Nevertheless, our findings are in Mineral N leaching  The key predictors contributing to the heterogeneity in the overall response of mineral N leaching to biochar application were found to be the biochar application rate, pyrolysis temperature, fertilizer application rate with biochar, and publication year. Higher fertilizer rates with biochar increased mineral N leaching, while lower rates had the opposite effect (Fig. 17). The Bekchanova et al. Environmental Evidence (2024) 13:3 Page 26 of 34 Bekchanova et al. Environmental Evidence Fig. 13  The results of randomized LASSO on the key predictors in ­N2O emission response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models Fig. 13  The results of randomized LASSO on the key predictors in ­N2O emission response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). Page 22 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Table 7  Coefficient signs following Randomized LASSO selection for each SPPs Soil total NPK Soil mineral nitrogen Plant nutrient level N2O emission NPK availability Potential CEC Effective CEC NUE Mineral N leaching Study location and Climate C ti t ± ± This visualization shows the variables selected in a minimum of one out of five LASSO models simplify the search string to "Biochar OR Charcoal OR Agrichar" for most of them (Additional file 2: Table S8). However, compared to other systematic reviews, the number of sources searched in this review was consid- erable [8, 38, 39]. Therefore, we argue that the existence of publication bias due to a lack of comprehensiveness is negligible. Our review was limited to the English lan- guage and, although most of the peer-reviewed journals were in English, we discovered during the screening process that some peer-reviewed and gray literature was published in other languages. However, at the full- text screening stage, only two articles (out of 1137) were found to be ineligible due to language. This result indi- cates that there is a very small chance of language bias. contrast to the results presented by Liu, Zhang [90], who suggest the potential advantages of low-pyrolyzed biochar for reducing N leaching. Our study specifically examines biochar’s ability to mitigate N leaching in sandy-textured soils, so direct comparisons with other studies may not be appropriate. Publication year was another predictor iden- tified in our analysis (Fig. 17), and it showed a decreasing trend in response over the years. Limitations of the review methodsh Throughout the systematic review processes, we sought to minimize potential biases regarding the review meth- odology. The regular consultations with the advisory committee and other experts facilitated the identification of relevant and reliable studies and the reduction of likely biases. We created comprehensive search strings with the aim of applying them to diverse search sources. However, the full search strings provided in Table 2 could only be used in some bibliographic databases. When applied to others, such as NDLTD (Networked Digital Library of Theses and Dissertations) and OATD (Open access the- ses and dissertations), simplified search strings had to be used (Additional file 2; Table 7) and the same was true for all organization websites. Hence, we were forced to During both screening stages (title and abstract and full-text screening), all studies were independently screened. In cases where there was uncertainty about excluding studies, both reviewers worked together to discuss and reach a consensus. The implementation of the screening procedures independently aimed to mitigate potential limitations linked to the screening process, including the risk of biased decisions, and to enhance the overall robustness of the screening. As mentioned in the section on deviations from the protocol, we applied text-mining after the title and Page 27 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Fig. 14  The results of randomized LASSO on the key predictors in NPK availability response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models Fig. 14  The results of randomized LASSO on the key predictors in NPK availability response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models were not well matched, or when the sampling method was not appropriate to collect data on the population of interest, the studies struggled with the risk of selec- tion bias or improper sampling. In this case, studies were excluded from the review. One hundred and seventy pub- lications were attributed a ‘moderate’ risk of bias, either because most of the effect modifiers were missing (Fig. Limitations of the review methodsh 2) or there was the risk of selection bias due to a mismatch between treatment and control. Based on the review pro- tocol, both studies with ‘low’ and ‘moderate’ risk of bias were supposed to be used for the data extraction. How- ever, only the former was included for data extraction and in the analyses, while the latter was excluded after discus- sion with the advisory committee. Due to the significant number of ‘low’ risks of bias studies, our focus remained on this category. The significant number of studies with a ’moderate’ and a ’high’ risk of bias prevented us from extracting data during the review, thus not allowing the implementation of additional sensitivity analyses. It is possible that some relevant studies were lost as a result of this decision. Also, the outcome might have been dif- ferent if the studies with a ‘moderate’ and ‘high’ risk of bias had been included. However, studies with a ‘moder- ate’ and ‘high’ risk of bias could have introduced bias and caused missing data. Therefore, we believe such studies abstract screening to reduce the number of studies for full-text screening. Although the text-mining followed rigid procedures, setting cut-off thresholds to exclude irrelevant papers may have led to the exclusion of some relevant studies as well [106]. We tried to minimize this bias by manually assessing 10% of the studies excluded at text-mining (randomly selected), which suggests there were few or no falsely excluded studies. It was also sometimes necessary to transform the data when there were several potential interventions or comparators in order to prevent duplicate extrac- tions or dependent data. For example, we averaged data when the data were provided for several years, months, or days. However, the effects of biochar application to the soil may have been different over time. Limitations of the evidence base Many articles (303) were excluded due to low validity or high risk of bias, mainly because of performance, sam- pling, and selection bias. Performance bias was the domi- nant reason for attributing a high risk of bias, mainly because studies were not based on randomization. Ran- domization decreases the likelihood of confounding fac- tors [107]. When the intervention and comparison sites Bekchanova et al. Environmental Evidence (2024) 13:3 Page 28 of 34 Bekchanova et al. Environmental Evidence Page 28 of 34 Fig. 15  The results of randomized LASSO on the key predictors in potential CEC response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models Fig. 15  The results of randomized LASSO on the key predictors in potential CEC response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models of articles and observations (5 articles and 44 observa- tions). Nevertheless, prior review studies have found that biochar addition to sandy-textured soils decreased N leaching by 44% [8], so we deem our results regard- ing the reduction of mineral N leaching to be reliable. Biochar had no influence on soil mineral nitrogen and NUE of sandy-textured soils. However, the number of observations for NUE in this review was relatively low. Therefore, it is possible that with a higher number of observations, an effect may have been found. Although NUE was not affected by biochar treatment in this study, food crop yields showed a contrasting response to biochar application. Again, this could be due to the lack of studies for NUE in this review, which future studies should address. However, for soil mineral nitro- gen, the number of studies and observations was large enough, so we can say with reasonable certainty that biochar has no effect on it. would have been excluded from the quantitative synthe- ses and, hence, we believe it is reasonable to assume the overall effect of biochar on SPPs would not change and results obtained without bias accurately reflect the true effect of biochar on SPPs. Limitations in generalizing the results Of the 109 articles included in this review, 17 were excluded at the data extraction stage and they were not included in both qualitative and quantitative synthe- sis largely due to data readability issues (the data were not readable with webplotdigitizer). Other than stated in the protocol [44], we only used the 92 ‘low’ risk of bias articles for both quantitative and qualitative syn- thesis, as we believed this could ensure consistency and comparability in the analyses. The overall effect of biochar on nine SPPs was computed in quantitative synthesis (Fig. 8) and we observed that biochar had a significant positive effect on soil total NPK, plant nutri- ent level, NPK availability, ­N2O emission, potential CEC, and mineral N leaching. However, the number of articles and observations among these SPPs differed. For example, soil total NPK had the highest number of articles and observations (61 articles and 505 observa- tions), while mineral N leaching had a lower number f The PET-PEESE method we used to correct for pub- lication bias is one of the recommended techniques for ecological review studies [41, 64]. However, PET-PEESE may perform poorly when the number of included stud- ies is small (< 20) and heterogeneity is very high. The number of unique articles recorded for some of the SPPs violated this rule, but the number of observations Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 29 of 34 Page 29 of 34 Fig. 16  The results of randomized LASSO on the key predictors in effective CEC response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models Fig. 16  The results of randomized LASSO on the key predictors in effective CEC response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models Fig. 16  The results of randomized LASSO on the key predictors in effective CEC response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models Fig. Implications for management and policy l d b h h h Estimating the variance based on the pooled CV when SD or SE was not given may raise concerns about the credibility of the results. A sensitivity analysis was per- formed by removing all observations from these vari- ances based on the pooled CV and the results differed considerably, as almost two-thirds of the observations were excluded from the analysis (Additional file  11). However, Nakagawa, Noble [60] proposed this method as one of the approved methods when the variance could not be calculated in a straightforward way. Furthermore, using this method meant we could avoid losing valuable studies for our review. Policy discussions on biochar have shown hesitancy, pri- marily arising from the prevailing uncertainty regard- ing biochar’s effects on ecosystem services [109]. Prior investigations into biochar’s role in the soil nutrient cycle highlighted the variability of relationships between some key components ­(N2O emission, N leaching, plant N uptake, and soil ­NH3 volatilization) due to diverse soil and biochar characteristics [8, 38, 39]. However, these studies did not specifically address the impact of biochar on the nutrient cycle in sandy-textured soils. While some of our findings align with previous reviews, our review distinguishes itself through its systematic approach and the provision of the most recent findings. According to our review, biochar offers a suite of benefits for address- ing the nutrient cycle problem. From enhancing nutrient retention and soil fertility to reducing nutrient runoff and greenhouse gas emissions, biochar can play an important role in promoting sustainable nutrient management prac- tices in future agriculture. In practice, the potential gen- eralizability of our findings regarding biochar’s impact on nutrient dynamics of sandy-textured soils functions as a strategic guide for agricultural policymakers and farmers, assisting their decision-making that addresses the com- plexities of biochar, such as different biochar types, soil management during and after biochar application, and optimal biochar application rates.ii Limitations in generalizing the results 17  The results of randomized LASSO on the key predictors in mineral N leaching response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models Fig. 17  The results of randomized LASSO on the key predictors in mineral N leaching response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models Fig. 17  The results of randomized LASSO on the key predictors in mineral N leaching response. The importance of a variable is quantified by running the LASSO model for five different model sizes (1–5 regressors). This visualization shows the variables selected in a minimum of one out of five LASSO models Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence Page 30 of 34 exceeded 20 for all SPPs (Additional file 13). Therefore, we assume that PET-PEESE is the right approach for our case. After correction for publication bias, effective CEC of sandy-textured soils did not appear to benefit from biochar treatment. To further our understanding of the potential benefits of biochar on effective CEC of sandy- textured soils, future review studies should explore this topic more, using a larger number of observations. addition, like tillage and irrigation, had minimal impact on SPP responses. The key strength of our systematic review, aiming to provide globally applicable outcomes, faced a hurdle due to the uneven distribution of observa- tions across different regions. Implications for future researchh Additional file 12. Meta-regression results. Contains the results of LASSO analyses for each SPP. Additional file 12. Meta-regression results. Contains the results of LASSO analyses for each SPP. Additional file 13. Correction for publication bias. Contains funnel plots for each SPP and PET-PEESE results. Given the complexity of studying all components of the soil nutrient cycle in one review study, it is likely that the response of other nutrient cycle components besides SPPs has not been specifically examined in this study. For instance, the responses of the microbial activity or soil mineralization to biochar application in sandy-textured soils, which are important indicators of soil quality and components of soil nutrient cycles [110, 111], are miss- ing in this review. Besides, biochar characteristics such as biochar porosity, its CEC, and its specific surface area can significantly affect the nutrients of sandy-textured soils [31, 112], which have not been investigated in this review. Furthermore, plant and/or crop ID was not included in the analysis of this study. Thus, future review studies could address these missing components of the soil nutri- ent cycle and biochar features to complement this review. Additional file 14. Consistency check results for all screening stages (title & abstract screening and full-text screening) and critical appraisal. Additional file 15. R code. Contains all codes used for meta-analysis, meta-regression and correction for publication bias. Additional file 15. R code. Contains all codes used for meta-analysis, meta-regression and correction for publication bias. Acknowledgements This review study was supported by the BASTA project and the authors would like to thank all project stakeholders who contributed to the development of the final review. Funding h The review is implemented as part of Madina Bekchanova’s PhD, which is funded through the BASTA project. Luca Campion also receives funding from the BASTA project. Abbreviations NUE Nutrient use efficiency CEC Cation exchange capacity SPPs Soil and plant properties NPK Nitrogen-phosphorus-potassium SD Standard deviation SE Standard error Author contributions MB and LC jointly worked on the screening and critical appraisal stages. MB extracted the data for the protocol. MB carried out narrative synthesis and meta-analyses. SB consulted on the meta-analysis. MB and RM took the lead in the preparation of the manuscript. All other authors contributed to the manuscript with their critical comments. The final manuscript has been read and approved by all authors. Conclusion According to our results, the nutrient cycle of sandy-tex- tured soils is changed by biochar application by increas- ing soil total NPK, plant nutrient level, NPK availability and potential CEC. At the same time, biochar application decreases ­N2O emissions and mineral N leaching. The results are also in reasonable agreement with previously performed meta-analyses [8, 38, 39]. However, we have focused on the effects of biochar on the nutrient cycle of sandy-textured soils, with the ability to compare different SPPs. In addition to SPPs, an increase in food crop yields is noted, while biomass production was not affected. The limited number of articles and observations for certain SPPs, such as ­N2O emissions, potential CEC, NUE, and mineral N leaching, limits the ability to draw strong con- clusions about their effects. More specifically, the findings of this review provide policymakers with valuable insights into the potential of integrating biochar into agricultural practices offering a sustainable approach to mitigating the impacts of nitrate pollution on both a local and global scale. Based on our findings, biochar application diminishes ­N2O emissions, particularly when employing a shortened experimental duration alongside a moderate biochar application rate. Additionally, a lower rate of biochar application has dem- onstrated a notable decrease in mineral N leaching from sandy-textured soils. These abilities of biochar showcase not only its potential to remedy environmental pollution but also its promising offer to address groundwater pol- lution in various countries [108]. This review highlights biochar’s ability to stimulate NPK availability in coarse- textured soils and intensify overall NPK content and potential CEC in sandy-textured soils at higher applica- tion rates. These findings not only show that biochar has f The change in these SPPs after biochar application depends on a number of factors. For example, in par- ticular, experimental continent, biochar application rate, soil pH, and publication year (Table 7) were the predic- tors that explained the heterogeneity in the response of many SPPs to biochar application. Unfortunately, rand- omized LASSO was not feasible for analyzing NUE due to insufficient observations, which could compromise the reliability of the results. Some predictors were not selected for SPP responses, likely due to missing values or their limited impact. Variables like average precipitation, annual temperature, and fertilizer application before or after biochar lacked variability, making their effect on the overall response uncertain. Conclusion LASSO results also showed that soil management practices during and after biochar Page 31 of 34 Bekchanova et al. Environmental Evidence (2024) 13:3 Bekchanova et al. Environmental Evidence potential to improve environmental sustainability but also underscores biochar’s promising potential in con- tributing to agricultural productivity. Implications for future researchh Additional file 2. Search strategy and results. Provides a description of the search strategy and results of the literature searches. For each source, we provided full details on the search date(s), search strings used, search settings and restrictions, subscriptions (if applicable), and the number of returns. Additional file 2. Search strategy and results. Provides a description of the search strategy and results of the literature searches. For each source, we provided full details on the search date(s), search strings used, search settings and restrictions, subscriptions (if applicable), and the number of returns. The geographical spread of the studies included in this review revealed that more research is needed on the effect of biochar on the nutrient cycling of sandy-tex- tured soils. In general, the evidence is especially lacking in continents such as North and South America and Oce- ania (Additional file  10: Table  S10.1). Relevant experi- mental studies were lacking for mineral N leaching, NUE, and potential and effective CEC of sandy-textured soils. Moreover, most experiments were carried out on either sandy soil or sandy loam, while very few studies were conducted on coarse loamy, coarse sand, and loamy soil. Unfortunately, some predictors such as climate type, compost application with biochar, or before biochar could not be included in the analyses due to the large amount of missing data in all SPPs. Therefore, future research should focus on filling these gaps. We encourage future experimental studies to incorporate true replica- tion and randomization methods to enhance the gener- alizability of their findings. Finally, we recommend that the research community presents the results in a readable form of figures and tables to further facilitate the use of data in meta-analyses. Additional file 3. Papers excluded after text-mining. Provided further keywords used in text-mining. Additional file 3. Papers excluded after text-mining. Provided further keywords used in text-mining. Additional file 4. The results of full-text screening included both excluded and included articles. Separate lists of unobtainable articles and duplicates in full-text screening. Additional file 8. Statistical analysis of variation in the results of different measurement methods of SPPs. Additional file 9. Data-extraction sheet. Contains the coding of extracted data for all articles included in both qualitative and quantitative synthesis. Additional file 10. Descriptive statistics. Contains further descriptions of data for narrative synthesis. Additional file 11. Sensitivity analyses. The effect of outlier removal and estimated SD from P value removal on the total outcome. The online version contains supplementary material available at https://​doi.​ org/​10.​1186/​s13750-​024-​00326-5. The online version contains supplementary material available at https://​doi.​ org/​10.​1186/​s13750-​024-​00326-5. 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Author details 1 Centre for Environmental Sciences, Research Group Environmental Econom- ics, UHasselt—Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium. 2 Centre for Environmental Sciences, Research Group Environmental Biology, UHasselt—Hasselt University, Agoralaan Gebouw D, 3590 Diepen- beek, Belgium. 3 Vrije Universiteit Brussel, Multidisciplinary Institute for Teacher Education (MILO), Pleinlaan 9, 1050 Brussels, Belgium. 4 School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA. 20. Kannan P, Paramasivan M, Marimuthu S, Swaminathan C, Bose J. Applying both biochar and phosphobacteria enhances Vigna mungo L. growth and yield in acid soils by increasing soil pH, moisture content, microbial growth and P availability. Agric, Ecosyst Environ. 2021;308:107258. 21. Azeem M, Hayat R, Hussain Q, Ahmed M, Pan G, Tahir MI, et al. 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Dislocation force of scleral flange-fixated intraocular lens haptics
BMC ophthalmology
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cc-by
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© The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Spela Stunf Pukl1,2,3, Martin Kronschläger1*, Manuel Ruiss1, Stéphane Blouin4, Emre Rüştü Akcan1 and Oliver Findl1 Abstract Purpose  To measure the dislocation forces in relation to haptic material, flange size and needle used. Setting  Hanusch Hospital, Vienna, Austria. Design  Laboratory Investigation. Methods, main outcome measures  30 G (gauge) thin wall and 27 G standard needles were used for a 2 mm tangential scleral tunnel in combination with different PVDF (polyvinylidene fluoride) and PMMA (polymethylmethacrylate haptics). Flanges were created by heating 1 mm of the haptic end, non-forceps assisted in PVDF and forceps assisted in PMMA haptics. The dislocation force was measured in non-preserved cadaver sclera using a tensiometer device. Results  PVDF flanges achieved were of a mushroom-like shape and PMMA flanges were of a conic shape. For 30 G needle tunnels the dislocation forces for PVDF and PMMA haptic flanges were 1.58 ± 0.68 N (n = 10) and 0.70 ± 0.14 N (n = 9) (p = 0.003) respectively. For 27 G needle tunnels the dislocation forces for PVDF and PMMA haptic flanges were 0.31 ± 0.35 N (n = 3) and 0.0 N (n = 4), respectively. The flange size correlated with the occurring dislocation force in experiments with 30 G needle tunnels (r = 0.92), when flanges were bigger than 384 micrometres. Conclusions  The highest dislocation forces were found for PVDF haptic flanges and their characteristic mushroom- like shape for 30 G thin wall needle scleral tunnels. Forceps assisted flange creation in PMMA haptics did not compensate the disadvantage of PMMA haptics with their characteristic conic shape flange. Keywords  Scleral fixation, Flange-fixated IOL, Yamane technique, Dislocation force Purpose  To measure the dislocation forces in relation to haptic material, flange size and needle used. Setting  Hanusch Hospital, Vienna, Austria. Design  Laboratory Investigation. Methods, main outcome measures  30 G (gauge) thin wall and 27 G standard needles were used for a 2 mm tangential scleral tunnel in combination with different PVDF (polyvinylidene fluoride) and PMMA (polymethylmethacrylate haptics). Flanges were created by heating 1 mm of the haptic end, non-forceps assisted in PVDF and forceps assisted in PMMA haptics. The dislocation force was measured in non-preserved cadaver sclera using a tensiometer device. Results  PVDF flanges achieved were of a mushroom-like shape and PMMA flanges were of a conic shape. For 30 G needle tunnels the dislocation forces for PVDF and PMMA haptic flanges were 1.58 ± 0.68 N (n = 10) and 0.70 ± 0.14 N (n = 9) (p = 0.003) respectively. Spela Stunf Pukl1,2,3, Martin Kronschläger1*, Manuel Ruiss1, Stéphane Blouin4, Emre Rüştü Akcan1 and Oliver Findl1 For 27 G needle tunnels the dislocation forces for PVDF and PMMA haptic flanges were 0.31 ± 0.35 N (n = 3) and 0.0 N (n = 4), respectively. The flange size correlated with the occurring dislocation force in experiments with 30 G needle tunnels (r = 0.92), when flanges were bigger than 384 micrometres. Conclusions  The highest dislocation forces were found for PVDF haptic flanges and their characteristic mushroom- like shape for 30 G thin wall needle scleral tunnels. Forceps assisted flange creation in PMMA haptics did not compensate the disadvantage of PMMA haptics with their characteristic conic shape flange. Keywords  Scleral fixation, Flange-fixated IOL, Yamane technique, Dislocation force Backgroundhl The flanged intra-scleral IOL (intraocular lens) fixation technique includes formation of two scleral tunnels, externalisation of the IOL haptics, and haptic end heating to create a flange that seals the scleral tunnel [1]. *Correspondence: Martin Kronschläger martin.kronschlaeger@gmx.at 1Vienna Institute for Research in Ocular Surgery (VIROS), A Karl Landsteiner Institute, Hanusch Hospital, Heinrich-Collin Str. 30, AT-1140 Vienna, Austria 2Medical Faculty, University of Ljubljana, Ljubljana, Slovenia 3Eye Hospital, University Clinical Centre Ljubljana, Ljubljana, Slovenia 4Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of OEGK and AUVA Trauma Centre Meidling, Medical Department Hanusch Hospital, Vienna, Austria l When performed appropriately, this technique has been shown to offer stable IOL positioning in eyes with­ out capsular support, however the surgical steps are chal­ lenged and are, along with the equipment and materials, still a matter of several modifications [2, 3]. i The most important risk after the surgery is erosion of the flange out of the scleral tunnel and through the © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. BMC Ophthalmology BMC Ophthalmology Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 https://doi.org/10.1186/s12886-024-03369-x Open Access Dislocation force of scleral flange-fixated intraocular lens haptics Spela Stunf Pukl1,2,3, Martin Kronschläger1*, Manuel Ruiss1, Stéphane Blouin4, Emre Rüştü Akcan1 and Oliver Findl1 Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 2 of 9 Page 2 of 9 Solutions Pack (MicroSurgical Technology, Redmond, USA). Previously studied techniques for flanging were used as follows: (i) for the IOL with PMMA, the hap­ tic was grasped with forceps 1 mm from the tip during flange formation; (ii) for the IOL with PVDF haptics a non-grasping technique was used. The flange was wedged into the outer ostia of the scleral tunnel. conjunctiva. On the contrary, during the surgery and immediately postoperatively, the meticulous surgical steps can be complicated by flange slippage trough the scleral tunnel into the eye. The stability of the IOL during the procedure and immediately after the surgery mostly depends on fixing force of the flange - its resistance to slip through the scleral tunnel. Experiments were carried on non-preserved human scleral tissue provided by the Vienna Eye Bank. Sclera is the opaque, firm collagenous outermost layer of the eye. Its stiffness and stress-stain properties differ at various regions of the eye, and they do change signifi­ cantly depending on the healing processes [4–7]. Scleral tissue has a non-linear behaviour with low stiffness at lower stress, and increasing stiffness at higher stress. Its in-vivo resistance thus depends also on the IOP changes [7]. i For measurement of the dislocation force of the intra-scleral flange fixated IOL haptic a bench setup was designed. An electronic force gauge instrument (PCE-DFG-N20, PCE Instruments) was secured in the horizontal plane. A straight clamp was attached to the instrument. The clamp was applied on the sclera parallel to the scleral tunnel. The haptic exiting the scleral tun­ nel at its interior was pulled with forceps while measur­ ing the applied force. The maximal force until the flange slipped though was recorded. The thickness of the pulled- out flange was then analysed with light microscopy and measured (Fig. 1).l Before the onset of scleral tunnel healing and fibrosis, and especially in cases of intra- or early post-operative lover IOP, the fixing force of the flanges depends exclu­ sively on the relationship of the scleral tunnel dimensions versus the flange size and shape. l Typically, the scleral tunnel in Yamane technique is positioned 2  mm behind the limbus, is angled slightly posteriorly, and is parallel to the limbus. For flange analysis and measurement, the haptics of the IOLs with dislocated flanges were observed in reflec­ tion mode by circular differential interference contrast using an optical upright microscope (Axio Scope.A1, Carl Zeiss Meditec AG, Jena, Germany) equipped with a 5x EC Epiplan Neofluar high-density differential interfer­ ence contrast lens (Carl Zeiss Meditec AG). A compact charge-coupled device monochrome camera (Lumenera Corp.) recorded 1392 × 1040 pixels images with a resolu­ tion of 1.3 mm/pixels. Microscopic images of each hap­ tic and flange were taken. The diameter of the peripheral end of each haptic and each flange were measured per­ pendicularly to the long axis of the haptic with the aid of the straight tool in ImageJ. Relationship between the diameter of the tunnel, which is initially determined by the needle thickness, versus the haptic and flange size, change after the surgery. However, during and immediately after the surgery, a suitable size relationship would add additional safety and stability of the flanges and IOL. l The present study was designed to measure the forces needed to dislocate haptic flanges of known dimension out of characteristic scleral tunnels in human autopsy eye sclera in order to better understand the potential impact of size matching of needle to haptic and flange dimen­ sions for scleral fixation. For statistical analysis the SPSS software (IBM, USA) was used, the groups were compared by the Mann-Whit­ ney U test, the diameter of flanges as well as the material of the haptics and size of the needle were correlated by the ANOVA test to the dislocation force measured. For correlation analysis the Pearson correlation coefficient was used. Methodsf Four different 3-piece IOLs, that are often used for the scleral fixation technique, were included in this experi­ mental study. The haptics were of two different materi­ als: Polyvinylidene fluoride– PVDF (n = 10): CT Lucia 202 (Carl Zeiss Meditec AG, Jena, Germany) and the Avansee Preset (Kowa, Tokyo, Japan), and Polymeth­ ylmethacrylate– PMMA (n = 9): Sensar AR40 IOL (Johnson&Johnson, Santa Ana, USA) and Tecnis ZA9003 IOL (Johnson&Johnson, Santa Ana, USA). Resultsh The mean dislocation force for PVDF haptic flanges from the 2 mm tangential scleral tunnel created with a 30 G thin wall needle was 1.58 ± 0.68 N (n = 10) and the mean dislocation force for PMMA haptic flanges under the same settings was 0.70 ± 0.14 N (n = 9). The difference was statistically significant, p = 0.003, Mann-Whitney U test (Fig. 1). A typical tangential 2 mm long scleral tunnel was cre­ ated with a 30 gauge (G) thin-wall needle with a length of 13 mm (TSK Laboratory Europe, Oisterwijk, Nether­ lands). For comparison of the fixing forces, a 27 gauge (G) standard needle, with a length of 12 mm (Sterican B. Braun, Hessen, Germany) was used alternatively. When the 2 mm long tangential tunnel was for com­ parison to the 30 G created with a 27 G standard needle, the flange slippage occurred in experiments with PMMA Flanging of the introduced haptic was done with a low- temperature cautery from the MST Scleral IOL Fixation Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 3 of 9 Fig. 1  Measurement of dislocation force: A: An electronic force gauge instrument was secured in the horizontal plane, B: scleral tissue fixated into a straight clamp, C: 30 G thin wall needle used for a 2 mm scleral tunnel, D: 1 mm haptic flanging with no-grasp technique, E: the flange, F to H: pulling of the haptic until dislocated Fig 1 Measurement of dislocation force: A: An electronic force gauge instrument was secured in the horizontal plane B: scleral tissue fixated An electronic force gauge instrument was secured in the horizontal plane, B: scleral tissue fixated into a Fig. 1  Measurement of dislocation force: A: An electronic force gauge instrument was secured in the horizontal plane, B: scleral tissue fixated into a straight clamp, C: 30 G thin wall needle used for a 2 mm scleral tunnel, D: 1 mm haptic flanging with no-grasp technique, E: the flange, F to H: pulling of the haptic until dislocated technique, as well as sizes and characteristic shapes of flanges for different IOLs are in Table 1; Fig. 3a and b.l haptics. The dislocation forces could be measured only in few experiments with the PVDF haptics (n = 3) and were substantially and statistically significantly lower compared to experiments with 30 G needles and PVDF haptics (Fig. Resultsh 2a): PVDF group, 0.31 ± 0.35  N (p = 0.011, Fig. 2b). lf PVDF flanges were of mushroom like shape and PMMA flanges were of conic like shape (Table 1; Fig. 3a). Flangesl Mean flange diameter of all analysed flanges (flanges that slipped through the tunnel and those that produced Mean values of dislocation force and standard devia­ tions when the tunnel was made with a thin wall 30 G Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 4 of 9 Page 4 of 9 Stunf Pukl et al. BMC Ophthalmology Fig. 2  (a) Dislocation forces measured in Newtons (N), 2 mm tangential scleral tunnel created with a 30 G thin wall needle or 27 G standard needle, mea­ surements for flanges of PVDF haptics. * p < 0.05. (b) Dislocation forces measured in Newtons (N), 2 mm scleral tunnel, 30 G thin wall needle and 3-piece IOLs with haptics of different materials: PVDF, PMMA. ** p < 0.01 Fig. 2  (a) Dislocation forces measured in Newtons (N), 2 mm tangential scleral tunnel created with a 30 G thin wall needle or 27 G standard needle, mea­ surements for flanges of PVDF haptics. * p < 0.05. (b) Dislocation forces measured in Newtons (N), 2 mm scleral tunnel, 30 G thin wall needle and 3-piece IOLs with haptics of different materials: PVDF, PMMA. ** p < 0.01 resistance) was 376 ± 27 μm for the Zeiss CT Lucia 202 IOLs (Figs. 4), 361 ± 14 μm for the in Kowa Avansee Pre­ set IOLs, 356 ± 18  μm for the Johnson&Johnson Tecnis ZA903 IOLs, and 409 ± 11 μm for the Johnson&Johnson Sensar AR40 IOLs. All of the flanges from PVDF hap­ tics were created without grasping the haptic, and result in a mushroom-like shape (Fig. 3a). On the other hand, flanges from PMMA haptics were performed by flang­ ing 1 mm from the haptic end and grasping the haptic 1 mm from the haptic tip. They were of a conic-like shape (Table 1; Fig. 3a). In 30 G thin-wall needle tunnels, a higher disloca­ tion force was measured in larger flanges in for most of the performed experimental dislocations (Fig. 5a: A-D). Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 5 of 9 Fig. 3  (a) Microscopic images of flanges of different IOLs: A– Zeiss CT Lucia 202, B– Kowa Avansee Preset, C– Johnson&Johnson Tecnis ZA9003, D– Johnson&Johnson Sensar AR40. Flangesl (b) Dislocation force in Newtons for different IOLs, 30 G thin wall needle tunnel (Zeiss CT Lucia 202: n = 6, Kowa Avansee Preset: n = 5, Johnson&Johnson Tecnis ZA9003: n = 5, Johnson&Johnson Sensar AR40: n = 4) Fig. 3  (a) Microscopic images of flanges of different IOLs: A– Zeiss CT Lucia 202, B– Kowa Avansee Preset, C– Johnson&Johnson Tecnis ZA9003, D– Johnson&Johnson Sensar AR40. (b) Dislocation force in Newtons for different IOLs, 30 G thin wall needle tunnel (Zeiss CT Lucia 202: n = 6, Kowa Avansee Preset: n = 5, Johnson&Johnson Tecnis ZA9003: n = 5, Johnson&Johnson Sensar AR40: n = 4) Table 1  Dislocation force and flange size for different IOLs IOL label IOL company Mean size of the flange, micrometres (µm) Dislocation force, New­ tons (N) Mean SD Mean SD Zeiss CT Lucia 202 Carl Zeiss Meditec (Jena, Germany) 376.40 26.9 1.31 1.0 Kowa Avansee Preset Kowa (Tokyo, Japan) 360.63 13.8 1.37 1.0 Johnson&Johnson Tecnis ZA9003 Johnson&Johnson, Abbott Medical Optics (Santa Ana, USA) 356.30 18.2 0.46 0.1 Johnson&Johnson Sensar AR40 Johnson&Johnson, Abbott Medical Optics (Santa Ana, USA) 409.05 10.4 0.99 0.5 * Scleral tunnel 2 mm, 30 G thin wall needle, heating 1 mm of haptic, non-forceps assisted in PVDF haptics and forceps assisted in PMMA haptics of haptic ends under and through the conjunctiva. The numerous combinations of different haptic materials and thicknesses of IOLs available, as well as the needles used for externalisation, make standardisation challenging. With all the IOLs, the correlation of size to force is a flat curve for all IOLs up to the flange size of 384 microme­ tres (correlation coefficient– 0.04). For flanges larger than 385 microns, flange size correlated with dislocation force (0.92) (Fig. 5b). According to the experimental study with cadaver sclera, the flange is an effective way to stabilize the haptic in the immediate post-implantation period [8]. Ma et al. further showed that the haptic material and flange to tun­ nel size coefficient do influence the dislocation of flanged haptic from cadaveric sclera [9]. In a 27 G needle tunnel no dislocation force could be obtained with PMMA haptic flanges since they all slipped through the tunnel and the mean dislocation force for PVDF haptic flanges was 0.31 ± 0.347 N, n = 3 (Fig. 2a). Discussionhi Among the PVDF haptic flanges, substantially higher dislocation forces were mea­ sured when a 30 G thin wall needle was used for creation of the 2 mm long tangential scleral tunnel as compared to the 27 G needle tunnel. The findings are in accordance with previously published results from Ma et al. However, in their study the scleral tunnel was not tangential and 2 mm long as described in the original technique report [1], and also the PMMA haptics were flanged without the forceps holding technique, which was proved to results in a broader flange [9]. We thus propose the scleral tunnel in Yamane style scleral fixation to be performed as origi­ nally described − 2 mm behind the limbus, angled slightly posteriorly, parallel to the limbus - with a 30 G thin wall needle, 2 mm tangentially trough the sclera in order to achieve the optimal flange fixation force.ll cone-like shaped flange, which was proposed to provide maximum hold in the scleral tunnel and minimum leak to the sub-conjunctival space [10]. Not using the forceps in PMMA haptics during heating, the flanges creates less prominent conic flanges [10]. Forceps assisted flange cre­ ation in PMMA haptics during the experiments reported here however, did not compensate the disadvantage of PMMA haptic characteristic conic shaped flange, result­ ing in lower dislocation forces, which means less stabil­ ity of the IOLs with PMMA haptics in the scleral tunnel. Appropriate type of IOL selection is thus also an impor­ tant step. A PVDF haptic IOL represents a more secure option for Yamane scleral fixation according to measure­ ments in the present study. Ma et al. performed a no-grasp haptic heating tech­ nique and reported flange sizes of 0.5–2.0  mm. They found that heating the haptic beyond 1.0  mm did not result in a larger or differently shaped flange [9]. Disloca­ tion forces in their experiments correlated to the flange to needle diameter ratio, speaking in favour of suffi­ ciently large flanges. Discussionhi Incorporating the knowledge of how to obtain an optimal flange [10], and imitating the surgical steps, as described by Yamane concerning the scleral tunnel preparation [1, 2], the present laboratory study was per­ formed to measure dislocation forces immediately after the haptic insertion and flanging.hl The scleral fixation technique with flanged intrascleral haptic fixation, first described by Yamane, has been an important addition to the techniques used for fixating IOLs in eyes without capsular support [1]. Standardi­ sation of the technique, however, may be needed for increasing safety, such as avoiding either haptic disloca­ tion or oversized flanges which may cause protrusion l The dislocation forces for PVDF haptic flanges were significantly higher, meaning more stable IOL, than Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 6 of 9 Fig. 4  Flange size in micrometres for all analysed flanges (Zeiss CT Lucia 202: n = 6, Kowa Avansee Preset: n = 9, Johnson&Johnson Tecnis ZA9003: n = 10, Johnson&Johnson Sensar AR40: n 3) Fig. 4  Flange size in micrometres for all analysed flanges (Zeiss CT Lucia 202: n = 6, Kowa Avansee Preset: n = 9, Johnson&Johnson Tecnis ZA9003: n = 10, Johnson&Johnson Sensar AR40: n = 3) Fig. 4  Flange size in micrometres for all analysed flanges (Zeiss CT Lucia 202: n = 6, Kowa Avansee Preset: n = 9, Johnson&Johnson Tecnis ZA9003: n = 10, Johnson&Johnson Sensar AR40: n = 3) for the PMMA haptic flanges. Among the PVDF haptic flanges, substantially higher dislocation forces were mea­ sured when a 30 G thin wall needle was used for creation of the 2 mm long tangential scleral tunnel as compared to the 27 G needle tunnel. The findings are in accordance with previously published results from Ma et al. However, in their study the scleral tunnel was not tangential and 2 mm long as described in the original technique report [1], and also the PMMA haptics were flanged without the forceps holding technique, which was proved to results in a broader flange [9]. We thus propose the scleral tunnel in Yamane style scleral fixation to be performed as origi­ nally described − 2 mm behind the limbus, angled slightly posteriorly, parallel to the limbus - with a 30 G thin wall needle, 2 mm tangentially trough the sclera in order to achieve the optimal flange fixation force.ll for the PMMA haptic flanges. Discussionhi The optimal shape of a prominent cone with PMMA haptics may be obtained with forceps- assisted heating [10], which however in the contrary to our expectations, did not prove higher dislocation forces li As far as flanges, the flange shape depends on the hap­ tic material and flanging technique [10, 11] and can, if not consistent, result in instability of the flange in the scleral tunnel, or on the other hand conjunctival erosions [12]. The flange shape of PVDF haptics appears to be inde­ pendent of whether forceps are used for assistance while heating. Conversely, with PMMA haptics, a forceps grip­ ping is needed to attain mushroom-like or a prominent Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 7 of 9 Page 7 of 9 Fig. 5  (a) Flange size in micrometres (left of double y axis) and dislocation force in Newtons (right of double y axis) for A: PVDF1 (Zeiss CT Lucia 20 n = 4; B: PVDF2 (Kowa Avansee Preset) n = 5; C: PMMA1 (Johnson&Johnson Tecnis ZA9004) n = 5; and D: PMMA2 (Johnson&Johnson Sensar AR40) n = (b) Flange size in micrometres (x axis) and dislocation force in Newtons (y axis) for all flanges, dislocated out for 30 G thin wall tunnels, which produce resistance Fig. 5  (a) Flange size in micrometres (left of double y axis) and dislocation force in Newtons (right of double y axis) for A: PVDF1 (Zeiss CT Lucia 202) n = 4; B: PVDF2 (Kowa Avansee Preset) n = 5; C: PMMA1 (Johnson&Johnson Tecnis ZA9004) n = 5; and D: PMMA2 (Johnson&Johnson Sensar AR40) n = 3. (b) Flange size in micrometres (x axis) and dislocation force in Newtons (y axis) for all flanges, dislocated out for 30 G thin wall tunnels, which produced resistance Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Page 8 of 9 Page 8 of 9 Stunf Pukl et al. BMC Ophthalmology in PMMA haptic IOLs compared to the published data [9]. in PMMA haptic IOLs compared to the published data [9]. elasticity change, if used beyond the first two days after retrieval, was noticed. This speaks for early processes of tissue degradation and/or hydration. Tissue quality is of course an important aspect when interpreting these labo­ ratory results concerning dislocation forces. Conclusionsh The present experimental study was performed to imi­ tate the intraoperative and early postoperative stability of flanged intrascleral fixation of three-piece IOL haptics in an aphakic eye. Using the model of non-preserved cadav­ eric sclera, the 2 mm tangential tunnel provided highest dislocation forces if created with a 30 G thin wall needle and when a PVDF haptic flange was used, suggesting that the scleral tunnel diameter, length, and direction, as well as proper IOL type selection are essential for the fixa­ tion force in Yamane scleral fixation. The post-dislocation analysis of flanges proved that a larger flange diameter resulted in higher dislocation forces independent to the haptic material when larger than 384 microns. Forceps assisted flange creation with PMMA haptics did not com­ pensate for the disadvantage of the less stable PMMA characteristic conic-shaped flange. However, flanging of 1 mm haptic end assures a sealing flange not smaller than 350 microns. fl Heating 1  mm of the haptic end in theory results in a flange diameter of approximately 350  μm [10]. The flanges performed showed a slight variability in flange size (Table 1). The largest diameters were measured for the Sensar AR40 IOLs, which does, however, have the thickest haptics compared to the other three IOLs used [14]. The flange should thus be performed by heating at least 1 mm of the haptic end in order not to be smaller than 350 μm. Being of the same importance as the flange, a precise sclera tunnel formation has several important impacts during and after the procedure. When a 30 G thin wall needle was used for the scleral tunnel, a larger flange size when more than 380 micrometres in diameter positively correlated to a higher dislocation force regardless of the IOL type. This suggest that independent of the hap­ tic material, a well-formed flange will provide enough stability of the IOL in a 30 G thin wall needle tunnel [10], which is long and deep in sclera enough. However, beyond the stability of the IOL, safety after the surgery in terms of postoperative leak and endophthalmitis risk depends also on long enough scleral tunnel (at least 2  mm) and sufficient flange burial [12]. To large flange diameter might not burry and seal and could represent a risk for flange erosions, postoperative leakage, invasion of microorganisms [12]. The length and orientation of the scleral tunnel additionally stabilise the flanged hap­ tic. Discussionhi Additionally, the clinical and long-term stability of flanged intrascleral fixation of three-piece IOL haptics also depend on the elastic and healing/scarring properties of the sclera. Measurements of the dislocation forces in this cadaver scleral model thus only applies to the specific aspect of the procedure and long-term clinical follow-up studies are needed. A mushroom-like shape of the PVDF haptics resulted in a better stability in our study. Even though the flange sizes were comparable to the flanges of the PMMA hap­ tics (Table 1), the dislocation forces were larger for PVDF haptics (Table  1). However, a grasp assisted prominent conic shape of the PMMA haptic according to intuitive thinking offers easier slip of the flange into the scleral tunnel and a good seal immediately after burial of the flange into the scleral tunnel. While mid-term flange sta­ bility, reported in the literature [13], results also from the fibrotic sclera response. Further studies are needed to assess the sealing properties of differently shaped flanges. Heating 1  mm of the haptic end in theory results in a flange diameter of approximately 350  μm [10]. The flanges performed showed a slight variability in flange size (Table 1). The largest diameters were measured for the Sensar AR40 IOLs, which does, however, have the thickest haptics compared to the other three IOLs used [14]. The flange should thus be performed by heating at least 1 mm of the haptic end in order not to be smaller than 350 μm.l A mushroom-like shape of the PVDF haptics resulted in a better stability in our study. Even though the flange sizes were comparable to the flanges of the PMMA hap­ tics (Table 1), the dislocation forces were larger for PVDF haptics (Table  1). However, a grasp assisted prominent conic shape of the PMMA haptic according to intuitive thinking offers easier slip of the flange into the scleral tunnel and a good seal immediately after burial of the flange into the scleral tunnel. While mid-term flange sta­ bility, reported in the literature [13], results also from the fibrotic sclera response. Further studies are needed to assess the sealing properties of differently shaped flanges. Abbreviations Abbreviations G Gauge IOL Intraocular lens PMMA Polymethylmethacrylate PVDF Polyvinylidene fluoride Abbreviations G Gauge IOL Intraocular lens PMMA Polymethylmethacrylate PVDF Polyvinylidene fluoride Conclusionsh The close-to-limbus tangential insertion [7], long scleral tunnel (at least 2 mm), and appropriate burial of the flange into the sclera covered with tenon’s capsule and conjunctiva provide stability, and appear to also be important to avoid flange erosions, act as an effective barrier to invasion of microorganisms, which may other­ wise result in postoperative endophthalmitis [12].h Competing interests 14. Stunf Pukl S, Kronschläger M, Ruiss M, Blouin S, Findl O. Size variability and fitting of 30-gauge thin-wall needles and 3-piece intraocular lens haptics for the flanged intrascleral fixation technique. J Cataract Refract Surg. 2023;49:874–8. p g Spela Stunf Pukl, Martin Kronschläger, Manuel Ruiss, Stephane Blouin, Emre Rüştü Akcan: The authors have no compending interests, no financial or proprietary interest in any material or method mentioned. Oliver Findl is a scientific advisor to Alcon, BVI, Carl Zeiss Meditec AG, Croma and Johnson&Johnson. Data availability 9. Ma KK, Yuan A, Sharifi S, Pineda R. A Biomechanical Study of Flanged Intra­ scleral Haptic fixation of three-piece intraocular lenses. Am J Ophthalmol. 2021;227:45–52. 9. Ma KK, Yuan A, Sharifi S, Pineda R. A Biomechanical Study of Flanged Intra­ scleral Haptic fixation of three-piece intraocular lenses. Am J Ophthalmol. 2021;227:45–52. The datasets analysed during the current study are available from the corresponding author on reasonable request. 10. Kronschläger M, Blouin S, Roschger P, Varsits R, Findl O. Attaining the optimal flange for intrascleral intraocular lens fixation. J Cataract Refract Surg. 2018;44:1303–5. Funding Funding There was no financial support for the study. Declarations 11. Agrawal V, Raju B. Creating the flange in Yamane’s technique. Indian J Oph­ thalmol. 2021;69:465. 11. Agrawal V, Raju B. Creating the flange in Yamane’s technique. Indian J Oph­ thalmol. 2021;69:465. Ethics approval and consent to participate Not applicable. Received: 13 December 2023 / Accepted: 25 February 2024 Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Consent for publication Not applicable. 13. Canabrava S, Rodrigues G, Halabi NN, Rezende AC, Cardoso M. 18-month results of double-flanged 5– 0 polypropylene suture transscleral bag fixation in subluxated cataracts. Arq Bras Oftalmol. 2022;7:0004–27492022005004205. 13. Canabrava S, Rodrigues G, Halabi NN, Rezende AC, Cardoso M. 18-month results of double-flanged 5– 0 polypropylene suture transscleral bag fixation in subluxated cataracts. Arq Bras Oftalmol. 2022;7:0004–27492022005004205. Author contributions The three-dimensional organization of collagen fibrils in the human cornea and sclera. Invest Ophthalmol Vis Sci. 1991;32:2244–58. 5. Kamma-Lorger CS, Boote C, Hayes S, et al. Collagen and mature elastic fibre organisation as a function of depth in the human cornea and limbus. J Struct Biol. 2010;169:424–30.i 6. Newton RH, Meek KM. Circumcorneal annulus of collagen fibrils in the human limbus. Invest Ophthalmol Vis Sci. 1998;39:1125–34. 7. Elsheikh A, Geraghty B, Alhasso D, Knappett J, Campanelli M, Rama P. Regional variation in the biomechanical properties of the human sclera. Exp Eye Res. 2010;90:624–33. 8. Stem MS, Wa CA, Todorich B, Woodward MA, Walsh MK, Wolfe JD. 27-gauge sutureless intrascleral fixaiton of intraocular lens with haptic flanging: short-term clinical outcomes and a Disinsertion Force Study. Retina. 2019;39:2149–54. 8. Stem MS, Wa CA, Todorich B, Woodward MA, Walsh MK, Wolfe JD. 27-gauge sutureless intrascleral fixaiton of intraocular lens with haptic flanging: short-term clinical outcomes and a Disinsertion Force Study. Retina. 2019;39:2149–54. Author contributions J Struct Biol. 2010;169:424–30. 6. Newton RH, Meek KM. Circumcorneal annulus of collagen fibrils in the human limbus. Invest Ophthalmol Vis Sci. 1998;39:1125–34. 7. Elsheikh A, Geraghty B, Alhasso D, Knappett J, Campanelli M, Rama P. Regional variation in the biomechanical properties of the human sclera. Exp Eye Res. 2010;90:624–33. 8. Stem MS, Wa CA, Todorich B, Woodward MA, Walsh MK, Wolfe JD. 27-gauge sutureless intrascleral fixaiton of intraocular lens with haptic flanging: short-term clinical outcomes and a Disinsertion Force Study. Retina. 2019;39:2149–54. 9. Ma KK, Yuan A, Sharifi S, Pineda R. A Biomechanical Study of Flanged Intra­ scleral Haptic fixation of three-piece intraocular lenses. Am J Ophthalmol. 2021;227:45–52. 10. Kronschläger M, Blouin S, Roschger P, Varsits R, Findl O. Attaining the optimal flange for intrascleral intraocular lens fixation. J Cataract Refract Surg. 2018;44:1303–5. 11. Agrawal V, Raju B. Creating the flange in Yamane’s technique. Indian J Oph­ thalmol. 2021;69:465. 12. Werner L. Flange erosion/exposure and the risk for endophthalmitis. J Cata­ ract Refract Surg. 2021;47:1109–10. 13. Canabrava S, Rodrigues G, Halabi NN, Rezende AC, Cardoso M. 18-month results of double-flanged 5– 0 polypropylene suture transscleral bag fixation in subluxated cataracts. Arq Bras Oftalmol. 2022;7:0004–27492022005004205. 14. Stunf Pukl S, Kronschläger M, Ruiss M, Blouin S, Findl O. Size variability and fitting of 30-gauge thin-wall needles and 3-piece intraocular lens haptics for the flanged intrascleral fixation technique. J Cataract Refract Surg. 2023;49:874–8. 2. Yamane S, Ito A. Flanged fixation: Yamane technique and its application. Curr Opin Ophthalmol. 2021;32:19–24. not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature.Emre Rüştü Akcan acquisition, analysis of data; interpretation of data; AND approved the submitted version; AND agreed both to be personally accountable for own contributions and ensured that questions related to the accuracy or integrity of any part of the work, even ones in which was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. Oliver Find conception, design of the work; interpretation of data; substantively revised the work AND approved the submitted version; AND agreed both to be personally accountable for own contributions and ensured that questions related to the accuracy or integrity of any part of the work, even ones in which was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. , , p ( ) ; 4. Komai Y, Ushiki T. Publisher’s Note Received: 13 December 2023 / Accepted: 25 February 2024 1. Yamane S, Sato S, Maruyama-Inoue M, Kadonosono K. Flanged intrascleral intraocular Lens fixation with Double-Needle Technique. Ophthalmology. 2017;124:1136–42. Author contributions Spela Stunf Pukl acquisition, analysis of data; interpretation of data; have drafted the work AND approved the submitted version; AND agreed both to be personally accountable for own contributions and ensured that questions related to the accuracy or integrity of any part of the work, even ones in which was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. Martin Kronschläger conception, design of the work; interpretation of data; substantively revised the work AND approved the submitted version;AND agreed both to be personally accountable for own contributions and ensured that questions related to the accuracy or integrity of any part of the work, even ones in which was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. Manuel Ruiss acquisition, analysis of data; interpretation of data; substantively revised the work AND approved the submitted version; AND agreed both to be personally accountable for own contributions and ensured that questions related to the accuracy or integrity of any part of the work, even ones in which was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. Stephane Blouin acquisition, analysis of data; interpretation of data; AND approved the submitted version; AND agreed both to be personally accountable for own contributions and ensured that questions related to the accuracy or integrity of any part of the work, even ones in which was The scleral tunnel length may result in instability of the IOL if too short resulting in slippage of the flange through the sclera post-operatively resulting in sub­ luxation of the IOL, or resulting in IOL decentration if unpaired to the contralateral tunnel length, During the experiments, the non-preserved cadaver sclera tissue Page 9 of 9 Page 9 of 9 Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Stunf Pukl et al. BMC Ophthalmology (2024) 24:103 Stunf Pukl et al. BMC Ophthalmology 2. Yamane S, Ito A. Flanged fixation: Yamane technique and its application. Curr Opin Ophthalmol. 2021;32:19–24. 3. Jacob S, Intrascleral IOL, Fixation. Asia Pac J Ophthalmol (Phila). 2017;6:381–7. 4. Komai Y, Ushiki T. The three-dimensional organization of collagen fibrils in the human cornea and sclera. Invest Ophthalmol Vis Sci. 1991;32:2244–58. 5. Kamma-Lorger CS, Boote C, Hayes S, et al. Collagen and mature elastic fibre organisation as a function of depth in the human cornea and limbus. Ethics approval and consent to participate Not applicable. 12. Werner L. Flange erosion/exposure and the risk for endophthalmitis. J Cata­ ract Refract Surg. 2021;47:1109–10. 12. Werner L. Flange erosion/exposure and the risk for endophthalmitis. J Cata­ ract Refract Surg. 2021;47:1109–10. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. References 1. Yamane S, Sato S, Maruyama-Inoue M, Kadonosono K. Flanged intrascleral intraocular Lens fixation with Double-Needle Technique. Ophthalmology. 2017;124:1136–42.
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Barnabas: Early Church leader and model of encouragement
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Barnabas: Early Church leader and model of encouragement Robin Gallaher Branch Research Associate, Joy Project North-West University POTCHEFSTROOM E-mail: robinbranch@yahoo.com rgbranch@crichton.edu Barnabas: Early Church leader and model of encouragement Barnabas: Early Church leader and model of encouragement Acts presents Barnabas, an early church leader, as a model of integrity and character. It loads him with accolades. It calls him a good man (Acts 11:24), a prophet and teacher (Acts 13:1), an apostle (Acts 14:14), and one through whom God worked miracles (Acts 15:12). It recounts the times he faced persecution (Acts 13:45; 14:19) and risked his life for the name of the Lord Jesus Christ (Acts 15:26). He believed Saul truly had been converted (Acts 9:27) and saw the potential of John Mark (Acts 12:25) and championed them both at different times (Acts 11:25-26; 15:36-41). 1 Corinthians 9:6 affirms his charac- ter by noting he worked while serving congregations in order not to burden them. Acts introduces him as Joseph, a Levite from Cyprus, and praises his generous spirit (Acts 4:36). Arguably, Acts portrays no one else – except the Lord Jesus – in such glowing terms. The apostles nicknamed him Barnabas, Son of Encouragement, probably because he earned it! Significantly, a passage relating the character attributes and big heartedness of Barnabas note that the disciples were called Christians first at Antioch (Acts 11:19-26). Because of its textual context, it may well be that the character traits of Barnabas defined the early use of the word Christian. Barnabas played a decisive role in the Early Church. Yet over two millennia, he has slipped into unjustified obscurity behind Paul, Peter, John, and James, the brother of Jesus. This article examines selected stories about him that showcase his contributions to the Early Church and establish his significant leadership role. In die Skriflig 41(2) 2007:295-322 295 Barnabas: Early Church leader and model of encouragement bas: leier van Vroeë Kerk en rolmodel vir motivering Handelinge beskryf Barnabas as ʼn kerkleier, ʼn mens met ’n sterk karakter en integriteit. Daar word ook na hom verwys as ʼn goeie man (Hand. 11:24), ʼn profeet en onderwyser (Hand. 13:1), ʼn dissipel (Hand. 14:14), en ʼn persoon deur wie God wonderwerke kon verrig (Hand. 15:12). Verder word ook verwys na die kere wat hy vervolging in die gesig gestaar (Hand.13:45; 14:19), en sy lewe in gevaar gestel het ter wille van die Naam van Jesus Christus (Hand. 15:26). Hy het waarlik geglo dat Saulus bekeerd geraak het (Hand. 9:27), en hy het ook die potensiaal in Johannes (Markus) raakgesien (Hand. 12:25), en het hulle albei lof toegesing op verskillende kere (Hand. 11:25- 26 en Hand. 15:36-41). 1 Korintiërs 9:6 belig Barnabas se karakter deur aan te toon dat terwyl hy sendingwerk by verskeie kerke verrig het, hy ook gewerk het, sodat hy nie ʼn geldelike las op hulle sou plaas nie. Handelinge stel hom voor as Josef, ’n Leviet van Siprus, en erken sy vrygewige karakter (Hand. 4:36). Handelinge verwys slegs na een ander persoon met soveel lof – Jesus Christus. Die apostels het hom die bynaam, Barnabas, Seun van Vertroosting gegee. Hy het hierdie naam heel- waarskynlik verdien! Handelinge verwys ook na Barnabas se karaktereienskappe en groothartigheid en noem dat die apostels die eerste keer in Antiochië Christene genoem is (Hand. 11:19-26). As gevolg van die tekstuele konteks van die Skrif, was dit heel waarskynlik dat Barnabas se karaktereienskappe die betekenis van die woord Christen geïnspireer het. Barnabas het ʼn belangrike rol gespeel in die ontwikkeling van die Vroeë Kerk. Hy is egter deur die eeue heen oorskadu in belangrikheid deur Paulus, Petrus, Johannes en Jakobus, die broer van Jesus. Hierdie artikel belig opnuut sy merkwaardige karaktereienskappe en sy belangrike bydra tot die Vroeë Kerk. 1 The elements of a short story include the central idea, character, conflict, point of view, setting, language, and tone (see Lostracco & Wilkerson, 1998). Literary 1. Introduction This article looks at the life of Barnabas as portrayed in Acts in terms of the leadership his life exhibited in the Early Church. This article employs a literary approach (Hill & Walton, 2000:575). Character development, setting, and conflict are among the literary and structural elements considered.1 Interpretation of the texts 1 The elements of a short story include the central idea, character, conflict, point of view, setting, language, and tone (see Lostracco & Wilkerson, 1998). Literary In die Skriflig 41(2) 2007:295-322 296 Robin Gallaher Branch about Barnabas from Acts comes from seeing the stories both contextually and as part of the whole canon. This article also employs a canonical approach because I favour allowing Scripture to interpret Scripture.2 The Biblical text portrays character in terms of actions and words. This article includes a brief survey of extra- canonical literature about Barnabas. Stories about him in Acts present workable models on how to use money, deal with the radical and amazing inclusion of new converts, and pastor a large and growing church. One story shows him and his fellow apostle Paul in a less-than-favorable light as leaders who strongly disagree with each other. Acts presents Barnabas and Peter, John, Paul and James, the brother of Jesus, as the primary Early Church leaders. Yet during the passing of two millennia, Barnabas and James have received less scholarly attention than have Peter, John, and especially Paul. Kollmann (2004:vii) notes that Barnabas unfortunately now resides in “undeserved obscurity” despite the fact that he “played a substantial role in every stage of early Christianity and had a decisive influence on the fate of the church in the first century”. Regarding James, Witherington (Shanks & Witherington, 2003:111) acknowledges that “there has been so much neglect of a figure like James, the brother of Jesus” and believes it is because Petrine Christianity (derived from Peter) became dominant in the West. This article seeks to retrieve Barnabas from “undeserved obscurity” and take a fresh look at his contributions. 2 See the Westminster Confession of Faith, I:6: “The whole counsel of God … is either expressly set down in Scripture or by good and necessary consequence may be deduced from Scripture” (italics added). 2. Barnabas, Son of Encouragement in Acts Presented as a “lovable character” (Winn, 1960:51), Barnabas is mentioned 24 times in Acts, in chapters 4, 9, 11, 12, 13, 14, and 15. Paul’s epistles mention him five times (1 Cor. 9:6; Gal. 2:1, 9, 13; Col. 4:10). Barnabas is introduced as Joseph Barnabas, a Levite and native of Cyprus; he sells a field and gives its proceeds to the apostles (Acts 4:36-37). These details, though meagre, help define him. elements also include the plot and structure of various stories, dramatic tension, impact on the reader, and the ordering of events (Elwell & Yarbrough, 2005:174). 2 See the Westminster Confession of Faith, I:6: “The whole counsel of God … is either expressly set down in Scripture or by good and necessary consequence may be deduced from Scripture” (italics added). In die Skriflig 41(2) 2007:295-322 297 Barnabas: Early Church leader and model of encouragement Acts speaks very favourably of Barnabas. Significantly, Acts never presents the older Barnabas as Saul/Paul’s subordinate or junior partner, although as their working relationship develops, Paul becomes the more talkative of the two (Acts 14:12). Barnabas is called a prophet and teacher (Acts 13:1), an apostle (Acts 14:14) and one through whom God worked miraculous signs and wonders (Acts 15:12). Barnabas faced persecution (Acts 13:45; 14:19), and risked his life for the name of the Lord Jesus Christ (Acts 15:26). Physical description and behavioral characteristics form part of characterisation (Lostracco & Wilkerson, 1998:12). Acts 14 provides clues to both for Barnabas. On a missionary journey with Paul to Lystra, a miracle takes place – a lame man walks! – and the astonished people call Barnabas Zeus and Paul Hermes, because Paul was the chief speaker (Acts 14:11-13). Something about Barnabas impressed the people to call him Zeus. Perhaps he was a very handsome man – or at least a big man with an impressive appearance. Typically, Zeus statues portray a man broad-chested and fiercely bearded (Wangerin, 2000:796). Busts of Zeus, the supreme ruler of Mount Olympus, depict a middle-aged but physically powerful and muscular man who is both regal and commanding. Perhaps because Barnabas is dubbed Zeus, he is the more imposing figure of the two (Gardner, 1995:76). Tribal affiliation also defines Joseph Barnabas. Acts introduces him as a Levite. 3 Mary, a home-owner, opened her house to believers for prayer despite the possibility of persecution by authorities (Acts 12:12-13). She is among wealthy and leading women mentioned by Luke (Joanna and Susanna: Luke 8:1-3; 2. Barnabas, Son of Encouragement in Acts As such, Barnabas performed routine tasks in the temple; he was not of Aaronic or Zadokite lineage, evidently, and therefore probably only served in a supportive role of slaughtering sacrificial animals or guarding the Temple forecourt and singing in the temple (Kollmann, 2004:7). Nevertheless, this lineage detail shows Barnabas held a certain status in the Jewish communities of the first century. Would Barnabas define himself as a Hebrew or a Hellenist? While his thought patterns are impossible to ascertain, it seems he was a man who, according to Acts, straddled both worlds. When intro- duced in Acts he probably would call himself a Hebrew. A Hebrew was a Diaspora Jew with strong ties to the motherland. Through Mary, his sister or close relative, he had ties with Jerusalem. Both were wealthy.3 John Mark was her son and Barnabas’ nephew (Acts 3 In die Skriflig 41(2) 2007:295-322 298 Robin Gallaher Branch 12:12; Col. 4:10). Probably over the years as Barnabas saw his ministry developing more internationally with the Greek-speaking Roman world, he arguably came to see himself as a Hellenist. A working definition of Hellenists is that they were Greek-speaking Jews in Jerusalem (Acts 6:1; 9:29).4 As a Hellenist, he likely adopted a broader, more liberal attitude toward the law (Paget, 1994:4). Location also plays a part in characterisation. Barnabas hailed from Cyprus, the third largest island in the Mediterranean. It had been ruled by Cleopatra. Following the deaths of Anthony and Cleopatra after the Battle of Actium, Octavian placed Cyprus under his direct control in 30 BC and made the island in 22 BC a senatorial province governed by a proconsul who was chosen annually (Kollmann, 2004:4). Cypriots worshipped Aphrodite, Zeus, Isis, and Apollo. In addition to profitable agricultural lands, Cyprus had forestry and copper and silver mining; many Roman ships were built from Cyprus lumber (Kollmann, 2004:5). Dates and settings likewise contribute to character development for they enhance the narrative’s meaning (Lostracco & Wilkerson, 1998:31). For example, c. AD 48 Barnabas, his cousin John Mark, and Saul embark on an evangelisation tour of Asia Minor cities. Acts (following Biblical narrative tradition) designates Barnabas as the initial leader of what has come to be known as Paul’s first missionary journey (Acts 13:1-3; Daniels, 1992:1:610). Prominence shifts back and forth, however, from here on in Acts. The order, Paul and Barnabas, appears three times in Acts 13 (v. 42, 46, 50), and the order, Barnabas and Paul, appears twice in Acts 15 (v. 12, 25). The tradition in Biblical narrative is that the most important figure is named first. 4 Hellenists may have interpreted the Torah less rigidly than did Aramaic- speaking Jewish believers in Jerusalem (Achtemeier, 1985:382). Hellenisation shaped the social consciousness of the day throughout the Mediterranean world. It fostered the spread of the Greek language, commerce, and the founding of cities. Military expansion, slavery, taxation, and ghettos within the cities were part of Hellenisation (see Elwell & Yarbrough, 2005:197-198.) 2. Barnabas, Son of Encouragement in Acts A third of the way through the chapter, Saul/Paul becomes the more prominent one.5 Significantly in terms of the later working relationship between the two strong leaders Barnabas and Paul, John Mark leaves them in Pamphylia and returns to Jerusalem (Acts 13:13). Mary: Acts 12:12-17; prominent women in Thessalonica and Berea: Acts 17:4, 12; Arlandson, 2004:155). 4 Hellenists may have interpreted the Torah less rigidly than did Aramaic- speaking Jewish believers in Jerusalem (Achtemeier, 1985:382). Hellenisation shaped the social consciousness of the day throughout the Mediterranean world. It fostered the spread of the Greek language, commerce, and the founding of cities. Military expansion, slavery, taxation, and ghettos within the cities were part of Hellenisation (see Elwell & Yarbrough, 2005:197-198.) 4 Hellenists may have interpreted the Torah less rigidly than did Aramaic- speaking Jewish believers in Jerusalem (Achtemeier, 1985:382). Hellenisation shaped the social consciousness of the day throughout the Mediterranean world. It fostered the spread of the Greek language, commerce, and the founding of cities. Military expansion, slavery, taxation, and ghettos within the cities were part of Hellenisation (see Elwell & Yarbrough, 2005:197-198.) 5 Prominence shifts back and forth, however, from here on in Acts. The order, Paul and Barnabas, appears three times in Acts 13 (v. 42, 46, 50), and the order, Barnabas and Paul, appears twice in Acts 15 (v. 12, 25). The tradition in Biblical narrative is that the most important figure is named first. 5 In die Skriflig 41(2) 2007:295-322 299 Barnabas: Early Church leader and model of encouragement In c. AD 52, Paul asks Barnabas to accompany him on a visit to the churches they had established during their earlier missionary journey. Barnabas wants to take John Mark with them. Paul and Barnabas quarrel strongly over John Mark and separate; Barnabas and John Mark sail for Cyprus and Paul and Silas go overland to Derbe on what became known as Paul’s second missionary journey (Acts 15:39-40). From Acts 16 on, the text focuses on Paul, and Barnabas drops out of Biblical record in Acts. In the Biblical text, names likewise play an important role in defining character. Barnabas’ Biblical name is Joseph. He is a Levite, a member of the priestly class, from Cyprus. Acts (4:36-37) introduces him in the context of giving and sharing, and indeed that was his life. The multiple entries in Acts show his generosity and unselfishness. 7 The word describing Barnabas is kin to paraclete, a word describing the Holy Spirit. It means “called to the side of” and carries the implication of one who is called alongside to help in various ways including being a legal assistant or advocate (Morris, 1986:263). 2. Barnabas, Son of Encouragement in Acts He was a “people person,” a natural minister and effective leader. His nickname, Barnabas Son of Encouragement (Acts 4:36), presents scholars with interesting possibilities. The bar could come from the Aramaic for son; the name could really mean son of prophecy (bar nebuah) or could refer to a heathen deity, Nabu. Scholars agree that Son of Encouragement is an inaccurate etymo- logy of Barnabas and should be seen rather as an endearment speaking of his character (Kollmann, 2004:13; Barnabas, 1995:75). Although no explanation accompanies his nickname, the apostles probably gave it to him because he earned it!6 Barnabas’ name also encompasses the ideas of refreshment and prophecy, exhortation and consolation (Bruce, 1954:109). 6 That the apostles changed Joseph’s name to Barnabas shows their authority as well as the social conventions of the day in the church (Wall, 2002:97). 8 Based on the Codex Bezae, there is some discussion that Barnabas may have been the Joseph who was proposed, along with Matthias, to replace Judas as an apostle (Acts 1:23-26); perhaps the nominee’s name was really Joseph Barnabas rather than Joseph Barsabbas (Read-Heimerdinger, 1998:41). Yet the consensus of scholarly debate refutes this, primarily because Joseph Barnabas was a Levite whose nickname was Son of Encouragement and Joseph Barsabbas, while not distinguished by tribe is distinguished by his nickname, Justus (Acts 1:23; Kollmann, 2004:13). 9 On the whole, scholars support the old view of Origen about Hebrews. Origen reportedly said that “who wrote the epistle is known to God alone” (Kollmann, 2004:53-4). 2.1 A canonical definition of encouragement What is a canonical definition of encouragement? Proverbs offers two verbal insights: “An anxious heart weighs a man down, but a kind word cheers him up” (Prov. 12:25); and, “A word aptly spoken is like apples of gold in settings of silver” (Prov. 25:11). The New Testament broadens the definition by linking encouragement to a trait and gift of the Holy Spirit. The word “encouragement” (paraklesis) occurs 29 times in the New Testament.7 It means “one In die Skriflig 41(2) 2007:295-322 300 Robin Gallaher Branch who comes alongside,” and carries the connotations of comforter and consoler. Acts 9:31 speaks of “the comfort of the Holy Spirit” and Romans 12:8 lists it as a gift of the Holy Spirit. Barnabas’ words, actions, and life combined human kindness and God’s blessings; quite likely, his nickname reflected what God was doing in him and through him. Since it was given to him by the apostles, it shows how he consistently related to others. 10 Significantly, the Gospel of Barnabas is well known among Muslim polemicists in Pakistan, India, Indonesia, and Egypt (Sox, 1994:1-2). 3. Extra-canonical traditions about Barnabas’ life Stories not included in the canon surround the lives of Barnabas and other Biblical characters. One legend says Barnabas studied with Gamaliel in Jerusalem and knew a younger student, Saul (Kollmann, 2004:6; Van Deun, 1993:188). According to early Christian tradition recorded by Clement of Alexandria, Barnabas knew Jesus. He became a follower of Jesus because he witnessed the healing of the lame man (John 5:2-9) and other miracles. Barnabas was one of the 70 sent out by Jesus to evangelise (Luke 10:1-24; Jeffreys, 1995:26- 28; Eusebius, 1986:98). This probably means he was about the same age as Jesus.8 Perhaps he numbered among the inter- nationals who experienced Pentecost (Acts 2:1-11). Although Tertullian names Barnabas as the writer of the epistle to the Hebrews (Richardson, 2000:151), the argument is not strong (Long, 1997:1).9 According to Christian tradition, Barnabas was the first bishop of Milan (Eusebius, 1986:98). His death, however, is shrouded in mystery. One tradition maintains he was martyred in Salamis in AD 55 and that John Mark brought news of his death to Paul in Ephesus (Van Deun, 1993:533-55). Another tradition says he was martyred in AD 61 in Syria; he was stoned to death and burned (Jeffreys, 1995:26-28). His feast day is June 11. This extra- canonical information helps to develop a portrait of Barnabas; it In die Skriflig 41(2) 2007:295-322 301 Barnabas: Early Church leader and model of encouragement complements the insights in the Biblical text that portray Barnabas as a fine man and significant leader of the Early Church. 4. Barnabas in extra-canonical literature Five books bearing his name or about him confirm the significance of Barnabas in Early Church tradition. The five are the Acts of Barnabas by John Mark, the Acta Bartholomaei et Barnabae, the Laudatio Barnabae by Alexander Monachus, the Gospel of Bar- nabas, and the Epistle of Barnabas. The Acts of Barnabas were composed under the fake authorship of John Mark probably toward the end of the 5th century; this volume ends with Barnabas’ death via martyrdom in Salamis; his ashes were buried with a copy of the Gospel of Matthew (Schneemelcher, 1989:465). The Acta Bartho- lomae et Barnabae are not apostolic works but instead are com- bined traditions about Bartholomew and Barnabas (Schneemelcher, 1989:466-7). In the Laudatio Barnabae of Alexander Monachus, a sixth century monk, details of Barnabas’ early life emerge. Taught by Gamaliel, he became a follower of Jesus. Among his first converts is Mary, his kinswoman and John Mark’s mother. Barnabas accompanies Jesus during his travels in Galilee and Jesus chooses him as one of the Seventy. Barnabas attempts to convert Saul, whom he knew be- cause of their association under Gamaliel, but these attempts fail, and Saul continues persecuting the church (Kollmann, 2004:58; Van Deun, 1983:83-122). The Gospel of Barnabas may well become a very important docu- ment in this century because of its Muslim influence and implications. It attacks and denies Jesus’ death and resurrection, ending with the view that Judas Iscariot was Jesus’ substitute on the cross and that Paul was deceived when he preached that Jesus was the Son of God (Sox, 1994:2, 20-21).10 The Epistle of Barnabas cannot be taken as written by Barnabas; it stands alone in Early Church literature because of its “uncom- promising antagonism of Judaism” and because its writer is unconnected with the apostles (Lightfoot, 1981:503-504). The writer of the Epistle of Barnabas takes passages from Daniel and ties them 10 In die Skriflig 41(2) 2007:295-322 302 Robin Gallaher Branch to the Roman emperors of his day but stops short of suggesting an overthrow of the government. Two other books also mention this leading apostle, Barnabas. The Acts of Peter, a non-canonical book dated to c. AD 260 also gives credence to Barnabas’ status. 4. Barnabas in extra-canonical literature For example, the sorcerer Simon came to Rome and caused confusion among the brethren because of the absence of the church leaders: “Paul was not at Rome, nor were Timothy and Barnabas, since they had been sent by Paul to Macedonia” (Schneemelcher, 1989:290). The Clement Romance, one of the Pseudo Clementine documents, presents evidence that Barnabas preached to a multitude in Rome about the Son of God who had appeared in the land of Judaea and “promises eternal life to everyone who will hear, provided that he fashions his doings according to the will of God the Father, by whom he has been sent” (Schneemelcher, 1989:505). Barnabas, a Hebrew, was part of the circle of disciples of this Son of God, according to the Clement Romance, and Barnabas spoke “without circumlocution what he had heard from the Son of God or had seen of him” (Schneemelcher, 1989:506). According to the story, when Barnabas faced an angry mob, Clement defended him because he sensed he was a sincere messenger of God. He and Barnabas became friends almost immediately because they were men of like character. Clement eventually sailed to Caesarea Stratonis, the largest city in Palestine, and met Peter and Barnabas there (Schneemelcher, 1989:506-8). Clement attested to the significance Barnabas’ words had on his conversion. 11 By general agreement throughout the centuries, Luke is considered the writer of the Gospel of Luke and the Acts of the Apostles (Matthews, 2000:15). This article does not tackle questions of authorship and treats Luke as the author. 5. Barnabas and money (Acts 4:37) Acts provides more authoritative, consistent, and credible infor- mation about Barnabas than do extra-canonical literature. Luke, the writer of Acts,11 introduces Barnabas during a time of economic stress and church growth. There were 3 000 new converts at Pente- cost (Acts 2:41) and more later. If these 3 000-plus represent only men, then quite possibly the Early Church faced the wonderful problem of what to do with perhaps 14 000 new believers. Arguably, Barnabas saw the church at its best – a whole body of believers united in heart and soul (Packer, 1966:43). The text records no In die Skriflig 41(2) 2007:295-322 303 Barnabas: Early Church leader and model of encouragement selfishness, no want, no division. This church expected the Holy Spirit to work in power within the community (Acts 3:1-10). The Early Church at this time lacked a formal, rigid ecclesiastical structure. Acts says the apostles continued preaching with great power; and outsiders looked on the new community with favor (Acts 2:40, 47). Significantly, this church had no needy persons (Acts 2:44; 4:34), for from time to time those who owned lands or houses sold them and brought the money from the sales and put it at the apostles’ feet (Acts 4:32-34). In this orderly, idyllic setting, Luke signals out one man who shares with abandonment and abundance, and yet with an attitude of humility: “Joseph, a Levite from Cyprus, whom the apostles called Barnabas (which means Son of En- couragement) sold a field he owned and brought the money and put it at the apostles’ feet” (Acts 4:37). Calvin (1965:130) believes Barnabas may have sold the only piece of land which he possessed, and is therefore signaled out by Luke as surpassing all the others in the Early Church for generosity.12 First impressions set the tone in a reader’s mind. Luke introduces this future church expositor as one whose humble- ness and generosity stand in sharp contrast to a subsequent example: the conniving attitude of Ananias and Sapphira (Acts 5:1- 11; Blaiklock, 1961:68). The story’s dramatic tension highlights their lie. The sin of Ananias and Sapphira was not in holding back part of the money but in pretending they had handed over the whole amount (Packer, 1966:43). In contrast, Barnabas’ gesture of planned giving indicates not only his ethics regarding finances but also the genuineness of his faith and character (Maclaren, 1944:175). 12 However, there is no way of knowing if this was his only field or if he had others. It is not a renunciation of wealth for a lifetime. Indeed, other indications through- out the epistles point to the fact that Barnabas enjoyed financial independence. Luke emphasises instead the qualities of openness and humility that accompany the gift. 5. Barnabas and money (Acts 4:37) Evidently the sale of the field and the donation of its proceeds put Joseph Barnabas in an immediate leadership position, even though he is not part of the original Twelve disciples nor a member of the Seven Greek-speaking servants of the widows who dealt with the daily distribution of food (Acts 6:1-2, 5). The Seven all bear Greek names and Nicolas from Antioch was a convert to Judaism (Acts 6:5b). Quite likely cosmopolitan Barnabas, because of his big- In die Skriflig 41(2) 2007:295-322 304 Robin Gallaher Branch hearted temperament, felt camaraderie with these men who were full of the spirit and wisdom (Acts 6:3). hearted temperament, felt camaraderie with these men who were full of the spirit and wisdom (Acts 6:3). The text gives no indication that Barnabas’ gift was a response to a call from church leadership for money. Unlike other New Testament situations (1 Cor. 16:1, 3), there seems to have been no pressing need for a financial contribution. Instead, Barnabas’ gesture sparkles with spontaneity and joy. In a public presentation, Bar- nabas gives the gift for the use of the community. Perhaps the gift represented a conviction of sin, for Pentateuchal regulations prohibited the Levites from holding property (Bruce, 1954:109). The Levites were to be dedicated to the land and Israel’s well being rather than to stewardship or cultivation of the land (Deut. 12:12; Josh. 14:3-4; Wall, 2002:97). Additionally, the fact that Barnabas is a Levite indicates how the new faith is creeping into the very heart of the old system (Maclaren, 1944:175). Dramatic tension increases. It is possible that Barnabas’ gift represented a considerable amount. Perhaps his field came from the rich fruit-growing lands of Cyprus (Neil, 1973:94); if so, his land probably was worth more than a stony field in Palestine. Along with Mary (the mother of John Mark), Joseph of Arimathea, and Nicodemus (John 12:1-5; 19:39-41), Barnabas is quite possibly the first giver of financial standing in the new church. Unlike Ananias and Sapphira, he gives without a backward glance; he leaves himself no options. Although probably a person of more financial standing than were the apostles, he puts his money at their feet – a gesture showing he sees rank in the kingdom as different from status in society. 13 The Biblical text frequently presents others who introduce those who sub- sequently take a more prominent position in the Biblical text, at least in terms of space. For example, the baby Moses was surrounded by three deliverers: his sister, his mother, and a princess of Egypt (Exod. 2:1-0; Branch, 2006:258). 5. Barnabas and money (Acts 4:37) Arguably, he considered the gift of the proceeds of the sale as a way to serve God in a monetary fashion; his action of giving, as do other episodes about him recorded in Acts, show his total commitment to Jesus Christ; his action, here and elsewhere, is both positive and generous – and marks him as a leader (Willimon, 1988:53). This single act of abandoned generosity unquestionably earned him lifelong favor and standing in the community. It probably led to his easy acceptance shortly thereafter (Acts 9:27) as a mediator between Saul and the apostles of the Jerusalem church (Wall, 2002:97). Significantly by his action, he acknowledges the authority of the apostles and submits to it. Barnabas leads by example. His action shows a disciple of Jesus at his best (Packer, 1966:43). Barnabas’ generosity shows he believes in the work of the kingdom. The setting is one in which believers shared a keen sense of responsibility for the welfare of each other – 305 In die Skriflig 41(2) 2007:295-322 Barnabas: Early Church leader and model of encouragement even to the point of giving all they had (Barclay, 1976a:43). It also shows a trust in God that Ananias and Sapphira lacked. Un- expectedly because of his action and Luke’s treatment of it, Barnabas becomes a Biblical model of good stewardship (see Rodin, 2000:14). His decision to give obviously was influenced by his relationship with God (see Hoge, 1994:205). Significantly, Barnabas’ action did not represent looking for praise, yet Luke ends up writing in such a way that he is praised. Evidently that’s what happens to encouragers: they receive unexpected praise and walk into positions of leadership. 6. Barnabas seeks out others One of the hallmarks of Barnabas, the Early Church leader and constant encourager, is that he repeatedly seeks out and champions others; often these others are believers in Jesus (both individuals and groups) who for whatever reason are running a bit against the current of mainstream thought and action. Instead of ostracising individuals and groups, Barnabas not only seeks them out but also listens to them and welcomes them warmly. He champions them when others exclude them. Barnabas adds openness to his earlier attribute of financial generosity by introducing the very suspect Saul to the apostles, and presenting Saul as one with the credential of boldness (Crowe, 1979:68). Barnabas believes in family loyalty, for he seeks out John Mark and puts his professional reputation on line by defending his ward against Paul’s strong denunciations. The references in Acts show Barnabas, a “people person,” believed in people. He believed the Lord could work with very unlikely candidates like a blood-thirsty persecutor and even with the un- circumcised gentiles. Barnabas changes the course of history because he befriends Saul. Twice he seeks out Saul. Another time he journeys to Antioch in Syria to see what’s happening in a gentile/Jewish congregation of believers. Each time Barnabas does these things his actions serve as a model of leadership, personal courage, and sound theology. Although a significant church leader, he ends up seeming to take a lesser position of vocal importance – and not seeming to mind it at all.13 Even in taking a second seat (perhaps especially so), his sterling character shows. 13 In die Skriflig 41(2) 2007:295-322 306 Robin Gallaher Branch 15 Barnabas believed that Saul, the former hot-headed persecutor of the church, had suddenly, amazingly, become its most eloquent advocate. Saul at this time in his life could well be called a loose canon and a lone ranger. He certainly acted independently. Later he kept a theological independence and even a physical distance from the Jerusalem church (Gal. 1:1-18). Moses grew to become known as the great lawgiver and Israel’s greatest prophet. Similarly, Andrew brought his brother Peter to Jesus (John 1:40-42), and Peter ended up being the more prominent of the two. 14 Canonical examples include Solomon and Jeroboam (1 Kings 11:26-40); Elijah and Elisha (1 Kings 19:16; 2 Kings 2:1-18); and Jesus’ calling his disciples (John 1:35-50). 6.1 Barnabas seeks out Saul – the first time (Acts 9:27) An established leader spots those with leadership abilities coming up in the ranks.14 Barnabas does this. He befriends Saul. Acts (7:58; 8:1-3) introduces Saul as one who hates the church and persecutes the new believers. He obtains letters from the high priest in Jerusalem to officials of Damascus synagogues authorising him to bind new believers and bring them to Jerusalem. On the way to Damascus, he has a “blinding” experience with the risen Lord Jesus, becomes a believer himself, and starts preaching that Jesus is the Son of God in the Damascus synagogues (Acts 9:1-20)! Saul preaches so boldly that the Jews in Damascus want to kill him, so he leaves Damascus and comes to Jerusalem (Acts 9:21-26). The disciples in Jerusalem face him fearfully, not believing he really is a disciple (Acts 9:26). Luke writes: “But Barnabas took Saul and brought him to the apostles. Barnabas told them how Saul on his journey had seen the Lord and that the Lord had spoken to him and how in Damascus he had preached fearlessly in the name of Jesus” (Acts 9:27).15 This significant verse merits scrutiny. Barnabas goes to Saul; he seeks him out. By this action, Barnabas puts himself and his reputation among the believing community on the line. More than that, Barnabas exhibits personal courage: he risks his life. Barnabas listens to Saul. Barnabas believes Saul. Barnabas, here an en- courager with a keen sense of ethics, backs up his encouragement with action. Barnabas’ ethical attitude of listening, believing, testing what he heard Saul say and then acting with words and deeds is consistent in the texts about him. Barnabas gives Saul a favorable introduction to the apostles (Daniels, 1992:1:610). Barnabas’ gesture expresses leadership in action. 14 Canonical examples include Solomon and Jeroboam (1 Kings 11:26-40); Elijah and Elisha (1 Kings 19:16; 2 Kings 2:1-18); and Jesus’ calling his disciples (John 1:35-50). 15 Barnabas believed that Saul, the former hot-headed persecutor of the church, had suddenly, amazingly, become its most eloquent advocate. Saul at this time in his life could well be called a loose canon and a lone ranger. He certainly acted independently. Later he kept a theological independence and even a physical distance from the Jerusalem church (Gal. 1:1-18). In die Skriflig 41(2) 2007:295-322 307 Barnabas: Early Church leader and model of encouragement Barnabas’ action is magnanimous (Longenecker, 1981:378). It changed the course of history, too. 16 Canonical examples abound. God sent Moses, Aaron, and Miriam to lead his people out of Egypt (Mic. 6:4). God promised Joshua that he would be with him as he was with Moses (Josh. 1:5). In the time of the Judges, God sent deliverers like Ehud and Gideon (Judg. 3:15; 6:14). Deborah, a prophetess who clearly has the backing of the tribes, serves as a leader in Israel (Judg. 4-5). Matthew presents Jesus as God’s choice of King of Israel (Branch, 2004:385-388). Paul lists himself and Barnabas as leaders within the context of discussions with the acknowledged leaders of the Jerusalem Council, James, Peter, and John (Gal. 2:9). Paul states so beautifully a truth about Jesus: “But when the time had fully come, God sent his Son, born of a woman, born under law, to redeem those under law, that we might receive the full rights of sons” (Gal. 4:4-5). 6.1 Barnabas seeks out Saul – the first time (Acts 9:27) Saul became a mighty apostle, the one who fashioned the church as we know it for the last 2 000 years. The New Testament credits thirteen books to him. By going to Saul, Barnabas acts like a modern-day coach who assists people to get from where they are after conversion to a new phase of their life in Christ, as Paul would come to say (Col. 1:14, 17, 19). Barnabas’ action shows he views the Holy Spirit’s work as big, creative, and open to new ways of doing things in the world. For example, Isaiah 43:19 (“See, I am doing a new thing!”) clearly holds true in terms of the life of Jesus, the work of the Holy Spirit at Pentecost (Acts 2), and the work of the Holy Spirit in the life of Saul the persecutor (Acts 9) and in the lives of those born outside the covenant, the gentiles (Acts 10). Leaders like Barnabas share a big vision about God’s big plans for the gospel and God’s big plans for individual lives. 7. How to deal with new converts (Acts 11:22-23) Throughout the Biblical text, God’s choice of a leader is backed up by recognition by people.16 The next story in Acts about Barnabas, his being sent by the Jerusalem Council to Antioch, re-affirms this Biblical principle. In this story, Acts shows that cosmopolitan Barnabas’ open attitude and encouragement extend to all who are new creatures in Christ Jesus, be they Jews or gentiles. In the first chapters of Acts, the church is confined to the Jews. Then Philip the evangelist goes to Samaria and shares the messianic news and meets an Ethiopian eunuch who requests water baptism (Acts 8). Then the apostle Peter, who is in Joppa, receives a revelation in a vision that the gentiles also can be cleansed (Acts 10:1-16). The Holy Spirit then falls on those gentiles listening to Peter in the house of a Roman, Cornelius (Acts 10:17-47). Simul- taneously, the Holy Spirit is working in Antioch, a city on the Orontes 16 In die Skriflig 41(2) 2007:295-322 308 Robin Gallaher Branch River in Cappadocia, a city known as luxurious and corrupt (Acts 10:19-21; Maclaren, 1944:324). The text says a great number of Jews and Greeks believed and turned to the Lord (Acts 10:21). The Jerusalem Council sends Barnabas to Antioch to see what is happening. The Council’s intent probably is not hostile; it is more likely one of inquiry (Maclaren, 1944:324). Barnabas with this assignment (possibly given because he is already an international person and can fund his own trip) begins his career as a missionary (Wagner, 2000:252). When Barnabas arrives in Antioch, he displays the same charac- teristics he had exhibited in the money incident. He acts openly. He listens to people. He makes ethical decisions. The text says he “saw the evidence and grace of God and was glad” (Acts 10:23). Calvin (1965:330) thinks Barnabas’ joy undisputedly shows his sincere godliness. Typical of a man of honorable character, Barnabas’ mind looks at the facts: these people – uncircumcised gentiles! – really are new converts! Barnabas sees that they were in possession, like himself and other Jewish converts to this radical new faith, of the visible and audible effects of the Holy Spirit’s gifts (Maclaren, 1944:325). The text indicates he carried no pre-conceived agenda. Evidently he widened his own theories about God’s actions to suit the new facts and circumstances (Maclaren, 1944:324). 7. How to deal with new converts (Acts 11:22-23) Bruce (1954:240) puts it this way: Barnabas’ “generous spirit was filled with joy at what he found” in Antioch. Then, true to character, he responds ethically and broadly and “encouraged them all to remain true to the Lord with all their hearts” (Acts 10:23). Barnabas leads the Antioch disciples in being steadfast in heart to the Lord. The text indicates Barnabas encourages the gentile believers in Antioch in three ways. First, he recognises God’s grace in others’ lives. Barnabas, instead of criticising a new work, has the maturity and discernment to recognise God’s good work and to encourage that work instead of putting a damper on it by judging it. Second, because Barnabas is focused, he helps others be focused. His focus, as he tells the Antioch believers, is “to remain true to the Lord” (Acts 11:23). Barnabas has a purpose of heart; in other words, he knows God has sent him to Antioch. He helps them have “purpose of heart,” too, and to focus on God’s will, God’s kingdom, and God’s purposes for this congregation in Antioch. Third, Barnabas is useable because he is available to God. Luke (11:24) calls him a good man, full of the Holy Spirit and faith. Throughout 309 In die Skriflig 41(2) 2007:295-322 Barnabas: Early Church leader and model of encouragement Acts, God empowers people beyond their natural abilities. This happens with Barnabas. The result of God’s empowerment is blessing and increase. The text says, “And considerable numbers were brought to the Lord” (Acts 11:24). Significantly, the name Joseph carries with it the ideas of God’s increase. Then Luke gives a surprising editorial comment about this man we can assume was his friend and brother in the Lord. Luke (Acts 11:24) writes that Barnabas “was a good man, full of the Holy Spirit and faith”. This is a significant statement. The only other time Luke uses “good” about a person other than Jesus is in connection with Joseph of Arimathea (Luke 23:50; Barrett, 1994:553). “Full of the Holy Spirit” can mean that the Lord worked miracles through Barnabas; a later text bears this out (Acts 15:12). Barnabas quite likely had what is called the gift of faith.17 Perhaps the character of Barnabas as the leader of the church overflowed to the believers in Antioch. Perhaps this spurred the Antioch community to nickname their neighbors Christians. 18 However, scholars speculate the new name also could be a derision, an insulting nickname and designation (Longenecker, 1981:402). A canonical precedent for a possible insulting appositive as an alien is “Ruth the Moabitess” (Ruth 1:22; 2:6, 21; 4:5; Roop, 2002:39-40, 48, 270-271). “Troubler of Israel” is an appositive Ahab and Elijah exchange (1 Kings 18:17-18). 7. How to deal with new converts (Acts 11:22-23) Luke (Acts 11:26b) says, “The disciples were called Christians first at Antioch”. However, given the context, it could very well be that the name (or nickname) Christian came into being because of Bar- nabas, this Christ-like man.18 Certainly it was his broad-mindedness and generous nature that led to the strengthening of the believers and a great extension of the work of the Holy Spirit (Erdman, 1929:94). 17 Paul writes that faith is one of the manifestations of the Spirit given to a person for the common good; other manifestations are the message of wisdom, the message of knowledge, and the gifts of healing, miraculous power, prophecy, distinguishing between spirits, speaking in different kinds of tongues, and interpretation of tongues (1 Cor. 12:7-10). 8. Barnabas seeks out Saul – the second time (Acts 11:25-26) The Antioch church expands. The work is more than one leader, Barnabas, can do. Barnabas seeks Saul yet a second time. Barnabas leaves Antioch, goes to Tarsus, and brings back Saul 17 Paul writes that faith is one of the manifestations of the Spirit given to a person for the common good; other manifestations are the message of wisdom, the message of knowledge, and the gifts of healing, miraculous power, prophecy, distinguishing between spirits, speaking in different kinds of tongues, and interpretation of tongues (1 Cor. 12:7-10). 18 However, scholars speculate the new name also could be a derision, an insulting nickname and designation (Longenecker, 1981:402). A canonical precedent for a possible insulting appositive as an alien is “Ruth the Moabitess” (Ruth 1:22; 2:6, 21; 4:5; Roop, 2002:39-40, 48, 270-271). “Troubler of Israel” is an appositive Ahab and Elijah exchange (1 Kings 18:17-18). 18 310 In die Skriflig 41(2) 2007:295-322 Robin Gallaher Branch (Acts 11:25-26). Barnabas’ action shows his humility and dis- cernment. The text indicates Barnabas’ overriding concerns were the needs of the people and the success of the gospel. Yet he must have realised that Saul’s skill in debate and his incredible mind might overshadow his own qualities. However, the possibility of sinking into second place didn’t seem to matter to Barnabas (Erdman, 1929:95). Barnabas offers the younger man a job: co-pastoring the dynamic Antioch disciples. Saul accepts. The young church is growing – and grows even more under their joint leadership. Barnabas and Saul met with the church for a year and taught great numbers (Acts 11:26). It must have been a glorious and fruitful time for both congregation and teachers. Quite likely, this time shaped much of Saul/Paul’s theology, especially that in 1 Thessalonians (Kollmann, 2004:50-1).19 Barnabas’ action of seeking Saul and bringing him to Antioch probably ties in with the Biblical concept of forgiveness. The church in Antioch sprang up because the Jews were scattered (Acts 11:19). Who scattered them? The Biblical text points to Saul. The Biblical text says he tried to destroy the young church and dragged off men and women and put them in prison (Acts 7:54-8:3). Chrysostom (1989:129) describes Saul as “terrible” when he is first presented in Acts. Within Acts’ context, it is possible that those who fled Saul’s on- slaught in Jerusalem settled far north in Antioch and discussed their new faith with their new neighbors. 20 An abuser is one who invades, trespasses, and violates the freedom and healthy boundaries of another (Wuellner, 2001:64). A root of violence is jealousy (Ochs, 2004:6). 19 It is thought that 1 Thessalonians may well be Paul’s first letter (especially if a later date for Galatians is allowed) (Arnold, 2002:405, 265). In die Skriflig 41(2) 2007:295-322 8. Barnabas seeks out Saul – the second time (Acts 11:25-26) Perhaps Saul instigated the confiscation of the properties of these early, spontaneous evan- gelists; perhaps he ordered the deaths of some believers. Saul, when he scattered the church, abused others; he admits this and calls himself a violent man (1 Tim. 1:13).20 In seeking Saul, Barnabas leads the Antioch disciples in new ways. He realises several things and was putting into practice Jesus’ In die Skriflig 41(2) 2007:295-322 311 Barnabas: Early Church leader and model of encouragement teaching on forgiveness (Luke 11:4).21 First, Saul needed to ask forgiveness and share his conversion experience; second, the new believers needed to practice forgiveness by forgiving their former oppressor. teaching on forgiveness (Luke 11:4).21 First, Saul needed to ask forgiveness and share his conversion experience; second, the new believers needed to practice forgiveness by forgiving their former oppressor. It would seem the Antioch believers also made a choice to forgive (Wuellner, 2001:63). Forgiveness can be an ethical adventure. It is also enlightened self-interest, because forgiveness frees the one wronged from the tyranny of being tied by unforgiveness to the guilty party. The believers in Antioch must forgive Saul for the destruction he caused in their lives years before. Evidently the adventure of forgiveness for Saul and the Antioch disciples was successful, for the text indicates growth and harmony prevailed (Acts 11:26). Furthermore, the text indicates a Christ-like spirit likewise domi- nated, because the disciples of Jesus were first called Christians in Antioch. Barnabas clearly gave both Saul and the new Antioch converts room to grow. He gave them the freedom of second chances. Leading in a big-hearted way, Barnabas consistently encouraged others to remain true to the Lord with all their heart; one way to do this was by forgiving mistakes. 22 Church growth is defined as a conscious effort to increase membership (Lim, 2004:125). It is hoped that people, once they are in church, will take advantage of programs for their spiritual growth. 23 Studies indicate church growth seems to be the result of concentrated effort and planning and takes place in an optimistic climate. Internal spiritual growth of the members shows itself in external numerical growth (Cummings, 1983:323). 21 The essence of forgiveness is knowing you are forgiven yourself (Jeffress, 2003:7-9). 9. How to pastor a large and growing church (Acts 11:25-30) Acts 11:25-30 offers a number of insights on leading a large, diverse, and growing church. First, get another pastor. Barnabas brought in a capable reinforcement, Saul. Together they organised a heavy routine of teaching the faith. Together they got those new converts rooted and grounded in sound doctrine. Together they and the congregation welcomed, encouraged, and taught new mem- bers.22 In other words, the new church of gentiles and Jews grew.23 Barnabas and Saul welcomed visiting prophets. Barnabas and Saul believed and acted quickly upon the prophetic word Agabus delivered. They decided to help their fellow believers in Jerusalem 21 The essence of forgiveness is knowing you are forgiven yourself (Jeffress, 2003:7-9). 22 Church growth is defined as a conscious effort to increase membership (Lim, 2004:125). It is hoped that people, once they are in church, will take advantage of programs for their spiritual growth. In die Skriflig 41(2) 2007:295-322 312 Robin Gallaher Branch with a monetary gift to prepare for the upcoming famine. The Antioch disciples immediately sent their gift to the elders in Jerusalem by dispatching Barnabas and Saul (Acts 11:30). From the Acts sketch, Barnabas and Saul had what modern missiologists call an educational model of a church (Hill, 2001:31).24 An educational model emphasises teaching. Barnabas and Saul gave teaching on what it meant to be a disciple in the Roman world, and what it meant to function as an individual in a church. Barnabas and Saul taught the heritage of the new faith from existing Scriptures.25 Barnabas and Saul as co-leaders pastored a large and growing church by adapting to meet the local cultural needs (Nyberg, 1999:24); this congregation mixed Jewish and gentile converts. The cosmopolitan Antioch congregation contained those of Cypriot and Libyan background (Walls, 2004:4). They began talking about Jesus in a new way – with little stress on the term Messiah. Jesus was presented as Lord, Kyrios, in a way more Hellenistic than Jewish (Walls, 2004:4). Ignatius (1989:63) sees this dynamic church as a fulfillment of Isaiah 62:2 and 12, namely that this combination of people is both righteous and holy. The text indicates Antioch was a lively, growing, excited church whose members constantly sought each other out and wanted to learn more. They talked about the Christ so much so that they were named Christians in Antioch for the first time (Acts 11:26). 9. How to pastor a large and growing church (Acts 11:25-30) The text indicates that Barnabas and Saul taught the people in a way that expected them to become leaders and to carry on the fellowship if the lead pastors left. 25 A modern educational model would indicate the confessions and catechisms were taught (Hill, 2001:31). 24 The other two models are informational and retreat (Hill, 2001:31). 24 The other two models are informational and retreat (Hill, 2001:31). 24 The other two models are informational and retreat (Hill, 2001:31). 25 A modern educational model would indicate the confessions and catechisms ( 2001 31) 24 The other two models are informational and retreat (Hill, 2001:31). 25 A modern educational model would indicate the confessions and catechisms were taught (Hill, 2001:31). 10. The first missionary journey, the Council in Jerusalem (Acts 13-15:35) When the Antioch church is in prayer and fasting, the Holy Spirit tells the church to “set apart for me Barnabas and Saul for the work to which I have called them” (Acts 13:2). This becomes what scholars term Paul’s first missionary journey; Paul’s name is changed from Saul midway through the journey’s account on Cyprus (Acts 13:9), In die Skriflig 41(2) 2007:295-322 313 Barnabas: Early Church leader and model of encouragement and Paul from here on in Acts becomes the more prominent or at least more vocal one (Acts 13:13a). Probably the name change reflects the emphasis of his life from here on: his outreach to the Roman world. Significantly, John Mark leaves them in Perga and goes back to Jerusalem (Acts 13:13b). Paul and Barnabas, now a missionary duo with perhaps ancillary companions, continue on preaching in Antioch – Pisida, Lystra, Iconium, and Derbe. In an exciting journey, they meet both conversions and antagonisms (Acts 13:42-51; 14:1-7, 19-21). Significantly, they plant churches and leave behind them an established system of elders for governing (Acts 14:23). In Lystra, the crowd to whom Paul and Barnabas speak witnesses a miracle and thinks that Paul and Barnabas (dubbed Hermes and Zeus respectively) are gods incarnate from Mount Olympus. Paul and Barnabas tear their clothes and rush into the crowd proclaiming they are merely men, too (Acts 14:15). Perhaps because Barnabas is called Zeus, he is the more imposing figure (Gardner, 1995:76). In Pisidian Antioch, Paul and Barnabas speak in a synagogue and receive abusive talk from hostile Jews (13:45). Luke (13:46) credits both apostles as answering the jealous Jewish opposition by promising they would now turn to the gentiles because the Jews had rejected the word of God and did not consider themselves worthy of eternal life. Paul and Barnabas then return to Antioch Syria. Men from Jeru- salem (who are not named by Luke) come to Antioch and say that the gentiles need to be circumcised in order to be saved (Acts 15:1- 2). Paul and Barnabas sharply dispute this and then are appointed to take their view to the Council in Jerusalem. Barnabas and Paul argue that the gentiles should be fully admitted into the new church (Acts 15:1-5, 12). Their argument prevails, thereby changing the course of history. 10. The first missionary journey, the Council in Jerusalem (Acts 13-15:35) What seems to turn the Council’s feeling is the description of the workings of the Holy Spirit among the gentiles that Barnabas and Paul recount (Acts 15:12). James, the Council leader, rules that life should not be made more difficult for their new gentile brothers by requiring circumcision. Instead he sends Barnabas and Paul back with a letter calling the two “dear friends” and containing three directives and encouragements for the gentile believers: abstain from food offered to idols; abstain from sexual immorality; abstain from the meat of strangled animals and blood (Acts 15:25, 29). Barnabas and Paul return to Antioch, where the Council’s decision is welcomed warmly (Acts 15:30-35). In die Skriflig 41(2) 2007:295-322 314 Robin Gallaher Branch 26 Canonical examples include Abram’s deception (Gen. 12:10-20); Moses’ anger (Num. 20:1-12); David’s adultery and murder (2 Sam. 12:7-9); and Peter’s cowardice (Matt. 26:69-75). 27 Calvin (1966:61) posits, on the one hand, that some great pride in Barnabas caused him to forsake the great honor of being Paul’s companion and, on the other hand, that Paul lacked kindliness in pardoning the mistake of a faithful assistant. Calvin (1966:61) warns that this example teaches Christians to be on the look-out for the chinks open to Satan. 11. Leadership disagreements (Acts 15:36-41) The Biblical text presents its heroes and heroines realistically. Biblical leaders have faults.26 Another story about Barnabas shows how he and Paul quarreled. It seems that their disagreement grew from their personality strengths. It also grew from their different perspectives (based on their personalities) of an earlier incident: John Mark’s action of leaving the first missionary journey in Pamphylia and returning to Jerusalem (Acts 13:13). Acts already had shown Barnabas’ loyalty to individuals and his big heartedness. Similarly, Paul’s boldness, fearlessness, tenacity under persecution, devotion to the gospel’s purity, and ability to count all obstacles as a loss for the joy of proclaiming Christ stand among his strong points already seen in Acts. These leadership attributes in both men clash head on. The issue, as Acts presents it, concerns their second missionary journey. Arguably, Barnabas, the “people person,” advocates giving John Mark another chance. The older Barnabas, seeing people as preeminent, seeks to include his cousin, perhaps to mentor him. Arguably, the easily irritated, feisty, younger Paul, however, sees the situation differently: the mission predominates. Research indicates that as first century people, Paul, Barnabas, and John Mark were sociocentric (group oriented) and not egocentric or individualistic in identity (Augsburger, 1996:150). Consequently, John Mark as a team member was there because he wanted to be; he was willing to make a commitment to its fellowship (Griswold et al., 1993:204). He chose not to exit – but Paul gave him the left foot of fellowship by demanding he leave the team (Acts 15:38). Paul seemingly recalled John Mark’s earlier desertion (Acts 13:13) and decided he could not be entrusted with the work of evangelism on another journey. This story in Acts illustrates that conflict between believers – even apostles – happens. Yet disagreement between Christians should not be seen as fatal to the proclamation of the Gospel. Neither should disagreement be seen in a win/lose mindset. However, the text in Acts reads as if Barnabas and Paul decided to argue first and talk later – something surely typical of church and denomination squabbles today (Stafford, 1997:33). 26 In die Skriflig 41(2) 2007:295-322 315 Barnabas: Early Church leader and model of encouragement The text omits two factors many find crucial to avoiding or mini- mising conflict. First, prayer: there is no evidence Barnabas and Paul prayed – and Acts abounds with examples of prayer (see Acts 1:14; 2:42; 6:4; 9:11). 28 Separation is a Biblical principle that is often overlooked. Genesis abounds with stories of friends and families who separate. Examples include Lot and Abraham, Esau and Jacob, Joseph and his brothers (see Petersen, 2005:31). 29 The idea in Acts is that the Holy Spirit is alive, is present, and is active in the lives of believers. Barnabas’ life as portrayed in Acts is one in which ministry to others flowed as a source of blessing to others). Barnabas is a man like 11. Leadership disagreements (Acts 15:36-41) Second, a mediator, a peacemaker, is absent. The text offers no indication that Barnabas and Paul sought peace or called in a peacemaker/mediator. This is ironic because they had served as peacemakers/mediators shortly before in the Council in Jerusalem (Acts 15:12-15). Peacemaking or mediation requires a number of characteristics. For example, all parties must want a constructive result. Selecting a neutral place is helpful. Parties must avoid rushing to a solution. Feelings must be listened to and vented. If the goal is conciliation, the parties must choose not to repay wrong with wrong (Stafford, 1997:32-34). Significantly, Luke indicates no direct benefit to either party re- garding the dispute and assigns no right or wrong to the dispute.27 With the exception of choosing to write from here on about Paul, Luke takes no sides. Reconciliation involves facing the tension that initially separates people (see Lyon, 1999:290). Barnabas and Paul choose to separate.28 They choose to part and to cool their tempers. The text indicates that Paul and John Mark later experienced reconciliation and a good working relationship (2 Tim. 4:11). There is no textual indication either way about Paul and Barnabas. The fine character traits of each man, however, lead readers to expect reconciliation. In addition, Pauline references in Galatians 2, 1 Corinthians 9:6, and Colossians 4:19 indicate the split probably was not final or terminal (Paget, 1994:4). In Biblical thought, forgiveness is a relational pro- cess between disputants. Indeed, years later Paul may have been writing to himself when he described the different dimensions of reconciliation, a word that occurs thirteen times in his writings. Augsburger (1996:151) outlines Paul’s three stages of reconciliation. First, a person must be reconciled to God; second, people are In die Skriflig 41(2) 2007:295-322 316 Robin Gallaher Branch reconciled to others from whom they were alienated, and third, people are called to be reconcilers and do the work of conciliation between those who are alienated and at enmity with each other (see 2 Cor. 5:18-19). 12. Conclusion The multiple New Testament entries about Barnabas portray a man of sterling character. These qualities make Barnabas a successful leader and one who merits the appositive of the Bible’s great encourager. Barnabas clearly and consistently recognised God’s grace in unlikely people – the murderer Saul, the uncircumcised gentiles in Antioch, and his cousin John Mark who seemed a fearful, spineless deserter, an early casualty on the mission field. He sought them out. His nickname Son of Encouragement also is sometimes translated Son of Consolation (Bruce, 1954:109). If consolation is the meaning, then Barnabas was a skilled, compassionate com- forter. The evidence given in Acts shows that Barnabas’ own life had a purpose. He decided to remain true to the Lord Jesus. His money backed up his commitment. From his own experience and purpose of heart, he convinced the new believers in Antioch also “to remain true to the Lord with all their hearts” (Acts 11:23). The focused, purposeful life is very attractive. The fact that Barnabas was focused meant he could lead others. Barnabas’ life with the new Antioch disciples showed his perseverance as an apostle. A principle among the apostles was this: follow me as I follow the Lord (John 10:27; 2 Thess. 3:9). Every instance in Acts presents Barnabas as one who whole- heartedly follows the Lord Jesus, is available for kingdom purposes, and readily gives himself to God’s service. The basis of Barnabas’ nickname, Son of Encouragement, needs to be considered. Yes, the text shows it both as a natural inclination – he was a “people person”, someone who genuinely liked people and enjoyed being around them – and a gift from the Holy Spirit (Rom. 12:8). Any gift of the Holy Spirit needs constant replenishment via prayer, study, and use.29 Barnabas could only give out what was 29 In die Skriflig 41(2) 2007:295-322 317 Barnabas: Early Church leader and model of encouragement given to him. Going on one’s own merit and energy makes a person “Mr. Nice Guy” or a “Ms. Congeniality” (see Hoyt-Oliver, 2006:21); there’s nothing wrong with these nicknames. But merely being nice doesn’t last for eternity. Barnabas’ work lasted. How did it last? Why does Luke cite it as an example again and again? Some clues stand out. Barnabas gave encouragement because he received encourage- ment. The text mentions he was a prophet, teacher, apostle, and miracle worker. Stephen who is described as one full of the Holy Spirit. Spiritual fullness speaks of God’s overflowing gift of the Holy Spirit. 12. Conclusion As a teacher he studied the Scrolls – the same way Paul did (2 Tim. 4:13). In order to teach sound doctrine, he con- stantly needed to study. He internalised, incorporated, and taught the Word of God he studied. Seeing God’s work made him glad (Acts 11:23) – it encouraged him. His glad countenance and big attitude were contagious; others became glad and glimpsed the big vision of God through him. From the Lord’s personal encouragement to him, Barnabas gave encouragement and provided a model of encouragement to others. Barnabas was equally at ease with the Hebrews and the Hellenists. He probably felt closer theologically to the Stephen group of inter- nationals than to the Twelve disciples (Kollmann, 2004:62). Barnabas sponsored his younger colleague, Saul, and championed him. For the majority of what came to be known as Paul’s first missionary journey, Barnabas led. True, gradually, but only gradually, Paul emerged from Barnabas’ shadow as the primary, vocal advocate of a gospel that was gentile-friendly and did not require circumcision. Despite the 29 New Testament entries about Barnabas attesting to his stature and importance in the Early Church, he is not too well known in modern Christian circles. His slide into obscurity was apparent even in the Middle Ages. For example, commenting on Acts 11:25-30, Gregory of Nazianzus said that “even though Barnabas stood by Paul during conflicts, he was indebted to Paul for choosing him and making him his partner” (italics added; Kollmann, 2004:61). According to the Biblical record, Gregory is incorrect. Barnabas chose Saul/Paul and championed him. They shared leadership. Calvin (1966:61) likewise errs when he writes that Paul bestowed “a great honor” on Barnabas when he suggested they “go back and visit the brothers in all the towns where we preached the Stephen who is described as one full of the Holy Spirit. Spiritual fullness speaks of God’s overflowing gift of the Holy Spirit. In die Skriflig 41(2) 2007:295-322 318 Robin Gallaher Branch word of the Lord and see how they are doing” (Acts 15:36). In addition, overlooking Barnabas continues in commentaries. Barclay (1966b:15-17), commenting on Galasians 2:1-10, a passage mentioning Barnabas twice, omits any reference to Barnabas and instead commends Paul for his refusal to be overawed by Judaisers advocating circumcision. Clearly, Barnabas, because there are no authenticating canonical writings ascribed to him, declined in importance quickly over two millennia. 30 Witherington (Shanks & Witherington, 2003:222) believes that a new millennia encourages scholars to take a new look at the significance of early Jews like James, and I would add, Barnabas. 12. Conclusion Yet careful study of texts in Acts (and elsewhere in Paul’s canonical epistles) as this article begins to show, demonstrates that at the time of the Early Church, Barnabas proved a key leader. His influence in the early history of Christian theology and the formation of the church structure has been bypassed by scholars who con- centrate on Paul, Peter, and John, and because of the recent dis- covery of the ossuary, on James (Shanks & Witherington, 2003).30 Perhaps Barnabas was martyred decades earlier than was Paul; perhaps his life was cut off soon after he and Paul separated. The text does not say. But what is known from Acts is that Barnabas was a fully recognised leader in the Early Church. As one splitting his time between Jerusalem and Antioch, he participated in Early Church councils and saw with vision that the New Covenant extended to the uncircumcised. Joseph Barnabas, Son of En- couragement, receives equal status with James, John, Peter, and Paul in the early sections of Acts and therefore not only should be honored as a founding leader of the Early Church but also should receive more scholarly scrutiny. List of references ACHTEMEIER, P., ed. 1985. Harper’s Bible dictionary. San Francisco: Harper & Row. ACHTEMEIER, P., ed. 1985. Harper’s Bible dictionary. San Francisco: Harper & Row. ARLANDSON, J.M. 2004. Lifestyles of the rich and Christian: women, wealth, and social freedom. (In Levine, Amy-Jill, ed. A feminist companion to the Acts of the Apostles. London: Clark International. p. 155-170.) ARLANDSON, J.M. 2004. Lifestyles of the rich and Christian: women, wealth, and social freedom. (In Levine, Amy-Jill, ed. A feminist companion to the Acts of the Apostles. London: Clark International. p. 155-170.) ARLANDSON, J.M. 2004. Lifestyles of the rich and Christian: women, wealth, and social freedom. (In Levine, Amy-Jill, ed. A feminist companion to the Acts of the Apostles. London: Clark International. p. 155-170.) p p ) ARNOLD, C.E., ed. 2002. Zondervan illustrated Bible backgrounds com- mentary: Romans to Philemon. Grand Rapids: Zondervan. p p ) ARNOLD, C.E., ed. 2002. Zondervan illustrated Bible backgrounds com- mentary: Romans to Philemon. Grand Rapids: Zondervan. p p ) ARNOLD, C.E., ed. 2002. Zondervan illustrated Bible backgrounds com mentary: Romans to Philemon. Grand Rapids: Zondervan. y p AUGSBURGER, D.W. 1996. Helping people forgive. Louisville: Westminster John Knox. y p AUGSBURGER, D.W. 1996. Helping people forgive. Louisville: Westminster John Knox. AUGSBURGER, D.W. 1996. Helping people forgive. Louisville: Westminste John Knox. BARCLAY, W. 1976a. The Acts of the Apostles. Philadelphia: Westminster. ARCLAY, W. 1976a. The Acts of the Apostles. Philadelphia: Westminster. BARCLAY, W. 1976a. The Acts of the Apostles. Philadelphia: Westminster. In die Skriflig 41(2) 2007:295-322 319 Barnabas: Early Church leader and model of encouragement BARCLAY, W. 1976b. The Letters to the Galatians and Ephesians. Phila delphia: Westminster. BARCLAY, W. 1976b. The Letters to the Galatians and Ephesians. Phila- delphia: Westminster. p BARRETT, C.K. 1994. Acts. Vol. 1: 1-14. Edinburgh: Clark. BLAIKLOCK, E.M. 1961. The Acts of the Apostles: an historical commentary. London: Tyndale. y BRANCH, R.G. 2004. The messianic dimensions of kingship in Deuteronomy 17:14-20 as fulfilled by Jesus in Matthew. Verbum et ecclesia, 25(2):378- 401. BRANCH, R.G. 2006. Understudy to Star: the courageous audacity of an Israelite slave girl. (In Niemann, H.M. & Augustin, M., eds. Stimulation from Leiden: collected communications of the XVIIIth Congress of the International Organization for the study of the Old Testament, Leiden 2004. Frankfurt am Main: Peter Lang. p. 257-269.) BRUCE, F.F. 1954. Commentary on the Book of Acts: the English text with introduction, exposition and notes. London: Eerdmans. CALVIN, J. 1965. List of references Calvin’s New Testament commentaries: Acts of the Apostles 1-13. Transl. by J.W. Fraser & W.J.G. McDonald. Grand Rapids: Eerdmans. CALVIN, J. 1966. Calvin’s New Testament commentaries: Acts of the Apostles 14-28. Transl. by J.W. Fraser. Grand Rapids: Eerdmans. y p CHRYSOSTOM. 1989. Nicene and post-Nicene Fathers. Vol. 12. Edinburgh: Clark. CROWE, J. 1979. The Acts. Wilmington: Glazier. CROWE, J. 1979. The Acts. Wilmington: Glazier. CUMMINGS, D. 1983. A study of factors relating to church growth in the North American division of Seventh-Day Adventists. Review of religious research, 24(4):322-333. ( ) DANIELS, J.B. 1992. Barnabas. Anchor Bible dictionary. Vol. 1. New York: Doubleday. ELWELL, W.A. & YARBROUGH, R.W. 2005. Encountering the New Testament: a historical and theological survey. 2nd ed. Grand Rapids: Baker Academic. ERDMAN, C.R. 1929. The Acts. Philadelphia: Westminster. EUSEBIUS. 1986. Nicean and post-Nicean Fathers. Vol. 1. Edinburgh: Clark. GARDNER, P.D., ed. 1995. New international encyclopedia of Bible c the complete who’s who in the Bible. Grand Rapids: Zondervan. GRISWOLD, W., KNISS, F. & NELSON, T. 1993. Straining at the tie that binds: congregational conflict in the 1980s. Review of religious research, 34(3):193-209. ( ) HILL, A.E., & WALTON, J. 2000. A survey of the Old Testament. Grand Rapids: Zondervan. HILL, J. 2001. Growing new members. Clergy journal, 77(8):31. HOGE, D.R. 1994. Determinants of religious giving in urban Presbyterian congregations. Review of religious research, 36(2):197-206. HOYT-OLIVER, J. 2006. Being nice or being His. College faith, 3:21-22. Berien: Andrews University Press. IGNATIUS. 1989. Ante-Nicean fathers: the writings of the fathers down to AD 325. Vol. 1. Edinburgh: Clark. g JEFFRESS, R. 2003. Developing the lost art of forgiveness. Southwester journal of theology, 35(3):6-17. j gy, ( ) JEFFREYS, M.A. 1995. Paul’s inner circle. Christian history, 14(3):26-28. In die Skriflig 41(2) 2007:295-322 320 Robin Gallaher Branch KOLLMANN, B. 2004. Joseph Barnabas: his life and legacy. Transl. by M. Henry. Collegeville: Liturgical Press. LIGHTFOOT, J.B., ed. & transl. 1981. The Apostolic fathers: Clement, Ignatius, and Polycarp. Vol. 2, part 1: Clement. Grand Rapids: Baker Book House. LIM, D.S. 2004. A missiological evaluation of church growth. Asian journal pentecostal studies, 7(1):125-147. p ( ) LONG, T.G. 1997. Hebrews. Louisville: John Knox. LONGENECKER, R.N. 1981. The Acts of the Apostles. (In Gaebelein, F.E., ed. The expositor’s Bible commentary. John-Acts. Grand Rapids: Zondervan. p. 207-573.) p ) LOSTRACCO, J. & WILKERSON, G. 1998. Analyzing short stories. Dubuque: Kendall. LYON, K.B. 1999. List of references Paranoid-schizoid phenomena in congregational conflict: some dilemmas of reconciliation. Pastoral psychology, 47(4):273-292. MACLAREN, A. 1944. Expositors exposition of Holy Scriptures. The Acts. chapters 1 to 12 verse 17. Grand Rapids: Eerdmans. MATTHEWS, C.R. 2000. Acts of the Apostles. (In Freedman, D.N., Myers, A.C. & Beck, A.B., eds. Eerdmans dictionary of the Bible. Grand Rapids: Eerdmans. p. 15-18.) MORRIS, L. 1986. New Testament theology. Grand Rapids: Zondervan NEIL, W. 1973. The Acts of the Apostles. London: Oliphants. NYBERG, R. 1999. Willow Creek’s methods gain German following. Christianity today, 43(5):24-25. y ( ) OCHS, P. 2004. The passion and repentance. The living pulpit, 13(3):6-8. PACKER, J.W. 1966. The Acts of the Apostles. Cambridge: Cambridge University Press. y PAGET, J.M. 1994. The epistle of Barnabas: outlook and background. Tubingen: Mohr. PETERSEN, D.L. 2005. Shaking the world of family values. (In Yoder, C.R., O’Connor, K.M., Johnson, E.E. & Saunders, S.P., eds. Shaking heaven and earth: essays in honor of Walter Brueggemann and Charles B. Cousar. Louisville: Westminster. p. 23-32.) READ-HEIMERDINGER, J. 1998. Barnabas in Acts: a study of his role in the text of Codex Bezae. Journal for the study of the Old Testament, 72(1):23- 66. RICHARDSON, P. 2000. Barnabas. (In Freedman, D.N., Myers, A.C. & Beck, A.B., eds. Eerdmans dictionary of the Bible. Grand Rapids: Eerdmans. p. 150-151.) p ) RODIN, R.S. 2000. Stewards in the kingdom: a theology of life in all its fullness. Downers Grove: InterVarsity. y ROOP, E.F. 2002. Ruth, Jonah, Esther. Scottsdale: Herald. SCHNEELMELCHER, W., ed. 1989. New Testament apocrypha. Vol. 2. Writings relating to the apostles, apocalypses and related subjects. Louisville: James Clark. SHANKS, H. & WITHERINGTON III, B. 2003. The brother of Jesus: the dramatic story and meaning of the first archaeological link to Jesus and his family. London: Continuum. y SOX, D. 1994. The gospel of Barnabas. London: Allen. STAFFORD, T. 1997. Why Christians fight Christians: the Spirit unites but the American Church divides. Christianity today, 41(11):28-34. In die Skriflig 41(2) 2007:295-322 321 Barnabas: Early Church leader and model of encouragement VAN DEUN, P., ed. 1993. Sancti Barnabae apostolie lavdatio autore Alexandro monacho et SS. Bartholomaei et Barnabae viat pro Menogloio imperiali conscrpta. Leuven: Leuven University Press. p y WAGNER, C.P. 2000. Acts of the Holy Spirit: a modern commentary on the Book of Acts. Ventura: Regal. WALLS, A.F. 2004. Converts or proselytes? The crisis over conversion in the Early Church. List of references International bulletin of missionary research, 28(1):2-6. WALL, R.W. 2002. The Acts of the Apostles: introduction, commentary and reflections. (In Keck, L., ed. The new interpreter’s Bible in twelve volumes. Vol. 10: Acts, introduction to epistolary literature, Romans, 1 Corinthians. Nashville: Abingdon. p. 1-368.) g p ) WANGERIN, W. 2000. On the road with Paul and Barnabas. Christian century, 117(22):796-800. g p ) WANGERIN, W. 2000. On the road with Paul and Barnabas. Christian century, 117(22):796-800. ( ) WESTMINSTER CONFESSION OF FAITH. www.pcanet.org/general/cof_ contents.htm 3rd ed. with corrections. Presbyterian Church in America. Date of access: 17 Oct. 2007. WESTMINSTER CONFESSION OF FAITH. www.pcanet.org/general/cof_ contents.htm 3rd ed. with corrections. Presbyterian Church in America. Date of access: 17 Oct. 2007. WILLIMON, W.H. 1988. Acts. Louisville: John Knox. WILLIMON, W.H. 1988. Acts. Louisville: John Knox. WINN, A.C. 1960. The Acts of the Apostles. Richmond: John Knox. p WUELLNER, F.S. 2001. Forgiveness, the passionate journey: nine steps to forgiving through Jesus’ beatitudes. Nashville: Upper Room Books. p WUELLNER, F.S. 2001. Forgiveness, the passionate journey: nine steps to forgiving through Jesus’ beatitudes. Nashville: Upper Room Books. Key concepts: Antioch Barnabas Early Church: leaders encouragement Jerusalem Council Saul/Paul Kernbegrippe: Antiochië Barnabas Jerusalem Raad Saulus/Paulus vertroosting Vroeë Kerk: leiers Key concepts: Antioch Barnabas Early Church: leaders encouragement Jerusalem Council Saul/Paul Kernbegrippe: Antiochië Barnabas Jerusalem Raad Saulus/Paulus vertroosting Vroeë Kerk: leiers In die Skriflig 41(2) 2007:295-322 322
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An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes
eLife
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Nathan D Lawson1*, Rui Li1, Masahiro Shin1, Ann Grosse1†, Onur Yukselen2, Oliver A Stone3, Alper Kucukural4,5, Lihua Zhu1,4,5 Nathan D Lawson1*, Rui Li1, Masahiro Shin1, Ann Grosse1†, Onur Yukselen2, Oliver A Stone3, Alper Kucukural4,5, Lihua Zhu1,4,5 1Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States; 2Bioinformatics Core, University of Massachusetts Medical School, Worcester, United States; 3Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom; 4Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States; 5Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States Abstract The zebrafish is ideal for studying embryogenesis and is increasingly applied to model human disease. In these contexts, RNA-sequencing (RNA-seq) provides mechanistic insights by identifying transcriptome changes between experimental conditions. Application of RNA-seq relies on accurate transcript annotation for a genome of interest. Here, we find discrepancies in analysis from RNA-seq datasets quantified using Ensembl and RefSeq zebrafish annotations. These issues were due, in part, to variably annotated 3’ untranslated regions and thousands of gene models missing from each annotation. Since these discrepancies could compromise downstream analyses and biological reproducibility, we built a more comprehensive zebrafish transcriptome annotation that addresses these deficiencies. Our annotation improves detection of cell type-specific genes in both bulk and single cell RNA-seq datasets, where it also improves resolution of cell clustering. Thus, we demonstrate that our new transcriptome annotation can outperform existing annotations, providing an important resource for zebrafish researchers. Competing interests: The authors declare that no competing interests exist. An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type- specific genes An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type- specific genes An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes Item Type Journal Article Authors Lawson, Nathan D.; Li, Rui; Shin, Masahiro; Grosse, Ann S.; Yukselen, Onur; Stone, Oliver A.; Kucukural, Alper; Zhu, Lihua Julie Citation <p>Lawson ND, Li R, Shin M, Grosse A, Yukselen O, Stone OA, Kucukural A, Zhu L. An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes. Elife. 2020 Aug 24;9:e55792. doi: 10.7554/eLife.55792. Epub ahead of print. PMID: 32831172. <a href="https://doi.org/10.7554/eLife.55792">Link to article on publisher's site</a></p> DOI 10.7554/eLife.55792 Rights Copyright Lawson et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. Download date 24/10/2024 04:11:15 Item License http://creativecommons.org/licenses/by/4.0/ Link to Item http://hdl.handle.net/20.500.14038/29570 TOOLS AND RESOURCES *For correspondence: nathan.lawson@umassmed.edu Present address: †Scholar Rock, Inc, Cambridge, United States Competing interests: The authors declare that no competing interests exist. Introduction Funding: See page 24 Received: 06 February 2020 Accepted: 21 August 2020 Published: 24 August 2020 Funding: See page 24 Received: 06 February 2020 Accepted: 21 August 2020 Published: 24 August 2020 The zebrafish has become an ideal animal model for studying processes related to developmental biology (e.g. Wilkinson and van Eeden, 2014). Due to its hardy nature and fecundity, it is highly amenable to a variety of manipulations, including both forward and reverse genetic approaches (Lawson and Wolfe, 2011). The power of these applications is enhanced by the unique characteris- tics of the zebrafish embryo. Most notably, zebrafish embryos are transparent and develop exter- nally, allowing direct observation and facile technical manipulation (Beis and Stainier, 2006). Moreover, the initial steps of zebrafish development are very rapid, with gastrulation completed by 24 hr post-fertilization (hpf) and a complete circulatory system online just 12 hr later. By 5 days post- fertilization (dpf), most organ systems are fully functional. Together, these characteristics of zebrafish life history have contributed to its establishment as a leading model to study developmental biology, while expanding its utility to the modeling of human diseases (Lam and Peterson, 2019). Reviewing editor: Elisabeth Busch-Nentwich, University of Cambridge, United Kingdom Copyright Lawson et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. Reviewing editor: Elisabeth Busch-Nentwich, University of Cambridge, United Kingdom Reviewing editor: Elisabeth Busch-Nentwich, University of Cambridge, United Kingdom Copyright Lawson et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. Copyright Lawson et al. This article is distributed under the In most model systems, a common analytical approach is to profile changes in gene expression following a particular experimental manipulation, or in comparison between wild type and mutant siblings. With the initial advent of microarrays and, more recently, RNA-sequencing (RNA-seq), this Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 1 of 28 Tools and resources Tools and resources Developmental Biology Developmental Biology approach can be applied at a transcriptome-wide level, enabling researchers to gain crucial insights into molecular defects associated with a particular experimental condition (Smith, 2003; Wang et al., 2009). Introduction Such analysis can reveal important effectors for signaling pathways, downstream targets for transcription factors, or identify changes in cellular composition in a complex tissue. More recently, several groups have adapted RNA-seq to allow molecular profiling of transcriptomes from single cells (Klein et al., 2015; Macosko et al., 2015). Regarding zebrafish, this powerful method has been applied in a number of novel ways. Initial efforts integrated single-cell RNA-seq (scRNA-seq) with a publicly available expression pattern database to provide a predictive spatial gene map for early stage zebrafish embryos (Satija et al., 2015). Recent application of scRNA-seq at successive developmental stages has allowed unprecedented molecular insights into lineage rela- tionships during embryogenesis (Farrell et al., 2018; Wagner et al., 2018). More advanced applica- tions have combined scRNA-seq with cas9-induced ‘scars’ to allow molecular lineage tracing and define cellular hierarchies in the brain (McKenna et al., 2016; Raj et al., 2018). Together, these studies demonstrate the power of combining the unique benefits of zebrafish embryogenesis with scRNA-seq to gain new insights into vertebrate development. The application of RNA-seq relies on the ability to accurately and reliably process large datasets consisting of millions of short fragment reads (Wang et al., 2009). This approach usually relies on the availability of a genomic sequence to which reads are initially mapped. Subsequently, the posi- tions of mapped reads matching a corresponding transcriptome annotation are used for gene assignment and quantification across different experimental conditions. For most commonly used model systems, gene models and transcriptome annotations are now generally robust, allowing the universal application of RNA-seq-based analysis with a variety of standardized computational pipe- lines. However, in this study, we have found several deficiencies in current transcriptome annotations for the zebrafish genome that can negatively impact RNA-seq analyses. To address these issues, we have generated a new zebrafish transcriptome annotation, and demonstrated its improved perfor- mance over existing annotations in several contexts, including analysis of bulk and scRNA-seq data- sets from multiple cell types. Together, our results demonstrate that this annotation will be a valuable resource for the zebrafish community. Discrepancies in RNA-seq analysis between zebrafish Ensembl and RefSeq annotations q We have previously used RNA-seq to profile endothelial cell gene expression in zebrafish embryos (Quillien et al., 2017; Whitesell et al., 2019). In unpublished observations from those studies, we noted discrepancies between identical datasets separately quantified using Ensembl (version 95, hereafter referred to as Ens95) and RefSeq (GCF_000002035.6_GRCz11) transcriptome annotations. For example, we performed RNA-seq on mCherry-positive (kdrlpos) and -negative (kdrlneg) cells iso- lated by fluorescence-activated cell sorting (FACS) from Tg(kdrl:HRAS-mCherry)s896 embryos, which express membrane-localized red fluorescence protein in endothelial cells (Chi et al., 2008; Whitesell et al., 2019). Use of the RefSeq annotation to quantify gene expression led to the identifi- cation of 1780 genes enriched in kdrlpos compared to kdrlneg cells, while Ens95 identified 1632 genes (log2 fold change >1, padj <0.05, n = 3; Figure 1A,B; Figure 1—source data 1; Table 1). The inter- section of kdrlpos-enriched genes from each dataset using NCBI ID as a common identifier yielded 132 and 222 genes that were identified only by Ens95 or RefSeq, respectively, while 1407 were com- monly identified as such in both annotation (Figure 1C, Figure 1—source data 2). Notably, common IDs were lacking for a sizable proportion of genes in both datasets (for example, 4215 out of 25704 in Ens95 lacked a matching NCBI ID; Table 1, Figure 1—source data 1), suggesting that each anno- tation may be missing genes. Importantly, genes detected as enriched only by Ens95 or RefSeq included those with previously known functional relevance. Among these were the artery-specific gene, ephrin-B2a (efnb2a; Lawson et al., 2001), and the SRY-box transcription factor 17 (sox17; Chung et al., 2011), which were only identified as differential by Ens95 (Figure 1A,B, Figure 1— source data 2). By contrast, slc2a1b, one of two duplicated zebrafish genes that encodes the GLUT1 glucose transporter, as well as other blood-brain barrier markers, such as solute carrier family 7 member 5 (slc7a5; Boado et al., 1999), were significantly enriched in kdrlpos cells using RefSeq, Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 2 of 28 Tools and resources Developmental Biology Figure 1. Comparison of Ensembl and RefSeq zebrafish transcriptome annotations for bulk RNA-seq analysis. (A, B) Volcano plots showing differentially expressed genes from Tg(kdrl:HRAS-mCherry)s896-positive and negative (kdrlpos and kdrlneg) cells identified using RNA-seq reads quantified with (A) RefSeq or (B) Ensembl, version 95 (Ens95) transcript annotations. Discrepancies in RNA-seq analysis between zebrafish Ensembl and RefSeq annotations Genes with significant enrichment (padj <0.05) are shown as red or blue (log2 fold change >1 or <-1, respectively) across replicate samples (n = 3). Grey dots are genes that fall below statistical cutoffs. Green dots indicate selected genes previously found to be enriched in endothelial cells in zebrafish or other models. (C) Venn diagram illustrating the intersection of genes with a common NCBI ID in Ens95 and RefSeq found significantly enriched in kdrlpos cells using either annotation. (D, E) Plots of commonly annotated genes identified as kdrlpos-enriched only by Ens95 with indicated values from (D) Ens95 or (E) RefSeq. (F, G) Correlation of expression levels from indicated annotation for kdrlpos-enriched genes identified (F) selectively as such by Ens95 (maroon) or RefSeq (grey) only, or (G) both annotations. Data are not normally distributed, Spearman correlation, r values are indicated. The online version of this article includes the following source data and figure supplement(s) for figure 1: Source data 1. DESeq2 output for kdrlpos and kdrlneg RNA-seq quantified with RefSeq (GCF_000002035.6_GRCz11; worksheet 1) or Ensembl, v95 (work- p gy efSeq zebrafish transcriptome annotations for bulk RNA-seq analysis. (A, B) Volcano plots showing differentially 896 Figure 1. Comparison of Ensembl and RefSeq zebrafish transcriptome annotations for bulk RNA-seq analysis. (A, B) Volcano plots showing differentially expressed genes from Tg(kdrl:HRAS-mCherry)s896-positive and negative (kdrlpos and kdrlneg) cells identified using RNA-seq reads quantified with (A) RefSeq or (B) Ensembl, version 95 (Ens95) transcript annotations. Genes with significant enrichment (padj <0.05) are shown as red or blue (log2 fold change >1 or <-1, respectively) across replicate samples (n = 3). Grey dots are genes that fall below statistical cutoffs. Green dots indicate selected genes previously found to be enriched in endothelial cells in zebrafish or other models. (C) Venn diagram illustrating the intersection of genes with a common NCBI ID in Ens95 and RefSeq found significantly enriched in kdrlpos cells using either annotation. (D, E) Plots of commonly annotated genes identified as kdrlpos-enriched only by Ens95 with indicated values from (D) Ens95 or (E) RefSeq. (F, G) Correlation of expression levels from indicated annotation for kdrlpos-enriched genes identified (F) selectively as such by Ens95 (maroon) or RefSeq (grey) only, or (G) both annotations. Data are not normally distributed, Spearman correlation, r values are indicated. Tools and resources Developmental Biology Developmental Biology Developmental Biology Figure 1 continued Figure supplement 1. Comparison of Ens95 and RefSeq zebrafish transcriptome annotations for bulk RNA-seq analysis. Figure supplement 1—source data 1. DESeq2 output for pdgfrbpos and pdgfrbneg RNA-seq quantified with RefSeq (GCF_000002035.6_GRCz11) or Ensembl, v95. ment 1. Comparison of Ens95 and RefSeq zebrafish transcriptome annotations for bulk RNA-seq analysis. Figure supplement 1—source data 1. DESeq2 output for pdgfrbpos and pdgfrbneg RNA-seq quantified with RefSeq (GCF_000002035.6_GRCz11) or Ensembl, v95. 2. Intersection of pdgfrbpos-enriched genes from RefSeq and Ens95 commonly annotated by NCBI ID. ment 1—source data 2. Intersection of pdgfrbpos-enriched genes from RefSeq and Ens95 commonly annotated Figure supplement 1—source data 2. Intersection of pdgfrbpos-enriched genes from RefSeq and Ens95 co but not Ens95 (Figure 1A,B, Figure 1—source data 2). Interestingly, slc2a1a, a second duplicate GLUT1 ortholog (previously referred to as ‘glut1b’; Tseng et al., 2009; Umans et al., 2017) was not identified as differential by either annotation, despite previous reports of its endothelial expression (Figure 1A,B, Figure 1—source data 1; Umans et al., 2017). By contrast, well-known endothelial markers, such as cadherin5 (cdh5) and kdrl itself, were robustly detected as enriched by both anno- tations (Figure 1A,B). g Subtle differences in Ens95 and RefSeq transcript annotations might affect data normalization and differential analysis, slightly shifting adjusted p-values and causing genes to fall just below statis- tical cutoffs. However, this was not the case for many of the genes identified selectively by either annotation. For example, 58 out of 132 commonly annotated kdrlpos genes enriched only in Ens95 showed an adjusted p-value over 5-fold greater than the standard cutoff (0.05) when quantified using RefSeq (compare Figure 1D,E, Figure 1—source data 2). Moreover, expression levels from each annotation for genes selectively identified as kdrlpos-enriched only using Ens95 or RefSeq showed a poor correlation, with significantly higher expression in the annotation in which the gene was identified as differential (Figure 1F, Figure 1—figure supplement 1A, Figure 1—source data 2). By contrast, levels of kdrlpos-enriched genes for genes commonly identified as differentially expressed displayed a high degree of correlation between Ens95 and RefSeq quantifications (Figure 1G). To rule out that these discrepancies were unique to endothelial genes, we analyzed RNA-seq data from TgBAC(pdgfrb:citrine)s1010 embryos. In this case, transgene-positive (pdgfrbpos) cells include epidermis, cartilage, pericytes, and vascular smooth muscle cells (Vanhollebeke et al., 2015). Discrepancies in RNA-seq analysis between zebrafish Ensembl and RefSeq annotations The online version of this article includes the following source data and figure supplement(s) for figure 1: S d t 1 DES 2 t t f kd lpos d kd lneg RNA tifi d ith R fS (GCF 000002035 6 GRC 11 k h t 1) E bl 95 ( k Figure 1. Comparison of Ensembl and RefSeq zebrafish transcriptome annotations for bulk RNA-seq analysis. (A, B) Volcano plots showing differentially expressed genes from Tg(kdrl:HRAS-mCherry)s896-positive and negative (kdrlpos and kdrlneg) cells identified using RNA-seq reads quantified with (A) RefSeq or (B) Ensembl, version 95 (Ens95) transcript annotations. Genes with significant enrichment (padj <0.05) are shown as red or blue (log2 fold change >1 or <-1, respectively) across replicate samples (n = 3). Grey dots are genes that fall below statistical cutoffs. Green dots indicate selected genes previously found to be enriched in endothelial cells in zebrafish or other models. (C) Venn diagram illustrating the intersection of genes with a common NCBI ID in Ens95 and RefSeq found significantly enriched in kdrlpos cells using either annotation. (D, E) Plots of commonly annotated genes identified as kdrlpos-enriched only by Ens95 with indicated values from (D) Ens95 or (E) RefSeq. (F, G) Correlation of expression levels from indicated annotation for kdrlpos-enriched genes identified (F) selectively as such by Ens95 (maroon) or RefSeq (grey) only, or (G) both annotations. Data are not normally distributed, Spearman correlation, r values are indicated. Th l f h l l d h f ll d d f l ( ) f f 1 3 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Incomplete 3’ UTRs models influence RNA-seq quantification using existing annotations existing annotations Since we constructed the RNA-seq libraries in the experiments noted above using oligo-dT priming (Quillien et al., 2017; Whitesell et al., 2019), they would yield reads with a bias to the 3’ end of transcripts. Therefore, we investigated whether discrepancies noted above were due to differences between 3’ untranslated region (UTR) annotations in Ens95 and RefSeq. For this purpose, we sought to assemble a reference set of transcripts with annotated 3’ UTRs from Ens95 and RefSeq. Strikingly, in the process of assembling this reference panel, we found that nearly 20% of all coding genes in Ens95 lacked any transcript with an annotated 3’ UTR, while a smaller proportion also lacked a stop codon (Table 2, Figure 2—source data 1). By contrast, only about 6% of RefSeq genes lacked a 3’ UTR, and 1% lack a stop codon (Table 2, Figure 2—source data 1). Importantly, missing 3’ UTRs appeared to contribute to the discrepancies observed in our RNA-seq analyses. For example, 64 of the 217 kdrlpos-enriched genes identified only using RefSeq lacked an Ens95 3’ UTR, and these were detected at significantly lower levels in Ens95 compared to RefSeq (Figure 2A, Figure 2—source data 1). Similar results were found for pdgfrbpos-enriched genes, where 94 out of 248 genes identi- fied only using RefSeq lacked a 3’ UTR annotation in Ens95 (Figure 2B, Figure 2—source data 1). Among the discrepant kdrlpos-enriched genes was the previously noted blood brain barrier (BBB) marker slc7a5, where lack of a 3’ UTR in Ens95 resulted in an approximately ten-fold difference in detected expression between the two annotations (Figure 2C; N.B.: unless otherwise indicated UCSC browser images show a single representative transcript bearing the longest 3’ UTR for a given gene; Figure 1—source data 2). Interestingly, the location of mapped reads from a publicly avail- able RNA-seq dataset (referred to as GSE32900), as well the genomic position of kdrlpos reads, sug- gested an even longer slc7a5 3’ UTR than that annotated in RefSeq (Figure 2C). A putative longer 3’ UTR would also be concordant with a ‘3P-seq’ feature on the same strand, which we annotated using a public dataset that defines genomic locations for 3’ transcript ends based on a biochemically strin- gent technique (Jan et al., 2011; Ulitsky et al., 2012). Tools and resources As above, most pdgfrbpos-enriched genes with a common NCBI identifier (1905) were differ- entially expressed compared to negative (pdgfrbneg) cells using both annotations, while 172 and 248 genes were selectively identified as such by only Ens95 or RefSeq, respectively (Figure 1—figure supplement 1B, Figure 1—figure supplement 1—source datas 1 and 2; Table 1). Among the dis- crepant genes were well-known pericyte markers, such as potassium inwardly-rectifying channel sub- family J member 8 (kcnj8) and chondroitin sulfate proteoglycan 4 (cspg4), which encodes the proteoglycan epitope NG2 (Bondjers et al., 2006; Ozerdem et al., 2001). Both kcnj8 and cspg4 were pdgfrbpos-enriched using RefSeq, but not Ens95 (Figure 1—figure supplement 1C,D, Fig- ure 1—figure supplement 1—source data 2). By contrast, angiopoietin 1 (angpt1) was identified as pdgfrbpos-enriched only using Ens95 (Figure 1—figure supplement 1C,D, Figure 1—figure supple- ment 1—source data 2). The pericyte marker ATP-binding cassette, sub-family C (CFTR/MRP), member 9 (abcc9), and pdgfrb itself, are found as pdgfrbpos-enriched with both annotations (Fig- ure 1—figure supplement 1C,D, Figure 1—figure supplement 1—source data 2). We noted Table 1. Numbers of detected and differential genes from RNA-seq datasets analyzed with Ens95 and RefSeq annotations with matched identifiers. Ens95 RefSeq All w/NCBI ID All w/Ens ID kdrlpos – all detected 25704 21489 27516 21903 kdrlpos-enriched 1632 1538 1780 1651 pdgfrbpos – all detected 25699 21480 27598 21903 pdgfrbpos-enriched 2186 2091 2323 2188 Nr2f2pos – all detected 20516 17867 21788 18164 Nr2f2pos-enriched 568 516 580 508 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Developmental Biology similar discrepancies for known smooth muscle genes, including the transcription factor myocardin (myocd), for which an annotation appears to be missing from Ens95 (data not shown), and calponin 1, basic, smooth muscle, b (cnn1b), both of which were selectively identified using RefSeq. Similar to kdrlpos-enriched genes, 80 out of 172 of pdgfrbpos-enriched genes identified using Ens95 showed padj values for matched RefSeq genes at least 5-fold over the statistical cutoff (Figure 1—figure supplement 1E, Figure 1—figure supplement 1—source data 2). Likewise, expression levels for genes selectively enriched using Ens95 or RefSeq showed poor correlation between annotations and higher expression levels in the respective annotation in which it was detected as differentially expressed (Figure 1—figure supplement 1F,G, Figure 1—figure supplement 1—source data 2). By contrast, the expression of pdgfrbpos-enriched genes identified by both annotations displayed a high degree of correlation (Figure 1—figure supplement 1F). Tools and resources Taken together, these observations suggest underlying differences in zebrafish Ensembl and RefSeq annotations that contribute to inconsistencies in differential gene analysis from RNA-seq data. Incomplete 3’ UTRs models influence RNA-seq quantification using existing annotations Thus, some of the discrepancies noted above are likely due to a lack of 3’ UTR annotation for a considerable proportion of Ensembl genes. We next compared 3’ UTR lengths in cases where there existed corresponding annotations for this feature in both Ens95 and RefSeq. For this purpose, we generated a reference set of transcripts for 16,558 genes (see Materials and methods for details; Figure 2—source data 2). In our reference panel, just over one-half of genes exhibited the same length 3’ UTR in both annotations (9077 out of ble 2. Number of coding genes and proportion without stop codon or 3’ UTR in indicated t ti Table 2. Number of coding genes and proportion without stop codon or 3’ UTR in indicated annotation. Ens95 RefSeq All Genes 32520 30445 annotated CDS 25592 26120 CDS, missing annotated stop codon 1585 269 CDS, missing annotated 3’ UTR 4703 1580 DOI: https://doi.org/10.7554/eLife.55792 5 of 28 Table 2. Number of coding genes and proportion without stop codon or 3’ UTR in indicated annotation. Tools and resources Figure 2. Incomplete 3’ UTRs annotations contribute to discrepancies in RNA-seq analysis. (A, B) Log10 average expression as quantified using indicated annotation for (A) kdrlpos- or (B) pdgfrbpos-enriched genes identified as such only in RefSeq and lacking an Ens95 3’ UTR annotation. Expression levels for genes from each annotation with matched NCBI ID are shown in each case. Data are normally distributed (Shapiro-Wilks test), paired t-test, p values are indicated; n = 3 (i.e. each point represents an average value from three separate RNA-seq replicates). (C) UCSC browser image of slc7a5 locus on the minus strand showing 3’ UTR annotations from Ens95 and RefSeq. Mapped read depth from kdrlpos cells on the genome, or assigned to each annotation are indicated, as is a 3P-seq feature. The GSE32900 track is consolidated RNA-seq reads from all stages indicated in Figure 3A. The location of a putative missing 3’ UTR is indicated. (D) Pie chart showing numbers of reference genes with the same or longer 3’ UTRs in each indicated annotation. (E) Pie charts showing the proportion of reference genes selectively identified as kdrlpos- or pdgfrbpos-enriched by Ens95 and RefSeq with indicated relative 3’ UTR length. Incomplete 3’ UTRs models influence RNA-seq quantification using existing annotations (F, G) Correlation plots showing log10 average expression from kdrlpos RNA-seq (n = 3) quantified with each annotation for matched reference genes with (F) longer Ens95 (maroon) or RefSeq (light blue) 3’ UTR, or (G) same 3’ UTR length. Data are not normally distributed, Spearman correlation, r values are indicated. (H, I) UCSC browser images of (H) sox17 and (I) cspg4 loci, both on the minus strand, showing 3’ UTR annotations from Ens95 and RefSeq. Mapped read depth of RNA-seq from (H) kdrlpos or (I) pdgfrbpos cells captured for each annotation is indicated. Consolidated reads from GSE32900 and location of 3P-Seq features are indicated, as is putative missing 3’ UTR in cspg4. The online version of this article includes the following source data and figure supplement(s) for figure 2: S d t 1 Mi i 3’ UTR t ti i R fS d E 95 Tools and resources Developmental Biology Figure 2. Incomplete 3’ UTRs annotations contribute to discrepancies in RNA-seq analysis. (A, B) Log10 average expression as quantified using indicated annotation for (A) kdrlpos- or (B) pdgfrbpos-enriched genes identified as such only in RefSeq and lacking an Ens95 3’ UTR annotation. Expression levels for genes from each annotation with matched NCBI ID are shown in each case. Data are normally distributed (Shapiro-Wilks test), paired t-test, p values are indicated; n = 3 (i.e. each point represents an average value from three separate RNA-seq replicates). (C) UCSC browser image of slc7a5 locus on the minus strand showing 3’ UTR annotations from Ens95 and RefSeq. Mapped read depth from kdrlpos cells on the genome, or assigned to each annotation are indicated, as is a 3P-seq feature. The GSE32900 track is consolidated RNA-seq reads from all stages indicated in Figure 3A. The location of a putative missing 3’ UTR is indicated. (D) Pie chart showing numbers of reference genes with the same or longer 3’ UTRs in each indicated annotation. (E) Pie charts showing the proportion of reference genes selectively identified as kdrlpos- or pdgfrbpos-enriched by Ens95 and RefSeq with indicated relative 3’ UTR length. (F, G) Correlation plots showing log10 average expression from kdrlpos RNA-seq (n = 3) quantified with each annotation for matched reference genes with (F) longer Ens95 (maroon) or RefSeq (light blue) 3’ UTR, or (G) same 3’ UTR length. Data are not normally distributed, Spearman correlation, r values are indicated. Tools and resources Taken together, these results suggest that a large proportion of genes in current zebrafish transcriptome annotations do not have accurate 3’ models, which can affect the interpretation of RNA-seq analysis. Our discovery of 3’ UTR discrepancies between Ens95 and RefSeq was likely facilitated by the 3’ end-bias inherent in our RNA-Seq libraries. Therefore, we compared annotation performance using RNA-seq data from a random-primed library. In this case, we performed RNA-Seq on endothelial cells positive for the vein-specific transcription factor, Nr2f2 (nuclear receptor subfamily 2, group F, member 2), versus those positive for the Tg(fli1a:egfp)y1 transgene (see Materials and methods). Accordingly, we detected several known vein-specific genes enriched in Nr2f2pos cells including fms related receptor tyrosine kinase 4 (flt4), lymphatic vessel endothelial hyaluronic receptor 1b (lyve1b), and nr2f2 itself (Figure 2—figure supplement 2A,B, Figure 2—source data 3). Genes identified as Nr2f2pos-enriched with matched NCBI IDs showed a similar degree of overlap from each annotation, as noted above for kdrlpos and pdgfrbpos analysis (Figure 2—figure supplement 2C). We also noted a poor correlation in detection levels for Nr2f2pos-enriched genes selectively identified by either Ens95 or RefSeq compared to commonly identified genes (Figure 2—figure supplement 2D). In addition, we detected higher expression for discrepant genes in the annotation where the gene was significantly enriched, although the magnitude of difference in these cases was less than that of the 3’ biased data (compare Figure 2—figure supplement 2E with Figure 1—figure supplement 1A, G). Accordingly, many of the discrepant Nr2f2pos-enriched genes were associated with small shifts in adjusted p-values or log2 fold change values. For example, only 10 out of 59 Nr2f2pos-enriched genes identified by only Ens95 showed a greater than 5-fold padj compared to RefSeq values for the same genes (Figure 2—figure supplement 2F, Figure 2—source data 3). Furthermore, a com- parison between discrepant reference Nr2f2pos genes did not show the same trend noted with kdrlpos and pdgfrbpos analysis regarding 3’ UTR differences (Figure 2—figure supplement 2G, com- pare with Figure 2E). We noted a high degree of correlation between expression levels detected in each annotation regardless of differences in 3’ UTR lengths, although we still noted a slight trend of longer 3’UTRs displaying slightly higher expression (Figure 2—figure supplement 2H, Figure 2— source data 3). These results suggest that differences in 3’ UTR annotations between Ensembl and RefSeq may be somewhat mitigated when analyzing RNA-seq data from libraries constructed using random priming. Tools and resources Developmental Biology Developmental Biology Figure 2 continued Source data 2. Reference gene set for 3’ UTR comparisons. Source data 3. RNA-seq analysis of Nr2f2pos and NR2f2neg cells. Source data 4. Transcript based-comparison of RefSeq and Ensembl annotations. Figure supplement 1. Differences in 3’ UTR lengths between Ens95 and RefSeq for discrepant kdrlpos- and pdgfrbpos-enriched genes. Figure supplement 2. Analysis of RNA-seq reads from a random-primed library. Source data 4. Transcript based-comparison of RefSeq and Ensembl annotations. Figure supplement 1. Differences in 3’ UTR lengths between Ens95 and RefSeq for discrepant kdrlpos- and pdgfrbpos-enriched genes. Figure supplement 2. Analysis of RNA-seq reads from a random-primed library. 16558), while 4923 and 2558 genes showed longer 3’ UTRs in Ens95 or RefSeq, respectively (Figure 2D, Figure 2—source data 2; ‘longer’ is defined as more than 50 nucleotides). Similar to genes with missing 3’ UTRs, a large proportion of discrepant kdrlpos- and pdgfrbpos-enriched genes identified only in Ens95 or RefSeq also had a longer 3’ UTR in the respective annotation (Figure 2E). Moreover, these 3’ UTRs were, on average, five times longer when comparing annotations (Fig- ure 2—figure supplement 1A,B, Figure 2—source data 2). Consistent with an effect on detection, levels of reference genes in kdrlpos and pdgfrbpos datasets quantified by Ens95 or RefSeq tended to be higher in the respective annotation predicting a longer 3’ UTR and showed a lower correlation between annotations than those with the same 3’ UTR length (Figure 2F,G, Figure 2—source data 2). Among these genes were several noted above as discrepant between Ens95 and RefSeq annota- tions when quantifying kdrlpos and pdgfrbpos datasets. For example, sox17 exhibits a longer 3’ UTR in Ens95, leading to improved detection at severalfold higher levels in kdrlpos cells (Figure 2H, Fig- ure 1—source data 2). We also noted additional cases where an accurate 3’ UTR model is likely missing from both annotations. For example, the pericyte marker cspg4 has a slightly longer 3’ UTR in the RefSeq annotation (Figure 2I), where it is also detected as significantly enriched in pdgfrbpos cells (Figure 1—figure supplement 1C,D). However, as noted above with slc7a5, the location of mapped reads from GSE32900 and our pdgfrbpos data, as well as a 3P-Seq feature on the same strand, suggest a much longer 3’ UTR (Figure 2I). Incomplete 3’ UTRs models influence RNA-seq quantification using existing annotations (H, I) UCSC browser images of (H) sox17 and (I) cspg4 loci, both on the minus strand, showing 3’ UTR annotations from Ens95 and RefSeq. Mapped read depth of RNA-seq from (H) kdrlpos or (I) pdgfrbpos cells captured for each annotation is indicated. Consolidated reads from GSE32900 and location of 3P-Seq features are indicated, as is putative missing 3’ UTR in cspg4. The online version of this article includes the following source data and figure supplement(s) for figure 2: S d t 1 Mi i 3’ UTR t ti i R fS d E 95 Source data 1. Missing 3’ UTR annotations in RefSeq and Ens95. Figure 2 continued on next page Source data 1. Missing 3’ UTR annotations in RefSeq and Ens95. Figure 2 continued on next page 6 of 28 6 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Ensembl and RefSeq annotations are missing genes During the analysis above, we noted that Ens95 and RefSeq zebrafish annotations lacked common identifiers for a sizable proportion of genes. Moreover, relevant lineage markers, such as the smooth muscle-specific gene myocd, were among genes missing from either annotation (see above and Table 1). To further investigate this issue, we performed a coordinate-based transcript-level compar- ison between Ens95 and RefSeq (see Materials and methods). This analysis revealed 3165 genes annotated by RefSeq that were missing from Ens95 (Table 3, Figure 2—source data 4). More than half of these missing genes encoded proteins and several hundred were curated in the Zebrafish Information Network (ZFIN; Figure 2—source data 4). Conversely, 2116 Ens95 genes were missing from RefSeq (Table 3, Figure 2—source data 4), including 670 protein-coding genes, 141 T-cell receptor genes, and 546 genes curated by ZFIN (Table 3, Figure 2—source data 4). These discrep- ancies may have been due to the older version of Ensembl that we used at the start of our studies. However, a comparison of Ens95 to a more current version (Ensembl, version 99; referred to as Ens99), revealed identical transcript models and no new genes that have been annotated in the intervening versions (Figure 2—source data 4), although some nomenclature has changed (data not shown). Thus, current zebrafish transcript annotations from RefSeq and Ensembl have considerable gaps that preclude a comprehensive assessment of gene expression and that may constrain follow- up studies when used for RNA-seq, or analyses focused on 3’ UTR sequences (e.g. miRNA target searches). Tools and resources Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 7 of 28 Tools and resources Tools and resources Developmental Biology As noted above, nearly 20% of Ens95 genes lack a 3’ UTR annotation (see Table 2). For these Nr2f2pos-enriched genes, we did detect significant differences in expression levels between Ens95 and RefSeq annotations (Figure 2—figure supplement 2I). Notably, among these discrepant genes was the essential endothelial Ets transcription factor, erg (Vijayaraj et al., 2012), which lacks any UTR annotations in Ens95 compared to RefSeq, resulting in undersampling in Nr2f2pos cells when using Ens95 (Figure 2—figure supplement 2J). As a result, erg is identified as differentially enriched when using RefSeq, but not Ens95 for quantification (Figure 2—source data 3). Thus, the analysis of RNA-seq data obtained from random-primed libraries is less dependent on 3’ UTR annotation in existing Ensembl and RefSeq transcriptome annotations than when using 3’ biased data. However, relevant functional genes may still be missed when using Ensembl for quantification due to the com- plete absence of 3’ UTR annotations for many genes. Tools and resources Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Assembly of an improved zebrafish transcriptome annotation Our analyses above demonstrated two major issues with existing zebrafish transcriptome annota- tions. First, 3’ UTR annotations are incomplete and differ between Ensembl and RefSeq. Second, each annotation is missing a sizable number of genes. To address these issues, we sought to con- struct a more complete zebrafish transcriptome annotation (Figure 3A). For this purpose, we used the GSE32900 RNA-seq datasets, which comprise libraries from zebrafish embryos at dome, bud, and shield stages, as well as 28 hr post-fertilization (hpf) and 2- and 5 days, post-fertilization (dpf). From these stages, we combined over 600 million paired-end, strand-specific reads (Figure 3— source data 1) and mapped them to GRCz11. We generated transcript and gene models using Table 3. Coordinate-based transcriptome comparisons. Annotation Ensembl 95 RefSeq V4.2 V4.3 # genes 32520 30445 39988 36351 # transcripts 59876 55182 115496 111842 # exons 335075 307538 414404 411330 # RefSeq genes missing 3165 - 173 7c # Ensembl genes missinga - 2116 1133b 957d a –RefSeq comparison with Ens95, V4 comparison with Ens99. b – 956/1133 classified as rRNA, snRNA, snoRNA or sRNA. c – left out from V4.2 add-back; see main text. d – 956/957 are rRNA, snRNA, snoRNA, sRNA, or miscRNA; remaining protein coding gene is a sequence duplicate. Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 8 of 28 Tools and resources Developmental Biology Figure 3. The V4.2 annotation improves detection of cell-type-specific genes from bulk RNA-seq data. (A) Schematic outline for generating a new zebrafish transcriptome annotation. See Results and Materials and methods sections for details. (B) Pie charts showing the proportion of reference genes with same, longer or shorter 3’ UTR in the V4.3 annotation compared to relative 3’ UTR length between Ens95 and RefSeq. (C, E) Venn diagrams howing intersection of reference genes with commonly annotated NCBI ID that are significantly enriched in (C) kdrlpos- or (E) pdgfrbpos-cells in each ndicated annotation. (D, F) Volcano plots of reference genes with common NCBI ID identified as (D) kdrlpos- or (F) pdgfrbpos-enriched only by Ens95 in comparison to RefSeq. Indicated values are from the same genes quantified using V4.3. Red dots indicate log2 fold change >1 and adjp <0.05. (G) 3’ UTR lengths and (H) log10 average expression (n = 3) using RefSeq and V4.3 for reference genes in the indicated dataset. (G, H) Data are not normally distributed, Wilcoxon matched-pairs signed-rank test, p values are indicated. Assembly of an improved zebrafish transcriptome annotation Error bars denote mean and standard deviation. (I) Log10 average Figure 3. The V4.2 annotation improves detection of cell-type-specific genes from bulk RNA-seq data. (A) Schematic outline for generating a new zebrafish transcriptome annotation. See Results and Materials and methods sections for details. (B) Pie charts showing the proportion of reference genes with same, longer or shorter 3’ UTR in the V4.3 annotation compared to relative 3’ UTR length between Ens95 and RefSeq. (C, E) Venn diag showing intersection of reference genes with commonly annotated NCBI ID that are significantly enriched in (C) kdrlpos or (E) pdgfrbpos cells in ea Figure 3. The V4.2 annotation improves detection of cell-type-specific genes from bulk RNA-seq data. (A) Schematic outline for generating a new zebrafish transcriptome annotation. See Results and Materials and methods sections for details. (B) Pie charts showing the proportion of reference genes with same, longer or shorter 3’ UTR in the V4.3 annotation compared to relative 3’ UTR length between Ens95 and RefSeq. (C, E) Venn diagrams showing intersection of reference genes with commonly annotated NCBI ID that are significantly enriched in (C) kdrlpos- or (E) pdgfrbpos-cells in each indicated annotation. (D, F) Volcano plots of reference genes with common NCBI ID identified as (D) kdrlpos- or (F) pdgfrbpos-enriched only by Ens95 in comparison to RefSeq. Indicated values are from the same genes quantified using V4.3. Red dots indicate log2 fold change >1 and adjp <0.05. (G) 3’ UTR lengths and (H) log10 average expression (n = 3) using RefSeq and V4.3 for reference genes in the indicated dataset. (G, H) Data are not normally distributed, Wilcoxon matched-pairs signed-rank test, p values are indicated. Error bars denote mean and standard deviation. (I) Log10 average expression (n = 3) and (J) 3’ UTR lengths across all annotations for reference genes uniquely identified as enriched in indicated transgene-positive cell type using V4.3 (log2 fold change >1, padj <0.05). Data are not normally distributed. Friedman test to assess variance (p<0.0001 in all cases). Dunn’s multiple comparison test was used for pairwise comparisons, p values are indicated. Error bars denote mean and standard deviation. The online version of this article includes the following source data and figure supplement(s) for figure 3: F 3 d Figure 3 continued on next page Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources These fusion transcripts led to misassignment of gene informa- tion in Ensembl and resulted in incorrect RNA-seq quantification, leading to shifts in detected gene expression (for examples, see Figure 3—figure supplement 1, Figure 3—source data 2). We also chose to remove ribosomal and small nuclear RNAs (but not miRNAs), which are present in Ensembl, but not in RefSeq. The first working version of our annotation, referred to as version 4.2 (V4.2), comprised 115,496 transcripts from over 400,000 unique exons that give rise to nearly 40,000 genes (Table 3). A coordi- nate-based transcript comparison with RefSeq showed good coverage by V4.2 with only 173 RefSeq genes missing (Table 3, Figure 3—source data 3). Comparison with a more recent Ensembl tran- scriptome annotation (Ensembl 99, released January 2020) shows nearly 1200 genes missing from V4.2, although the majority of these (957/1133) are ribosomal or small nuclear RNAs, which we had removed from our annotations (Table 3, Figure 3—source data 3) and which are also absent from RefSeq. Over 6000 gene models in V4.2 did not overlap with existing annotations and are referred to using arbitrary ‘XLOC’ numbers assigned by Cufflinks (Figure 3—source data 4). Of these, approximately 1300 are transcripts that encode amino acid homology to zebrafish or human pro- teins, suggesting that these are previously unidentified paralogs or orthologs, although we cannot rule out the possibility that they may be pseudogenes. Of the XLOC genes, we also identified 45 that match previously annotated long non-coding RNAs not present in Ensembl or RefSeq (Fig- ure 3—source data 4). We subsequently added annotations for the missing Ens99 and RefSeq genes noted above from V4.2 (see Table 3; Figure 3—source data 3) to yield a V4.3 annotation. We also limited inclusion in V4.3 of XLOC genes to those that were supported by secondary analyses (see Materials and methods for details; Figure 3—source data 4). For end users concerned with poten- tial mapping or quantification issues arising from novel gene annotations (e.g. due to the presence of pseudogenes, or repeat elements), XLOC genes can be easily removed from the annotation. Except for the cases noted above, V4.3 is missing only a single Ens99 gene (exclusive of small RNAs noted above) and 7 RefSeq genes (Table 3). Tools and resources Developmental Biology Developmental Biology Figure 3 continued Figure 3 continued Source data 1. List of SRA accession numbers, stages, and read numbers from GSE32900 for associated RNA-seq datasets used in this study. Source data 2. List of manually-identified discrepancies in Ensembl gene annotation due to spurious fusionor overlapping transcripts. urce data 1. List of SRA accession numbers, stages, and read numbers from GSE32900 for associated RNA-seq d Source data 3. RefSeq (worksheet 1) and Ens99 (worksheet 2) genes missing from the V4.2 annotation. . RefSeq (worksheet 1) and Ens99 (worksheet 2) genes missing from the V4.2 annotation. Source data 3. RefSeq (worksheet 1) and Ens99 (worksheet 2) genes missing from the V4.2 annotation. Source data 5. V4.3 gene information table, including unique LL ID numbers, associated Ens99 gene ID, NCBI ID, and ZFIN gene ID numbers, gene symbols, and gene names. able, including unique LL ID numbers, associated Ens99 gene ID, NCBI ID, and ZFIN gene ID numbers, gene Source data 5. V4.3 gene information table, including unique LL ID numbers, associated Ens99 gene ID, NCBI ID, and ZFIN gene ID numbers, gene symbols, and gene names. Source data 6. Output from DESeq2 analysis comparing kdrlpos and kdrlneg RNA-seq. Source data 7. Output from DESeq2 analysis comparing pdgfrbpos and pdgfrbneg RNA-seq. Source data 8. Worksheet 1 - Output from DESeq2 analysis comparing Nr2f2pos and Nr2f2neg RNA-seq. Figure supplement 1. Ensembl naming conflicts and improved transcript diversity in V4.3. Figure supplement 2. The V4.3 annotation improves the detection of cell-type-specific genes from bulk RNA-seq data. Figure supplement 3. Analysis of Nr2f2pos and Nr2f2neg datasets using V4.3. Cufflinks (Trapnell et al., 2010) and applied Cuffmerge (Trapnell et al., 2010) to combine them with Ens95 and RefSeq. With this approach, the naming conventions from the Ens95 annotation were applied to all gene models and remaining known genes named with RefSeq nomenclature. Ini- tial transcriptome versions (versions 1 through 3; V1-V3) were generated to test and identify optimal parameters for transcript assembly (data not shown and see Materials and methods for details). Dur- ing this process, we noted several nomenclature conflicts that arose due to spurious fusion tran- scripts. These were identified and removed through automated and manual annotation (see Materials and methods for details). Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 9 of 28 9 of 28 Tools and resources Tools and resources Therefore, we also include comments in the information table regarding how Ensembl and RefSeq gene assignments were made. We rec- ommend that users consider these when performing follow-up analyses to confirm that matching data imported from other sources is accurate. Since our annotation comprises genes missing from Ensembl or RefSeq, as well as potentially novel genes (e.g. those identified with ‘XLOC’ assign- ments), and would lack a corresponding identifier from those annotations, we also assigned a unique arbitrary gene identifier to every gene (referred to as an ‘LL’ ID number). The LL ID number is also assigned to entries annotated in the GTF allowing easy integration of information from this table (Figure 3—source data 5) with RNA-seq outputs following analysis. The gene information tables for both annotations are also available for download at zf-transcriptome.umassmed.edu. Improved 3’ UTR coverage in the V4.3 transcriptome annotation To quantify improvements in 3’ UTR coverage in V4.3, we again relied on the reference gene set described above. For those reference genes where 3’ UTR lengths were the same between Ens95 and RefSeq, we found that 17% (1584/9077) possessed a longer 3’ UTR in the V4.3 annotation (Figure 3B, Figure 2—source data 2). Moreover, a notable proportion of reference genes with lon- ger 3’ UTRs in either Ens95 (688/4923) or RefSeq (865/2558), exhibited still longer 3’ UTR annota- tions in V4.3 (Figure 3B, Figure 2—source data 2). In total, we identified 3129 genes out of the reference gene set (16558 total genes), where V4.3 predicted a longer 3’ UTR than previously found in Ens95 or RefSeq for matching genes. To determine how these extended annotations affect RNA-seq analysis, we quantified the 3’ biased kdrl:mcherry and pdgfrb:citrine datasets using V4.3 and compared the output to that obtained from Ens95 and RefSeq. We observed a 20% to 30% increase in the number of kdrlpos- or pdgfrbpos-enriched genes over that identified when using Ens95 or RefSeq (Figure 3—figure sup- plement 2A,B; Figure 3—source datas 6 and 7; Table 4). The majority of these genes were those commonly annotated in both existing annotations, while a smaller proportion was present in only Ens95 or RefSeq. Only about 60 kdrlpos- or pdgfrbpos-enriched genes identified by V4.3 were those not previously identified in Ens95 or RefSeq annotations (i.e. XLOC-annotated genes; Table 4). Tools and resources The single Ens99 gene is an exactly duplicated sequence while missing RefSeq genes are those whose annotations are split between multiple chro- mosomes, with most cases having just a single or partial 5’ exon as the second annotation (data not shown; Figure 3—source data 3). In these cases, we kept the larger annotation, which had been present in V4.2, that included the 3’ UTR. The V4.3 annotation contains 111,842 transcripts from over 400,000 unique exons that comprise 36351 genes (Table 3). The transcript number in V4.3 is nearly double that in Ensembl or RefSeq and is accompanied by a considerable increase in the num- ber of transcripts per gene (Figure 3—figure supplement 1D), suggesting increased transcript Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 10 of 28 Tools and resources Tools and resources Developmental Biology Developmental Biology isoform diversity. For example, Ensembl and RefSeq each predict a single transcript for the erg gene, each of which differs in intron-exon structure, as well as both 5’ and 3’ UTR (Figure 3—figure supplement 1E). The V4.3 annotation predicts four transcripts for erg, including the Ensembl and RefSeq transcripts, as well as new additional isoforms with alternative promoter or exon usage (Fig- ure 3—figure supplement 1E). isoform diversity. For example, Ensembl and RefSeq each predict a single transcript for the erg gene, each of which differs in intron-exon structure, as well as both 5’ and 3’ UTR (Figure 3—figure supplement 1E). The V4.3 annotation predicts four transcripts for erg, including the Ensembl and RefSeq transcripts, as well as new additional isoforms with alternative promoter or exon usage (Fig- ure 3—figure supplement 1E). To facilitate the use of V4.3 by researchers, we have made Gene Transfer Format (.gtf) files with exon, transcript, and gene-level coordinate annotations for both V4.2 and V4.3 available for down- load at zf-transcriptome.umassmed.edu. These files can be used for standard bulk or single-cell RNA-seq pipelines, with appropriate modification. We recommend that users apply the V4.3 annota- tion for their studies, given that it is more complete, although we include both for those interested in replicating studies described below. We have also compiled a gene information table containing matching Ensembl and RefSeq gene identifiers, along with ZFIN gene IDs, and chromosomal coordi- nates (Figure 3—source data 5). As described above, we noted some nomenclature conflicts between Ensembl and RefSeq, and there are likely to be more. doi.org/10.7554/eLife.55792 11 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources By contrast, the number of Nr2f2pos-enriched genes, identified using data from random-primed librar- ies, was similar when using V4.3 (Figure 3—figure supplement 3A, Figure 3—source data 8), Table 4. Numbers of genes identified as enriched in indicated genotype with each annotation. kdrlpos-enriched pdgfrbpos-enriched Nr2f2pos-enriched Ens95 1632 2186 568 RefSeq 1780 2323 580 V4.3 2141 2794 613 annotated in Ens95 and RefSeq 1938 2612 523 not annotated in Ens95 144 131 67 not annotated in RefSeq 119 113 54 only annotated in V4.3 60 62 31 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 11 of 28 11 of 28 Tools and resources Tools and resources Developmental Biology suggesting the improvements noted above were due, in part, to the expanded 3’ UTR coverage in our annotation. To broadly compare the enriched genes from each annotation, we again utilized our reference gene set, which also contains information on 3’ UTR lengths. As noted above, there were discrepan- cies between differentially called reference genes between Ens95 and RefSeq for the kdrl:mcherry and pdgfrb:citrine datasets (108 Ens95 only, 139 RefSeq only for kdrlpos-enriched; 123 Ens95 only and 114 RefSeq only for pdgfrbpos-enriched). Importantly, the majority of these discrepancies were eliminated by using V4.3. For example, 77 out of 108 genes identified as enriched only by Ens95 in kdrlpos cells were now called as significant using V4.3 (Figure 3C,D). Similar results were observed with pdgfrbpos-enriched genes, where 110 out of 139 genes detected in Ens95 only were also now detected as significant with V4.3 (Figure 3E,F). In both cases, these genes were detected at signifi- cantly higher levels using the V4.3 annotation compared to RefSeq and exhibited much longer 3’ UTR annotations (Figure 3G,H, Figure 2—source data 2). We also noted that approximately 10% of all differentially called kdrlpos (153) and pdgfrbpos (189) genes found in our reference gene set were uniquely identified using V4.3, but not Ens95 or RefSeq, despite their presence in all three annota- tions (Figure 3C,E; Figure 3—source datas 6 and 7). As above, these genes were detected at sig- nificantly higher levels and displayed much longer 3’ UTRs in the V4.3 annotation, compared to Ens95 or RefSeq, (Figure 3I,J; Figure 2—source data 2). Tools and resources Although we noted similar discrepancies between Ens95 and RefSeq annotations in the Nr2f2pos datasets (Figure 3—figure supplement 3B, Figure 3—source data 8), many of these were not resolved using V4.3, with most discrepant genes found just below statistical thresholds used to call Nr2f2pos-enriched genes (for example, see Fig- ure 3—figure supplement 3C, Figure 3—source data 8). However, we did note a number of cases where longer 3’ UTR annotations in V4.3 helped to identify genes not otherwise detected as Nr2f2pos-enriched by one of the other annotations (Figure 3—figure supplement 3D,E, Figure 3— source data 8). Among the genes identified as significantly enriched by V4.3 were all of the individual examples noted above as discrepancies between Ens95 and RefSeq (Figure 3—figure supplement 2A,B). These included endothelial genes such as slc7a5, which possessed a longer 3’ UTR in RefSeq and was initially identified as kdrlpos-enriched only in that annotation. In V4.3, slc7a5 has a 3’ UTR approximately 5 kb longer than Ens95 or RefSeq and is detected at much higher levels (Figure 3— figure supplement 2C). Consequently, it is detected as significantly enriched in kdrlpos cells when using V4.3 (Figure 3—figure supplement 2A). We also identified genes expected to be in endothe- lial cells but missed as significantly enriched by both Ens95 and RefSeq. This included slc2a1a, which has a 3’ UTR approximately 3 kb longer in V4.3 than Ens95 and RefSeq (Figure 3—figure supple- ment 2D). Accordingly, we detected slc2a1a at significantly higher levels in V4.3 than the other annotations and as significantly enriched in kdrlpos cells when using V4.3 (Figure 3—figure supple- ment 2A,D). We noted similar improvements with discrepant pdgfrbpos genes, such as cspg4, which has a longer 3’ UTR in V4.3 when compared to Ens95 and RefSeq, concomitant with much higher levels of expression detected by V4.3 (Figure 3—figure supplement 2B,E). Notably, in each of these cases, the longer 3’ UTRs identified by V4.3 were supported by the presence of a 3P-seq fea- ture (Figure 3—figure supplement 2C–E). Taken together, these results suggest that analysis of bulk RNA-seq data using the V4.3 annotation can provide a more comprehensive and consistent out- put than Ensembl or RefSeq annotations. V4.2 improves analysis of single-cell RNA-seq data in zebrafish Single-cell RNA-seq (scRNA-seq) is increasingly being applied to zebrafish to address relevant devel- opmental questions. In most cases, scRNA-seq relies on 3’ end-sequencing to identify and count transcripts in each cell. Tools and resources Based on the increased 3’ UTR coverage in our V4 annotations, we reasoned that they could provide improvements for analyzing scRNA-seq data. To determine if this was the case, we used a publicly available 3’ scRNA-seq dataset obtained from zebrafish embryos at five dpf using the 10x Genomics platform (Farnsworth et al., 2020). In this case, we separately quantified mapped reads from this dataset to Ens95 and V4.2 annotations using the CellRanger pipeline fol- lowed by filtering, clustering, and differential expression analysis using Seurat (Stuart et al., 2019). For cell clustering, we utilized the first 75 principal components, which contributes to a comparable amount of the cumulative variation in both cases (see Materials and methods, Source code 1, Fig- ure 4—figure supplement 1). 12 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Developmental Biology Developmental Biology Developmental Biology After initial mapping with Cell Ranger, we observed an increase in the number of genes and unique molecular identifiers (UMI) captured per cell, along with an increase in total genes detected when using V4.2 compared to Ens95 (Figure 4—source data 1). Most other standard metrics were comparable between the two annotations. We subsequently identified 54 cell clusters from a total of 9373 cells when using Ens95-quantified data (Figure 4A). With V4.2, both the number of cells (11630) and the number of clusters (62) was increased (Figure 4B). This suggested that the increased 3’ UTR coverage in V4.2 allowed more reads to be captured and used for quantification, thereby increasing the number of gene and cell calls used for clustering. Accordingly, we observed notable increases in the number of cluster-specific genes per cluster and numbers of cells per cluster when comparing Ens95- and V4.2-quantified data (Figure 4—figure supplement 1C,D). p g q ( g g pp ) The increased number of cell clusters from the V4.2 annotation versus Ens95 suggested that some clusters may be split as a consequence of the increased numbers of genes and cells (see below). This makes a more granular cluster-to-cluster comparison challenging. Therefore, to further compare differences between scRNA-seq output using the two annotations, we identified cell clus- ters that could be unambiguously identified and matched between Ens95 and V4.2. We identified two such clusters for further analysis from browsing cluster-specific gene expression signatures from each dataset (Figure 4—source datas 2 and 3). Tools and resources The first was a cartilage cell cluster defined by expression of mia (MIA SH3 domain-containing) in both Ens95 and V4.2-annotated datasets (Figure 4A–C; cluster 18 in Figure 4—source data 2, cluster 22 in Figure 4—source data 3). In each annotation, mia-positive (miapos) cells expressed several other genes found in cartilage or cor- responding pharyngeal arch progenitors, including matrilin 1 (matn1), collagen, type II, alpha 1a (col2a1a), and fibroblast growth factor binding protein 2b (fgfbp2; Figure 4—figure supplement 2A, Figure 4—source datas 2 and 3; Askary et al., 2017; Xu et al., 2018). We could similarly define an epidermis cell population in both annotations by actinodin1 (and1) expression (Figure 4A, B,D; identified as cluster 11 in Figure 4—source data 2 and cluster 15 in Figure 4—source data 3), along with co-expression of actinodin2 (and2), and muscle segment homeobox 2b (msx2b; Fig- ure 4—figure supplement 2B; Figure 4—source datas 2 and 3; Akimenko et al., 1995; Zhang et al., 2010). The cartilage cluster comprised a similar number of cells regardless of annota- tion (197 with Ens95, 196 with V4.2), while V4.2 identified more cells in the epidermis cluster com- pared to Ensembl (268 for V4.2, 240 for Ens95). The intersection of cluster-specific genes for cartilage and epidermis from each annotation indicated that most genes identified by Ensembl were likewise detected with V4.2 (Figure 5A; 139 cartilage genes, 104 epidermis genes, Figure 5— source data 1). However, 25% more cartilage- and 15% more epidermis-specific genes were detected when using V4.2 (Figure 5A). Reference genes from both clusters identified only using V4.2 exhibited significantly longer 3’ UTR length in that annotation compared to Ens95 (Figure 5B). By contrast, those few cluster-specific genes identified only using Ens95 largely fell just below statis- tical cutoffs or were cases of gene names assigned to more than one Ens95 locus that collapsed into a single gene in V4.2. For example, carboxypeptidase N (cpn1) is assigned to two closely adjacent genes in Ens95 and this locus is considered as a single cpn1 gene in V4.2, where it is detected as cluster-specific by V4.2 (data not shown and Figure 5—source data 1). To further characterize the cluster-specific genes uniquely identified by V4.2, we took advantage of the fact that the TgBAC(pdgfrb:citrine)s1010 transgene is expressed in both cartilage and epider- mis (Vanhollebeke et al., 2015, data not shown). Tools and resources Tools and resources Therefore, corresponding cell type-specific genes identified by scRNA-seq should be represented and will likely be enriched in the corresponding pdgfrbpos bulk RNA-seq analysis described above. Notably, the majority of cartilage (41 out of 57) and epidermis (20 out of 30) cluster-specific genes identified by V4.2 were also significantly enriched in pdgfrbpos cells (Figure 5C; Figure 5—source datas 1 and 2). Thus, these are likely to be bona fide cartilage and epidermis genes that are uniquely detected only by V4.2 in scRNA-seq data, despite most being commonly annotated in Ens95 as well. Interestingly, many of these genes were also detected as pdgfrbpos-enriched in bulk RNA-seq data quantified using Ens95 (Figure 5—figure supplement 1A,B, Source datas 1 and 2), despite the failure to identify them as such by scRNA- seq. This is likely due to the more restricted location of reads in a 3’ scRNA-seq library (i.e. at the terminal 3’ end of the transcript) versus bulk RNA-seq, where even in the case of 3’ biased libraries reads can still be found distributed throughout the transcript. Among the genes selectively identified by V4.2 were those encoding notable signaling molecules, such as SRY-box transcription factor 9a (sox9a) and the Wnt signaling inhibitor frizzled class receptor Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 13 of 28 Tools and resources Developmental Biology Figure 4. The V4.2 annotation increases the number of cells and clusters detected in single cellingle-cell RNA-seq analysis. (A, B) tSNE plots of cells from 5 day post fertilization (dpf) zebrafish embryos from the same mapped scRNA-seq reads quantified with (A) Ens95 or (B) V4.2. The total number of clusters and cells that passed filtering are shown. Clusters of interest noted in the text are named. Cartilage and epidermis clusters are circled. (C, D). tSNE plots showing restricted expression of (C) mia in cartilate cells and (D) and1 in epidermis cells for both Ens95 and V4.2 annotations. Each cluster is indicated by a circle. Legends indicate log-transformed and normalized expression values. The online version of this article includes the following source data and figure supplement(s) for figure 4: Source data 1. Metrics from CellRanger output for data quantified using Ens95 and V4.2. Figure 4 continued on next page Tools and resources Developmental Biology Figure 4. The V4.2 annotation increases the number of cells and clusters detected in single cellingle-cell RNA-seq analysis. Tools and resources (A, B) tSNE plots of cells from 5 day post fertilization (dpf) zebrafish embryos from the same mapped scRNA-seq reads quantified with (A) Ens95 or (B) V4.2. The total number of clusters and cells that passed filtering are shown. Clusters of interest noted in the text are named. Cartilage and epidermis clusters are circled. (C, D). tSNE plots showing restricted expression of (C) mia in cartilate cells and (D) and1 in epidermis cells for both Ens95 and V4.2 annotations. Each cluster is indicated by a circle. Legends indicate log-transformed and normalized expression values. The online version of this article includes the following source data and figure supplement(s) for figure 4: Source data 1. Metrics from CellRanger output for data quantified using Ens95 and V4.2. Figure 4 continued on next page Tools and resources Developmental Biology Developmental Biology Developmental Biology Figure 4 continued Source data 2. Cluster-specific genes from whole embryo scRNA-seq at 5 days post fertilization (dpf) identified using Seurat from data quantified with Ens95. Source data 3. Cluster-specific genes from whole embryo scRNA-seq at five dpf identified using Seurat from data quantified with V4.2. Figure supplement 1. Standard variance and principal component comparisons for scRNA-seq analysis. Figure supplement 2. Identification of cartilage and epidermis cell clusters in scRNA-seq data. Figure 4 continued Source data 2. Cluster-specific genes from whole embryo scRNA-seq at 5 days post fertilization (dpf) identified using Seurat from data quantified with Ens95. Source data 3. Cluster-specific genes from whole embryo scRNA-seq at five dpf identified using Seurat from data quantified with V4.2. Figure supplement 1. Standard variance and principal component comparisons for scRNA-seq analysis. Figure supplement 2. Identification of cartilage and epidermis cell clusters in scRNA-seq data. Ens95. Source data 3. Cluster-specific genes from whole embryo scRNA-seq at five dpf identified using Seurat from data quantified with V4.2. Figure supplement 1. Standard variance and principal component comparisons for scRNA-seq analysis. Figure supplement 2. Identification of cartilage and epidermis cell clusters in scRNA-seq data. 9b (fzd9b). Both of these genes have been previously found in cartilage cells or their progenitors (Askary et al., 2017; Xu et al., 2018) and were readily detected as significantly enriched in the carti- lage cluster from V4.2-quantified data, but not Ens95 (Figure 5D,E, Figure 5—source data 1). 9b (fzd9b). Both of these genes have been previously found in cartilage cells or their progenitors (Askary et al., 2017; Xu et al., 2018) and were readily detected as significantly enriched in the carti- lage cluster from V4.2-quantified data, but not Ens95 (Figure 5D,E, Figure 5—source data 1). Figure 5. The V4.2 annotation increases the quantity of cell type-specific genes identified by scRNA-seq. (A) Venn diagrams illustrating intersection by common LL gene ID of genes enriched in mia-positive cartilage cells and and1-positive epidermis cells by both indicated annotations. (B) 3’ UTR lengths from Ens95 and V4.2 for reference genes identified as cartilage or epidermis-specific uniquely by V4.2. Data are not normally distributed (Shapiro-Wilks test), comparison by Wilcoxon matched-pairs signed-rank test, p-values are shown. (C) Volcano plots showing cartilage- or epidermis- specific genes identified selectively by V4.2 with corresponding values from bulk RNA-seq comparison of pdgfrbpos and pdgfrbneg cells. Red indicates log2 fold change >1 (pdgfrbpos/pdgfrbneg), padj <0.05. Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 14 of 28 Tools and resources Tools and resources Tools and resources DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Tools and resources Developmental Biology Developmental Biology Developmental Biology Accordingly, both sox9a and fzd9b showed longer 3’ UTR annotations in V4.2 compared to Ens95 (Figure 5F). Similar results were noted for selected genes in the V4.2 epidermis cluster (Figure 5— figure supplement 1C, Figure 5—source data 2). In all of these examples, the extended 3’ UTR annotations in V4.2 were supported by 3P-seq features and would be expected to capture the majority of reads from scRNA-seq. Notably, the 3’ UTR annotated in V4.2 for fzd9b, which is also supported by a 3P-Seq feature, is only 350 bp longer than that in Ens95 (Figure 5F). Thus, even a modest increase in 3’ UTR length can have a significant impact on gene detection, especially in the case for 10x Genomics libraries where short reads are anchored at the 3’ end. We also noted cases where use of the V4.2 annotation could improve clustering resolution over Ens95-quantified scRNA-seq data. For example, we identified several groups of blood cells, which included cells within two clusters expressing leukocyte-specific genes (e.g. coronin, actin-binding protein, 1A [coro1a] and Rac family small GTPase 2 [rac2]; Jones et al., 2013; Song et al., 2004; Tell et al., 2012; Figure 6A,B) and erythroid cells expressing hemoglobin (hbae1.1; Galloway et al., 2005; Oates et al., 1999; Figure 6A–C). The two leukocyte clusters could be further distinguished by expression of src-like adapter 2 (sla2, Figure 6D), which is expressed in T and B cells in mammals (Pandey et al., 2002). Interestingly, the sla2-positive (sla2pos) leukocyte cluster was split on the tSNE plot when using Ens95-quantified reads, such that some cells were more closely associated with the erythroid cluster (denoted by two circles connected by a line in Figure 6A,B and G). Despite their assignment to the sla2pos leukocyte cluster, these separate cells failed to express sla2 and distinctly expressed hbae1.1, similar to cells in the adjacent erythroid cluster (Figure 6C,D). This subset of sla2pos cells also did not express leukocyte-specific genes, but shared expression of v-myb avian myeloblastosis viral oncogene homolog (myb) and proliferating cell nuclear antigen (pcna), sugges- tive of a common proliferative or progenitor-like state (Figure 6E; Liu et al., 2017; Soza-Ried et al., 2010). Using reads quantified with the V4.2 annotation, we identified a group of cells that were simi- larly located adjacent to, but separate from an erythroid cluster. Tools and resources However, in this case, the erythroid- adjacent cells were also classified as separate from sla2pos-leukocytes (Figure 6F). Mapping of cell barcodes from this V4.2 cluster onto cells clustered using Ens95-quantified reads revealed that these are the same cells clustered with, but split from, sla2pos leukocytes (Figure 6G). This suggested that these cells were mis-classified during clustering using Ens95-quantified data. Based on the expres- sion of hbae1.1 in these cells (Figure 6C) and analysis presented below using V4.2, we refer to this cluster as ‘erythroid-2’. To identify a potential source for distinct cell clustering using V4.2, we intersected cluster-specific genes from the Ens95 and V4.2 sla2pos leukocytes, along with those from V4.2 erythroid-2 cells. Fol- lowing intersection based on gene symbol, only a small number of genes were common to all three clusters, including pcna and myb, which were noted above (Figure 6E,H, Figure 6—source data 1). Similarly, erythroid markers, such as hbae1.1, were shared between the erythroid-2 V4.2 and sla2pos- leukocyte Ens95 clusters, consistent with the latter being a likely mix of the two cell populations (Figure 6H). Importantly, the erythroid-2 cluster displayed many more unique genes than those that were shared with the sla2pos Ens95 cluster. These included known erythroid-expressed genes such as solute carrier family 25 member 37 (slc25a37), which encodes the Mitoferrin iron transporter, transferrin receptor 1a (tfr1a), and integrin alpha 4 (itga4), which is expressed in hematopoietic pro- genitor cells (Li et al., 2018; Liao et al., 2000; Shaw et al., 2006; Wingert et al., 2004). Expression of these genes was generally low and detected in very few cells in any of these clusters when using the Ens95 annotation, but all were readily detected with V4.2 (Figure 7A). Notably, all of these genes appear preferentially expressed in the erythroid-2 cluster (Figure 7A). Furthermore, V4.2 shows annotated 3’ UTRs for these genes that are much longer than Ens95 and supported by the concordance of 3P-Seq features (Figure 7B). Taken together, these observations suggest that increased 3’UTR coverage and improved cell type-specific gene detection using the V4.2 annotation can contribute to more accurate clustering of cells from scRNA-seq data than existing annotations. Tools and resources Tools and resources (D, E) tSNE plots of the mia-positive cartilage cluster showing expression levels of sox9a and fzd9b using scRNA-seq data quantified using (D) Ens95 and (E) V4.2. Legends indicate log-transformed and normalized expression levels per cell. (F) UCSC browser image of sox9a and fzd9b loci showing 3’ UTR annotations from V4.2 and Ens95. Both loci are located on the negative strand. Mapped read depth from kdrlpos cells on the genome, or assigned to each annotation are indicated, as are 3P-seq features, all of which reside in the same orientation as the genes themselves. The online version of this article includes the following source data and figure supplement(s) for figure 5: S d t 1 C til ifi id tifi d b RNA Figure 5. The V4.2 annotation increases the quantity of cell type-specific genes identified by scRNA-seq. (A) Venn diagrams illustrating intersection by common LL gene ID of genes enriched in mia-positive cartilage cells and and1-positive epidermis cells by both indicated annotations. (B) 3’ UTR lengths from Ens95 and V4.2 for reference genes identified as cartilage or epidermis-specific uniquely by V4.2. Data are not normally distributed (Shapiro-Wilks test), comparison by Wilcoxon matched-pairs signed-rank test, p-values are shown. (C) Volcano plots showing cartilage- or epidermis- specific genes identified selectively by V4.2 with corresponding values from bulk RNA-seq comparison of pdgfrbpos and pdgfrbneg cells. Red indicates log2 fold change >1 (pdgfrbpos/pdgfrbneg), padj <0.05. (D, E) tSNE plots of the mia-positive cartilage cluster showing expression levels of sox9a and fzd9b using scRNA-seq data quantified using (D) Ens95 and (E) V4.2. Legends indicate log-transformed and normalized expression levels per cell. (F) UCSC browser image of sox9a and fzd9b loci showing 3’ UTR annotations from V4.2 and Ens95. Both loci are located on the negative strand. Mapped read depth from kdrlpos cells on the genome, or assigned to each annotation are indicated, as are 3P-seq features, all of which reside in the same orientation as the genes themselves. Th li i f thi ti l i l d th f ll i d t d fi l t( ) f fi 5 Source data 1. Cartilage-specific genes identified by scRNA-seq. Source data 2. Epidermis-specific genes identified by scRNA-seq. Source data 2. Epidermis-specific genes identified by scRNA-seq. ure supplement 1. Improved detection of cartilage and epidermis genes in scRNA-seq data using V4.2. 15 of 28 Lawson et al. eLife 2020;9:e55792. Discussion In this study, we describe an improved transcriptome annotation for the zebrafish genome. We doc- ument several discrepancies and deficiencies in the existing Ensembl and RefSeq annotations, includ- ing incomplete 3’ UTR annotations and missing gene models. Our new transcriptome annotation addresses many of these issues and performs better than existing annotations for the analysis of 16 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Developmental Biology Figure 6. The V4.2 annotation improves cluster resolution in scRNA-seq data. (A) tSNE plot of all clusters from Ensembl (Ens95)-quantified scRNA-seq of zebrafish embryos at 5 days post fertilization with one erythroid and two leukocyte clusters indicated. (A–E, G) Circled clusters denote sla2pos leukocyte cells. Asterisk marks cells spuriously assigned to sla2pos leukocytes, but identified as erythroid two when using the V4.2 annotation. (B–E) tSNE plots showing only sla2pos leukocyte (circled) and erythroid clusters with expression of (B) known leukocyte markers, coro1a, and rac2, (C) erythroid marker hbae1.1, and (D) sla2. (E) tSNE plots showing expression of pcna and myb in sla2pos and erythrocyte clusters. (B–E) Legends indicate log-transformed and normalized expression values. (F) Erythroid and sla2pos (leukocyte) clusters identified using the same scRNA-seq dataset as in (A) but quantified using V4.2. A unique erythroid-like cluster (erythroid 2) is circled. (G) tSNE plot of erythroid and sla2pos leukocyte clusters identified with Ens95 quantified data. Dark green denotes cells with identical barcodes as those in the erythroid two cluster identified using V4.2 shown in (F). (H) Three-way Venn diagram intersecting cluster-specific genes of indicated clusters by gene symbol. Selected genes are shown. The online version of this article includes the following source data for figure 6: Figure 6. The V4.2 annotation improves cluster resolution in scRNA-seq data. (A) tSNE plot of all clusters from Ensembl (Ens95)-quantified scRNA-seq of zebrafish embryos at 5 days post fertilization with one erythroid and two leukocyte clusters indicated. (A–E, G) Circled clusters denote sla2pos leukocyte cells. Asterisk marks cells spuriously assigned to sla2pos leukocytes, but identified as erythroid two when using the V4.2 annotation. (B–E) tSNE plots showing only sla2pos leukocyte (circled) and erythroid clusters with expression of (B) known leukocyte markers, coro1a, and rac2, (C) erythroid marker hbae1.1, and (D) sla2. (E) tSNE plots showing expression of pcna and myb in sla2pos and erythrocyte clusters. (B–E) Legends indicate log-transformed and normalized expression values. Discussion (F) Erythroid and sla2pos (leukocyte) clusters identified using the same scRNA-seq dataset as in (A) but quantified using V4.2. A unique erythroid-like cluster (erythroid 2) is circled. (G) tSNE plot of erythroid and sla2pos leukocyte clusters identified with Ens95 quantified data. Dark green denotes cells with identical barcodes as those in the erythroid two cluster identified using V4.2 shown in (F). (H) Three-way Venn diagram intersecting cluster-specific genes of indicated clusters by gene symbol. Selected genes are shown. The online version of this article includes the following source data for figure 6: 17 of 28 17 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Developmental Biology Figure 7. Improved detection of erythroid markers in V4.2. (A) tSNE plots of blood cell clusters from Ens95- and V4.2-quantified data showing expression of slc25a37, tfr1a, and itga4. Erythroid 2 cells spuriously identified as leukocyte using Ens95 quantification are circled. Legends indicate log- transformed and normalized expression values. (B) 3’ UTR annotations from Ens95 and V4.2 for slc25a37 (on the positive strand), tfra1a (on the negative strand), and itga4 (positive strand). The 3’ end of the cerkl gene on the negative strand overlaps the itga4 3’ UTR. Therefore, in this case we show read densities split based on strand. Figure 7. Improved detection of erythroid markers in V4.2. (A) tSNE plots of blood cell clusters from Ens95- and V4.2-quantified data showing expression of slc25a37, tfr1a, and itga4. Erythroid 2 cells spuriously identified as leukocyte using Ens95 quantification are circled. Legends indicate log- transformed and normalized expression values. (B) 3’ UTR annotations from Ens95 and V4.2 for slc25a37 (on the positive strand), tfra1a (on the negative strand), and itga4 (positive strand). The 3’ end of the cerkl gene on the negative strand overlaps the itga4 3’ UTR. Therefore, in this case we show read densities split based on strand. both bulk and single-cell RNA-seq datasets, especially in cases where RNA-seq libraries exhibit reads biased toward the 3’ ends of transcripts. Annotation discrepancies proved to be less noticeable when analyzing RNA-seq libraries constructed using a random primed method. However, we noted failure to detect important functional genes and well-known lineage markers even in this case. This issue was especially noticeable in the Ensembl transcriptome annotation, where nearly 20% of all coding genes lack an annotated 3’ UTR. Discussion Future studies that take advantage of long-read sequencing, along with addi- tional 5’ and 3’ anchored sequencing, will prove helpful at further verifying and improving the tran- script models predicted in our annotation. annotations. Therefore, we reasoned that the incorporation of existing high-quality RNA-seq data- sets would provide an evidence-guided approach to extend 3’ UTR annotations. Indeed, our new annotation exhibits extended 3’ UTR models for a large proportion of existing genes and improves performance for RNA-seq analysis. Moreover, transcript diversity is drastically increased in our anno- tation, with evidence of many more splice isoforms not evident in Ensembl or RefSeq. While we have not comprehensively addressed the depth of isoform diversity in this study, we believe that our improved annotation will prove useful for better characterizing splice isoform and differential 3’ UTR usage in the zebrafish. Future studies that take advantage of long-read sequencing, along with addi- tional 5’ and 3’ anchored sequencing, will prove helpful at further verifying and improving the tran- script models predicted in our annotation. p p The increased application of scRNA-seq for molecular analysis in the zebrafish model underscores the need for a transcriptome annotation with accurate 3’ UTR annotations. This is especially impor- tant given the reliance on 3’ end sequencing in most scRNA-seq studies. As we show, a 3’ UTR anno- tation missing just a few hundred nucleotides can lead to drastic differences in gene expression. With the limited sequence space captured in most scRNA-seq libraries, along with the large propor- tion of incomplete 3’ UTRs in existing zebrafish annotations, many previous studies may be missing a large number of cell type-specific genes. This issue subsequently has a direct impact on cell cluster- ing. In our example, we show how improvements in 3’ UTR annotation lead to a detection of impor- tant erythroid-specific genes that guide more accurate assignment of distinct, but related, cell types. Indeed, scRNA-seq analysis with the V4.2 annotation increased the number of clusters called by Ens95 by fifteen percent, suggesting there are numerous examples where improved gene quantifica- tion likely led to more refined cell clustering. Whether the V4.2 annotation might also provide similar improvements with scRNA-seq libraries anchored at the 5’ end is not known. Anecdotally, we have noted several genes where V4.2 shows an extended 5’ UTR annotation when compared to RefSeq and Ensembl (e.g. fzd9b, see Figure 5F). Discussion Moreover, we also show that integration of bulk RNA-seq and scRNA-seq from common cell types is more consistent when both datasets are mapped to the same annotation. Thus, similar approaches to integrate bulk RNA-Seq from random-primed libraries with scRNA-seq would still benefit from mapping both datasets on an annotation with more accurate 3’ UTR models. For these reasons, we believe that our improved annotation will be a valuable tool for zebrafish researchers to apply in the context of their ongoing and planned RNA-seq experiments. In the course of our previous efforts in applying RNA-seq, we had generated a custom annotation by simply extending the existing Ensembl UTR annotations by 5 kb (previously only described as a ‘custom’ annotation in the Materials and methods section of Quillien et al., 2017). However, we found that this could lead to several secondary issues regarding RNA-seq read and gene assign- ment, especially in cases where an extension merged with an adjacent gene on the same strand. Indeed, as we find in this study, this is currently an issue with several loci in the recent Ensembl anno- tations, leading to mis-quantification of RNA-seq data, aberrant assignment of gene information, and apparent loss of genes (for examples see Figure 3—figure supplement 1A–C). We have also found that some Ensembl genes are missing terminal exons, such that a simple 3’ extension could lead to quantification of otherwise spurious intronic RNA-seq reads from pre-mRNA (data not shown). In addition, several hundred genes from the reference gene set we generated here possess 3’ UTRs in the V4 annotation that are more than 5 kb longer than existing Ensembl or RefSeq Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 18 of 28 Tools and resources Tools and resources Developmental Biology Developmental Biology annotations. Therefore, we reasoned that the incorporation of existing high-quality RNA-seq data- sets would provide an evidence-guided approach to extend 3’ UTR annotations. Indeed, our new annotation exhibits extended 3’ UTR models for a large proportion of existing genes and improves performance for RNA-seq analysis. Moreover, transcript diversity is drastically increased in our anno- tation, with evidence of many more splice isoforms not evident in Ensembl or RefSeq. While we have not comprehensively addressed the depth of isoform diversity in this study, we believe that our improved annotation will prove useful for better characterizing splice isoform and differential 3’ UTR usage in the zebrafish. Zebrafish lines and maintenance All studies were performed under the auspices of animal protocols approved by the University of Massachusetts Medical School Institutional Animal Care and Use Committee. The Tg(fli1a:egfp)y1 and TgBAC(pdgfrb:citrine)s1010 trangenic lines have been described elsewhere (Lawson and Wein- stein, 2002; Vanhollebeke et al., 2015). Discussion DOI: https://doi.org/10.7554/eLife.55792 19 of 28 Materials and methods Tools and resources Developmental Biology Materials and methods Materials and methods Materials and methods Key resources table Reagent type (species) or resource Designation Source or reference Identifiers Additional information Genetic reagent (Danio rerio) Tg(fli1a:egfp)y1 Lawson and Weinstein, 2002 RRID:ZFIN_ZDB-ALT-011017-8 Genetic reagent (Danio rerio) TgBAC(pdgfrb:citrine)s1010 Vanhollebeke et al., 2015 RRID:ZFIN_ZDB-ALT-150922-2 Antibody anti-NR2F2 NR2F2 D16C4, rabbit monoclonal Cell Signaling Technology Cat #6434; RRID:AB_11220428 used at 1:100 Antibody Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Cyanine3-conjugated Thermo Fisher Scientific Cat #A10520; RRID:AB_2534029 used at 1:1000 Software, algorithm DolphinNext Yukselen et al., 2020; https://github.com/UMMS- Biocore/dolphinnext Software, algorithm In-house bulk RNA-seq pipeline https://github.com/UMMS- Biocore/rnaseq Software, algorithm DEBrowser Kucukural et al., 2019; https://github.com/UMMS- Biocore/debrowser Software, algorithm Intervene Khan and Mathelier, 2017 https://intervene.readthedocs. io/en/latest/install.html Software, algorithm gffcompare Pertea and Pertea, 2020; https://github.com/ gpertea/gffcompare Software, algorithm GenomicFeatures Lawrence et al., 2013; https://bioconductor.org/ packages/release/bioc/html/ GenomicFeatures.html RRID:SCR_016960 Software, algorithm bedtools Quinlan and Hall, 2010; https://bedtools.readthedocs. io/en/latest/content/ installation.html RRID:SCR_006646 Software, algorithm GSNAP Wu and Nacu, 2010; http://research-pub. gene.com/gmap/src/gm ap-gsnap-2019-09-12.tar.gz RRID:SCR_005483 Software, algorithm Cufflinks/Cuffmerge Trapnell et al., 2010; http://cole-trapnell-lab. github.io/cufflinks/cuffmerge/ RRID:SCR_014597 Software, algorithm Cell Ranger 10x Genomics; https://support. 10xgenomics.com/single-cell- gene-expression/software/ downloads/latest RRID:SCR_017344 Software, algorithm Seurat Stuart et al., 2019; https://satijalab.org/ seurat/install.html RRID:SCR_007322 Zebrafish lines and maintenance All studies were performed under the auspices of animal protocols approved by the University of Massachusetts Medical School Institutional Animal Care and Use Committee. The Tg(fli1a:egfp)y1 and TgBAC(pdgfrb:citrine)s1010 trangenic lines have been described elsewhere (Lawson and Wein- stein, 2002; Vanhollebeke et al., 2015). Zebrafish lines and maintenance Tools and resources Developmental Biology Discussion However, we have not quantified whether this observation holds across most of the transcriptome. With the availability of cap analysis of gene expression (CAGE) datasets that define the transcriptional start sites of genes in zebrafish (Haberle et al., 2014), it would be possible in future studies to assess how complete the 5’ ends of gene models might be across the different transcriptome annotations. The use of our annotation for read quantification can improve RNA-seq interpretation through a more accurate estimation of gene expression. However, there remain issues to be improved addressed in future versions. Despite improvements, our annotation is likely limited by the use of short-read sequencing libraries. For example, in cases where genes encode multiple transcript iso- forms with both variable 3’ UTR length and exon usage, it is not possible to accurately assign which splice isoforms have particular 3’ UTRs. We would note that this same deficiency applies to Ensembl and RefSeq annotations when quantifying data from RNA-seq libraries generated through short- read deep sequencing. We also noted that some predicted XLOC loci removed from V4.2 were located immediately adjacent and downstream of existing or extended 3’ UTR annotations, suggest- ing that they were likely longer 3’ UTRs (data not shown). The prevalence of repetitive elements in these 3’ UTR sequences may preclude dense enough mapping of short-read sequences to connect these downstream annotations. As noted above, future integration of our annotation with long-read sequencing will likely further improve both isoform assignment and 3’ UTR models. Likewise, 3’- anchored sequencing efforts, along with more rigorous computational analysis could also better define differential polyadenylation sites and allow improved characterization of differential 3’ UTR usage. We would also point out that the RNA samples we used for reconstructing the V4 transcrip- tome were limited to embryonic and early larval stages. As such, genes restricted to late larval and adult stages may still have a preponderance of incomplete 3’ UTRs. There are also likely to be some remaining nomenclature issues, particularly in the case of duplicated genes where official name des- ignations have not yet been assigned, or in cases where a gene is split between remaining non-chro- mosomal contigs. Despite these remaining issues, the current iteration of our transcriptome annotation represents an improvement over existing annotations and will provide a valuable resource for the zebrafish community. Lawson et al. eLife 2020;9:e55792. Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 20 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Developmental Biology Developmental Biology Bulk RNA-seq analysis We ran mapping and quantification pipelines described below in the DolphinNext environment (https://github.com/UMMS-Biocore/dolphinnext; Yukselen et al., 2020) using the Massachusetts Green High Performance Computing Cluster (GHPCC). Triplicate samples of paired-end reads from kdrl-positive and kdrl-negative cells were downloaded from GEO (GSE119718). For bulk RNA-seq we utilized a standardized pipeline in the DolphinNext environment (https://github.com/UMMS-Bio- core/rnaseq, Yukselen et al., 2020). Briefly, reads were mapped to GRCz11 using STAR (Dobin et al., 2013) with default parameters to generate BAM files, which were subsequently used for transcript quantification with RSEM (Li and Dewey, 2011) using Ensembl, version 95, RefSeq (GCF_000002035.6_GRCz11), or V4.3 transcript annotations. We identified differentially expressed genes using DESeq2 with gene-mapped expected count files from RSEM. DESeq2 was run using the DEBrowser interface (Kucukural et al., 2019). We applied the Low count filtering method to remove features with counts per million of less than 10 in at least three samples and median ratio normaliza- tion was applied in all cases. The dispersion was estimated using a parametric fit and hypothesis testing performed using the likelihood ratio test. p-values obtained by the Wald test were adjusted for multiple testing using the Benjamini and Hochberg method (Benjamini and Hochberg, 1995). Differentially expressed genes were defined as those with log2 fold change less than 1 or greater than one and adjusted p-value less than 0.05. We ran the same pipeline with identical parameters for each annotation (RefSeq, Ens95, or V4.3). Volcano plots were generated using DESeq2 in the DEBrowser interface. RNA-seq sample preparation For pdgfrb:citrine analysis, citrine-positive and -negative cells were obtained by fluorescent activated cell sorting (FACS) from dissociated TgBAC(pdgfrb:citrine)s1010 embryos at five dpf and used to gen- erate RNA-seq libraries as previously described (Quillien et al., 2017; Whitesell et al., 2019). To isolate venous endothelial cells, we applied a modification of the MARIS protocol that we previously adapted to zebrafish (Hrvatin et al., 2014; Quillien et al., 2017). Briefly, dechorionated and deyolked Tg(fli1a:egfp)y1 embryos at 38 hr post-fertilization were dissociated by immersing in 1 x TrypLE Express for 15 min at 28.5˚C. All subsequent steps took place at 4˚C. Cells were filtered through a 70 mm cell strainer, centrifuged at 3,000 rpm for 3 min, and resuspended in 4% Parafor- maldehyde/0.1% Saponin in phosphate buffer saline (PBS) for 30 min with rotation. Cells were washed twice (0.25% BSA/0.1% Saponin in PBS with RNAsinPlus (280 U/mL)) to remove fixative and then incubated with anti-NR2F2 (D16C4) Rabbit mAB (#6434, Cell Signaling) at 1:100 in blocking buffer (1% BSA/1% Saponin in PBS with RNAsinPlus (400 U/mL)) with rotation for 15 min. Cells were washed for 5 min twice and incubated with goat anti-rabbit IgG(H+L)-Cy3 (A10520, Invitrogen) at 1:1000 in blocking buffer for 1 hr. Cells were then washed twice and resuspended in wash buffer. Fluorescence-activated cell sorting (FACS) was performed by the UMassMed Flow Cytometry Core to separately isolate Nr2f2/EGFP double-positive (red/green) and Nr2f2-negative/EGFP-positive (green) cells. Total RNA was purified from double- and single-positive cells using RecoverAll Total Nucleic Acid Isolation Kit (AM1975, Ambion), then concentrated using RNA Clean and Concentra- tor-5 Kit (11–325, Zymo Research). After the elimination of ribosomal RNAs using mammalian Ribo- Gone Kit (634846, Clontech), RNAseq libraries were prepared using SMARTer Stranded RNA-Seq Kit (634836, Clontech) and deep sequencing performed on a HiSeq2000 (UMass Med Deep Sequencing Core Facility). Libraries were constructed from Nr2f2/EGFP-positive and EGFP-positive cells isolated from clutches of embryos generated on three different days. Comparison of 3’ UTR coverage between annotations Comparison of 3 UTR coverage between annotations To assess the presence or absence of 3’ UTR models in coding genes in Ens95 and RefSeq, we relied on the annotation of these features in column 3 of each respective gene transfer format file (GTF). Each feature was extracted from the respective GTF, collapsed to novel gene ID to avoid spuriously counting alternatively spliced multi-exon 3’ UTRs, and counted. To compare 3’ UTR length, we chose to generate a reference gene set with a single representative transcript per gene. This approach reduces the potential for spuriously matching or assigning differentially spliced or alternative 3’ UTR isoforms across annotations. All 3’ UTR lengths were obtained from each annotation by using GenomicFeatures in R (Lawrence et al., 2013) with GTFs for each annotation containing only the 3’ UTR annotated entries. We next extracted all terminal exons from the Ens95 GTF annotated as a 3’ UTR. For each Ens95 gene, we then identified and chose a single transcript with the longest 3’ UTR as representative. To accurately match a RefSeq transcript to each representative Ens95 transcript, we first identified and extracted the longest terminal 3’ UTR exon for each RefSeq transcript. In cases where there were identical overlapping transcript coordinates, these were collapsed into a sin- gle entry and arbitrarily assigned one of the duplicate transcript IDs. Matching transcripts from RefSeq were integrated using bedtools by intersecting on the last exon start coordinates on the same strand (i.e. start coordinate on the positive stand, end coordinate on the minus strand). To incorporate V4.3 genes, we identified the longest terminal exon for each gene, collapsed duplicates, and assigned an arbitrary transcript ID as above for RefSeq entries. V4.3 transcripts matching the ref- erence gene were then incorporated using bedtools to intersect on exon start coordinates on the same strand as above. V4.3 3’ UTR lengths were then calculated based on the differences between RefSeq or Ens95 (see Figure 2—source data 2). To visualize 3P-Seq location, we downloaded BED files from GEO (GSE37453, Ulitsky et al., 2012) and merged these into a single file after filtering for expression level. We then sequentially lifted these coordinates over from Zv9 to GRCz10 and then to GRCz11 using the UCSC browser interface (http://genome.ucsc.edu/cgi-bin/hgLiftOver). For com- parison of gene-level expression between annotations, we imported values from DESeq2 output for indicated dataset mapped to each respective annotation using the appropriate matched ID. Annotation comparisons A GTF for RefSeq (GCF_000002035.6_GRCz11) was downloaded from the UCSC Table browser, while Ens95 was downloaded from the Ensembl FTP site (ftp.ensembl.org:21/pub/release-95/gtf/danio_rerio/Danio_ rerio.GRCz11.95.gtf.gz). Before running gffcompare, Ensembl-annotated GTF files were modified to match UCSC-based chromosome annotation, while ‘alt’ chromosome variants in RefSeq were removed. Each pairwise comparison was run with default settings using each annotation as a refer- ence to identify relative missing and matching transcript models. To confirm that missing transcripts represented actual missing genes, reference genomes in each case were subsequently re-searched for matching gene IDs corresponding to each missing transcript. We subsequently surveyed between 10 to 20 missing genes manually through individual visualization of their loci on the UCSC genome browser to confirm the results. Matched transcript outputs from gffcompare, along with missing gene lists can be found in the associated source data files. Annotation comparisons To compare RNA-seq analyses from Ens95 and RefSeq, we downloaded matching NCBI IDs for Ensembl-annotated genes using Biomart from the Ens95 archive (http://jan2019.archive.ensembl. org/Danio_rerio/Info/Index). Our gene-level DEbrowser output listed gene symbol with all associ- ated transcripts. Since a number of Ens95 and RefSeq genes have identical gene symbol annota- tions, we incorporated matching Ens95 gene and NCBI IDs using a representative transcript ID for each gene to ensure correct matches. We then applied Intervene (Khan and Mathelier, 2017) for intersections based on common NCBI ID and generation of Venn diagrams. Proportional Venn dia- grams were generated using eulerr (Larsson, 2020, https://github.com/jolars/eulerr.co). A similar 21 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Developmental Biology Developmental Biology approach was applied for comparison of RNA-seq outputs from V4.2 and V.3, except that LL gene ID was used. All corresponding NCBI, Ensembl, and LL gene IDs for RNA-seq output are included in the corresponding source data tables. To identify matching and missing genes between different annotations, we applied gffcompare (Pertea and Pertea, 2020), which provides a coordinate-based comparison of transcript intron/exon structure using GTF files as input. A GTF for RefSeq (GCF_000002035.6_GRCz11) was downloaded from the UCSC Table browser, while Ens95 was downloaded from the Ensembl FTP site (ftp.ensembl.org:21/pub/release-95/gtf/danio_rerio/Danio_ rerio.GRCz11.95.gtf.gz). Before running gffcompare, Ensembl-annotated GTF files were modified to match UCSC-based chromosome annotation, while ‘alt’ chromosome variants in RefSeq were removed. Each pairwise comparison was run with default settings using each annotation as a refer- ence to identify relative missing and matching transcript models. To confirm that missing transcripts represented actual missing genes, reference genomes in each case were subsequently re-searched for matching gene IDs corresponding to each missing transcript. We subsequently surveyed between 10 to 20 missing genes manually through individual visualization of their loci on the UCSC genome browser to confirm the results. Matched transcript outputs from gffcompare, along with missing gene lists can be found in the associated source data files. approach was applied for comparison of RNA-seq outputs from V4.2 and V.3, except that LL gene ID was used. All corresponding NCBI, Ensembl, and LL gene IDs for RNA-seq output are included in the corresponding source data tables. To identify matching and missing genes between different annotations, we applied gffcompare (Pertea and Pertea, 2020), which provides a coordinate-based comparison of transcript intron/exon structure using GTF files as input. Comparison of 3’ UTR coverage between annotations Since our annotation comprises genes missing from both Ensembl and RefSeq annotations, as well as novel genes (see below), we assigned a unique identifier (prefix ‘LL’ followed by an arbitrary number) to each entry, which can be used as a common link for the relation between the gene information file and the resulting output from the GTF follow- ing its application in RNA-seq analysis. The GTF and gene information files for V4.2 and V4.3 are available at http://zf-transcriptome.umassmed.edu. Comparison of 3’ UTR coverage between annotations Further details are available upon request. Assembly of an improved zebrafish transcriptome annotation We downloaded 75 bp Paired-end stranded RNA-seq reads from embryos staged at 28hpf, 2dpf, 5dpf, bud, dome, and shield from GEO (Accession no.: GSE32898, Pauli et al., 2012). Reads were trimmed with Trimmomatic (adaptor removal, headcrop, and crop to retain position 10–50 bp only along with default quality trimming) and reads shorter than 32 bp after trimming were discarded. Trimmed reads were aligned to Danio rerio genome GRCz11 with GSNAP (Wu and Nacu, 2010) allowing 5% mismatches. Our anecdotal observations suggested a prevalence of incomplete and spurious partial transcripts in Ensembl. Therefore, the alignment was guided by splicing sites extracted from refseq_mRNA (GCF_000002035.6_GRCz11). We filtered alignment results so that 22 of 28 Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 Tools and resources Tools and resources Developmental Biology Developmental Biology only properly paired reads with MQ 30 and more than 35 bp of mapped regions were retained. An in-house perl script was used to add strand information and format the filtered alignment results (Source code 2). We used mapped reads to assemble transcript and gene models using Cufflinks and Cuffmerge (Trapnell et al., 2010). Preliminary versions of our transcriptome annotation (v1, v2) were used to identify parameters that optimally captured isoform diversity and 3’ UTR lengths. Ver- sion 3.1.2 (v3.1.2) used Cufflinks with the following parameters: -F 0.2 j 0.3 -a 0.0001 -A 0.4 –min- frags-per-transfragX20 –overhang-toleranceX20 –overlap-radius 50 -3-overhang-tol- erance 50 to assemble transcripts for samples from each embryonic stage. Cufflinks assembly for v3.1.2 was guided (using the -g argument in Cufflinks) by the most recently available zebrafish RefSeq annotation (GCF_000002035.6_GRCz11). We next integrated trans-fragments assembled by Cufflinks for each stage using Cuffmerge. We chose to use Ensembl annotations (version 95) to guide the integration of the transcript models generated above using Cuffmerge. At this step, we allowed low abundance transcripts to be retained in the final annotation (‘–min-isoform-frac- tion 0.00’). Initial gene nomenclature assignments were made using v3.1.2. For this purpose, all rel- evant matching gene information was extracted from the GTF output from Cuffmerge for v3.1.2 and used to assign gene information to transcript ID (TCONS) generated by Cufflinks. At this point, over 1000 gene symbol conflicts were identified by comparing assigned gene names for comparing RefSeq and Ens95 transcript IDs to those assigned by Cufflinks. Comparison of 3’ UTR coverage between annotations In many cases, these were due to spurious fusion transcripts linking adjacent genes. Therefore, we sought to remove these using a cus- tomized Python script (Source code 3). We also manually removed non-miRNA small RNAs. Given the nomenclature conflicts noted above, we utilized gffcompare to accurately import matched gene identifiers from RefSeq and a more recent Ensembl annotation (version 99, released January 2020). In cases where a perfect transcript match was not available, we subsequently compared gene coordi- nates to further confirm overlap; we include a qualitative description for each entry in this case for RefSeq and Ens99 matches in the V4.3 gene information file. In the course of investigating the nature of the nomenclature conflicts noted above, we also manually corrected several incorrect gene names assigned by Ensembl that resulted from persistent overlapping transcripts between two separate genes that evaded filtering noted above, causing a single gene ID to be assigned to two genes (see main text and Figure 3—source data 2). In these cases, spurious overlapping transcripts were removed to give V4.2. To identify any remaining Ensembl or RefSeq genes missing from V4.2, we performed pairwise comparisons with each annotation using gffcompare. The resulting missing genes were then manually added to give V4.3. Since our annotation comprises genes missing from both Ensembl and RefSeq annotations, as well as novel genes (see below), we assigned a unique identifier (prefix ‘LL’ followed by an arbitrary number) to each entry, which can be used as a common link for the relation between the gene information file and the resulting output from the GTF follow- ing its application in RNA-seq analysis. The GTF and gene information files for V4.2 and V4.3 are available at http://zf-transcriptome.umassmed.edu. only properly paired reads with MQ 30 and more than 35 bp of mapped regions were retained. An in-house perl script was used to add strand information and format the filtered alignment results (Source code 2). We used mapped reads to assemble transcript and gene models using Cufflinks and Cuffmerge (Trapnell et al., 2010). Preliminary versions of our transcriptome annotation (v1, v2) were used to identify parameters that optimally captured isoform diversity and 3’ UTR lengths. Ver- sion 3.1.2 (v3.1.2) used Cufflinks with the following parameters: -F 0.2 j 0.3 -a 0.0001 -A 0.4 –min- frags-per-transfragX20 –overhang-toleranceX20 –overlap-radius 50 -3-overhang-tol- erance 50 to assemble transcripts for samples from each embryonic stage. Comparison of 3’ UTR coverage between annotations Cufflinks assembly for v3.1.2 was guided (using the -g argument in Cufflinks) by the most recently available zebrafish RefSeq annotation (GCF_000002035.6_GRCz11). We next integrated trans-fragments assembled by Cufflinks for each stage using Cuffmerge. We chose to use Ensembl annotations (version 95) to guide the integration of the transcript models generated above using Cuffmerge. At this step, we allowed low abundance transcripts to be retained in the final annotation (‘–min-isoform-frac- tion 0.00’). Initial gene nomenclature assignments were made using v3.1.2. For this purpose, all rel- evant matching gene information was extracted from the GTF output from Cuffmerge for v3.1.2 and used to assign gene information to transcript ID (TCONS) generated by Cufflinks. At this point, over 1000 gene symbol conflicts were identified by comparing assigned gene names for comparing RefSeq and Ens95 transcript IDs to those assigned by Cufflinks. In many cases, these were due to spurious fusion transcripts linking adjacent genes. Therefore, we sought to remove these using a cus- tomized Python script (Source code 3). We also manually removed non-miRNA small RNAs. Given the nomenclature conflicts noted above, we utilized gffcompare to accurately import matched gene identifiers from RefSeq and a more recent Ensembl annotation (version 99, released January 2020). In cases where a perfect transcript match was not available, we subsequently compared gene coordi- nates to further confirm overlap; we include a qualitative description for each entry in this case for RefSeq and Ens99 matches in the V4.3 gene information file. In the course of investigating the nature of the nomenclature conflicts noted above, we also manually corrected several incorrect gene names assigned by Ensembl that resulted from persistent overlapping transcripts between two separate genes that evaded filtering noted above, causing a single gene ID to be assigned to two genes (see main text and Figure 3—source data 2). In these cases, spurious overlapping transcripts were removed to give V4.2. To identify any remaining Ensembl or RefSeq genes missing from V4.2, we performed pairwise comparisons with each annotation using gffcompare. The resulting missing genes were then manually added to give V4.3. Data access New raw datasets (pdgfrb:citrine and Nr2f2 RNA-seq), and associated processed data files, gener- ated for this manuscript, including the V4.3 GTF, are available at the Gene Expression Omnibus (GSE152759). All other raw datasets were otherwise obtained from GEO. Additional support files are available at http://zf-transcriptome.umassmed.edu. Additional information Funding Funder Grant reference number Author National Heart, Lung, and Blood Institute R35HL140017 Nathan D Lawson National Human Genome Re- search Institute U01HG007910 Onur Yukselen Alper Kucukural National Center for Advancing Translational Sciences UL1TR001453 Onur Yukselen Alper Kucukural National Institute of Neurolo- gical Disorders and Stroke R21NS105654 Nathan D Lawson The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. Acknowledgements We thank members of the UMass Med GHPCC group, including Lewis Robbins and Chris Hull for their support. We are also grateful to Yu-Huan Shih and William Frantz for their helpful comments on the manuscript. This work was supported by NIH R35HL140017 and R21NS105654 to N D L and U01HG007910 from NHGRI and National Center for Advancing Translational Sciences grant UL1 TR001453, which supported A K and O Y. Additional information Single-cell RNA-seq analysis Single-cell RNA-seq analysis We downloaded scRNA-seq reads from whole zebrafish embryos at five dpf from the Sequence Read Archive (SRR10095965, Farnsworth et al., 2020). Paired-end reads were split from this file using the SRA toolkit (https://github.com/ncbi/sra-tools; SRA Toolkit Development Team, 2020). We used Cell Ranger (10x Genomics, v3.1.0) in the DolphinNext environment (see above) for read mapping, filtering, and counting using default parameters. We ran Cell Ranger separately with the same set of reads and parameters for Ens95 and V4.2. Cell Ranger output files (barcodes, genes, and matrix files) were loaded into Seurat (v3.1, Stuart et al., 2019) for clustering, identification of differential genes, and visualization. All parameters and variables can be found in the accompanying R file (Source code 1). Seurat was run in RStudio through a web-based portal on the GHPCC using Open OnDemand (Hudak et al., 2018). Annotation of novel loci Our annotation yielded just over 6000 novel loci with no initial match to Ensembl or RefSeq genes. These are annotated using gene abbreviations with an ‘XLOC’ prefix assigned by cufflinks. To inves- tigate whether these represent new genes, we took several steps. First, we used transcript sequen- ces from each locus in blastx searches against zebrafish and human proteins. Second, we determined whether any overlapped previously long non-coding RNAs identified in previous studies. For this purpose, we used an integrated annotation published elsewhere that includes lincRNAs not found in Ensembl or RefSeq (Hu et al., 2018). This annotation was converted to a standard BED for- mat, lifted from Zv9 to GRCz10, then to GRCz11 and used to generate a GTF file. We used gffcom- pare with the lincRNA GTF file and a parallel file containing only XLOC V4.2 annotations to identify matching or overlapping transcripts. Finally, we determined exon numbers for each XLOC entry. In V4.2, all XLOC entries were maintained in the associated GTF and gene information files. For V4.3, we retained XLOCs that matched one of the following criteria: 1. exhibited exact, moderate, or high-confidence blast hits with a zebrafish or human protein, 2. exhibited matched or overlapping intron-exon structure with the lincRNAs noted above, or 3. comprised more than one exon. We also identified approximately 200 loci that exhibited complete overlap with existing RefSeq-annotated transcripts already present in V4.2. These redundant XLOC loci were also removed in the update to V4.3. Lawson et al. eLife 2020;9:e55792. DOI: https://doi.org/10.7554/eLife.55792 23 of 28 Tools and resources Developmental Biology Developmental Biology Ethics Animal experimentation: Zebrafish studies were performed in accordance with protocols #A2613 and #A2632 approved by the University of Massachusetts institutional animal care and use commit- tee (IACUC). Decision letter and Author response Decision letter and Author response Decision letter and Author response Decision letter https://doi.org/10.7554/eLife.55792.sa1 Author response https://doi.org/10.7554/eLife.55792.sa2 Decision letter and Author response Decision letter https://doi.org/10.7554/eLife.55792.sa1 Author response https://doi.org/10.7554/eLife.55792.sa2 Decision letter and Author response Decision letter https://doi.org/10.7554/eLife.55792.sa1 Author response https://doi.org/10.7554/eLife.55792.sa2 ec s o ette ttps //do o g/ 0 55 /e e 55 sa Author response https://doi.org/10.7554/eLife.55792.sa2 Additional files Supplementary files . Source code 1. List of R commands used to run Seurat for clustering Ens95 and V4.2. . Source code 2. Perl script used to add strand information and filter read GSNAP. . Source code 3. Python script to identify and remove spurious fusion trans . Source data 1. Zebrafish transcriptome annotation V4.2. Contains geno MB, md5sum:44c87a2bdd19ccfd9f7cd526f9e21498) and gene information .xlsx file). . Source data 2. Zebrafish transcriptome annotation V4.3.1. Contains gen MB, md5sum: 19759898187c47edfd9c216162851e31) and gene informat and .xlsx file). . Transparent reporting form Data availability All data generated in this study are available in accompanying source data tation files described in this study are available for download at http://zf- edu. Raw and processed RNA-seq data generated in this study are availab The following dataset was generated: Author(s) Year Dataset title Dataset URL Lawson ND 2020 Bulk RNA-seq data to assess an improved zebrafish transcriptome annotation https://www.ncbi.nl nih.gov/geo/query/ cgi?acc=GSE152759 The following previously published datasets were used: Author(s) Year Dataset title Dataset URL Whitesell TR, Chrystal PW, Ryu JR, Munsie N, Grosse A, French CR, Workentine ML, Li R, Zhu LJ, Waskiewicz A, Leh- mann OJ, Lawson ND, Childs SJ 2019 Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish https://www.ncbi.nl nih.gov/geo/query/ cgi?acc=GSE119718 Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Sandelin A, Rinn JL, Regev A, Schier AF 2011 Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis https://www.ncbi.nl nih.gov/geo/query/ cgi?acc=GSE32900 Author contributions Nathan D Lawson, Conceptualization, Data curation, Formal analysis, Supervision, Funding acquisi- tion, Validation, Investigation, Visualization, Methodology, Writing - original draft, Project adminis- tration, Writing - review and editing; Rui Li, Data curation, Software, Formal analysis, Methodology, Writing - review and editing; Masahiro Shin, Ann Grosse, Investigation, Methodology; Onur Yukse- len, Lihua Zhu, Resources, Software, Methodology, Writing - review and editing; Oliver A Stone, Resources; Alper Kucukural, Resources, Software, Visualization, Methodology, Writing - review and editing Author ORCIDs Nathan D Lawson https://orcid.org/0000-0001-7788-9619 Alper Kucukural http://orcid.org/0000-0001-9983-394X Author ORCIDs Nathan D Lawson https://orcid.org/0000-0001-7788-9619 Alper Kucukural http://orcid.org/0000-0001-9983-394X 24 of 28 Tools and resources Tools and resources Developmental Biology Developmental Biology Additional files . Source code 1. List of R commands used to run Seurat for clustering of data quantified using Ens95 and V4.2. . Source code 2. Perl script used to add strand information and filter reads in BAM file output from GSNAP. . Source code 3. Python script to identify and remove spurious fusion transcripts. . Source data 1. Zebrafish transcriptome annotation V4.2. Contains genomic annotation file (153.8 MB, md5sum:44c87a2bdd19ccfd9f7cd526f9e21498) and gene information (as tab-delimited file and .xlsx file). . Source data 2. Zebrafish transcriptome annotation V4.3.1. Contains genomic annotation file (152 MB, md5sum: 19759898187c47edfd9c216162851e31) and gene information (as tab-delimited file and .xlsx file). Data availability Data availability All data generated in this study are available in accompanying source data files. Transcriptome anno- tation files described in this study are available for download at http://zf-transcriptome.umassmed. edu. Raw and processed RNA-seq data generated in this study are available at GEO (GSE152759). The following dataset was generated: The following dataset was generated: Author(s) Year Dataset title Dataset URL Database and Identifier Lawson ND 2020 Bulk RNA-seq data to assess an improved zebrafish transcriptome annotation https://www.ncbi.nlm. nih.gov/geo/query/acc. cgi?acc=GSE152759 NCBI Gene Expression Omnibus, GSE152759 The following previously published datasets were used: Author(s) Year Dataset title Dataset URL Database and Identifier Whitesell TR, Chrystal PW, Ryu JR, Munsie N, Grosse A, French CR, Workentine ML, Li R, Zhu LJ, Waskiewicz A, Leh- mann OJ, Lawson ND, Childs SJ 2019 Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish https://www.ncbi.nlm. nih.gov/geo/query/acc. cgi?acc=GSE119718 NCBI Gene Expression Omnibus, GSE119718 Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Sandelin A, Rinn JL, Regev A, Schier AF 2011 Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis https://www.ncbi.nlm. nih.gov/geo/query/acc. cgi?acc=GSE32900 NCBI Gene Expression Omnibus, GSE32900 DOI: https://doi.org/10.7554/eLife.55792 25 of 28 The following dataset was generated: Author(s) Year Dataset title Dataset URL Database and Identifier Lawson ND 2020 Bulk RNA-seq data to assess an improved zebrafish transcriptome annotation https://www.ncbi.nlm. nih.gov/geo/query/acc. cgi?acc=GSE152759 NCBI Gene Expression Omnibus, GSE152759 Author(s) Year Dataset title Dataset URL Database and Identifier Whitesell TR, Chrystal PW, Ryu JR, Munsie N, Grosse A, French CR, Workentine ML, Li R, Zhu LJ, Waskiewicz A, Leh- mann OJ, Lawson ND, Childs SJ 2019 Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish https://www.ncbi.nlm. nih.gov/geo/query/acc. cgi?acc=GSE119718 NCBI Gene Expression Omnibus, GSE119718 Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Sandelin A, Rinn JL, Regev A, Schier AF 2011 Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis https://www.ncbi.nlm. nih.gov/geo/query/acc. cgi?acc=GSE32900 NCBI Gene Expression Omnibus, GSE32900 Lawson et al. eLife 2020;9:e55792. 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In Vitro Evaluation of Biomaterials for Vocal Fold Injection: A Systematic Review
Polymers
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  Citation: Wan-Chiew, N.; Baki, M.M.; Fauzi, M.B.; Lokanathan, Y.; Azman, M. In Vitro Evaluation of Biomaterials for Vocal Fold Injection: A Systematic Review. Polymers 2021, 13, 2619. https://doi.org/10.3390/polym13162619 Keywords: vocal fold augmentation; functional voice disorder; preliminary study; characterization; material Academic Editors: Rossella Dorati, Enrica Chiesa and Silvia Pisani Review In Vitro Evaluation of Biomaterials for Vocal Fold Injection: A Systematic Review Wan-Chiew 1 , Marina Mat Baki 1 , Mh Busra Fauzi 2 , Yogeswaran Lokanathan 2 Mawaddah A man 1,* Ng Wan-Chiew 1 , Marina Mat Baki 1 , Mh Busra Fauzi 2 , Yogeswaran Lokanathan 2 and Mawaddah Azman 1,* 1 Department of Otorhinolaryngology—Head and Neck Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; wanchiew1997@gmail.com (N.W.-C.); marinamatbaki@ppukm.ukm.edu.my (M.M.B.) 1 Department of Otorhinolaryngology—Head and Neck Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; wanchiew1997@gmail.com (N.W.-C.); marinamatbaki@ppukm.ukm.edu.my (M.M.B.) pp y 2 Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; fauzibusra@ukm lyoges@ppukm ukm edu my (YL ) 2 Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; fauzibusra@ukm.edu.my (M.B.F.); 2 Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; fauzibusra@ukm.edu.my (M.B.F.); lyoges@ppukm.ukm.edu.my (Y.L.) * Correspondence: mawaddah@ukm.edu.my * Correspondence: mawaddah@ukm.edu.my Abstract: Vocal fold injection is a preferred treatment in glottic insufficiency because it is relatively quick and cost-saving. However, researchers have yet to discover the ideal biomaterial with properties suitable for human vocal fold application. The current systematic review employing PRISMA guidelines summarizes and discusses the available evidence related to outcome measures used to characterize novel biomaterials in the development phase. The literature search of related articles published within January 2010 to March 2021 was conducted using Scopus, Web of Science (WoS), Google Scholar and PubMed databases. The search identified 6240 potentially relevant records, which were screened and appraised to include 15 relevant articles based on the inclusion and exclusion criteria. The current study highlights that the characterization methods were inconsistent throughout the different studies. While rheologic outcome measures (viscosity, elasticity and shear) were most widely utilized, there appear to be no target or reference values. Outcome measures such as cellular response and biodegradation should be prioritized as they could mitigate the clinical drawbacks of currently available biomaterials. The review suggests future studies to prioritize characterization of the viscoelasticity (to improve voice outcomes), inflammatory response (to reduce side effects) and biodegradation (to improve longevity) profiles of newly developed biomaterials. 1. Introduction The ECM in the vocal fold consists of collagen and elastin as the fibrous proteins proteoglycan and glycoprotein, as interstitial proteins. These proteins play vital roles in maintaining the viscoelasticity of the human vocal fold [17]. Elastin enables vocal fold tissue to possess elastic properties and is more abundant in the superficial parts of the lamina propria than its deeper layers [18]. On the other hand, collagen in the vocal fold functions as a mechanical support to withstand high-frequency vibration and stretching [13]. The abundance of collagen was found in the deep layer of the lamina propria. Due to its non-linear properties, it remains unclear whether current quantification methods used by recent studies suit the viscoelasticity of native vocal fold tissue. The vocal fold is very sensitive towards any intrusion. A previous study has ex- plained that airborne particulate matter significantly upregulated interleukin-6 (IL-6) and IL-1β which mounts a pro-inflammatory response. In addition, these particles could ini- tiate mitogen-activated protein kinase (MAPK) and necrosis factor kappa beta (NF-kB) pathways [19]. Furthermore, a recent clinical study reported that the most frequent compli- cation after vocal fold injection was inflammation at the injection site [20]. Activation of inflammation in the vocal fold increases fibrosis formation leading to vocal fold scarring, subsequently causing dysphonia [21,22]. Therefore, unregulated inflammatory response is shown to be an adverse event in the vocal fold. The molecules involved in the inflammatory response in the vocal fold have been extensively studied for at least a decade [23,24]. The consistency of studies in quantifying IL-1β, NF-kB, tumor necrosis factor-alpha (TNF- α), interferon-gamma (IFN-γ), transforming growth factor-beta (TGF-β), cyclooxygenase (COX2), HA and procollagen expression indicated that these molecules are closely related to inflammation in the vocal fold [25]. Inflammation starts with the accumulation of IL-1β, NF-kB and TNF-α, activating fibroblasts and promoting collagen deposition, leading to scar formation [24]. Multiple biomaterials have been used in vocal fold injections but only CaHA and autologous fat have a long duration without resorption [26]. However, application of CaHA imposed the risk of migration and granuloma formation [27]. Even though HA possesses the most favorable properties, its inconsistent resorption is the main drawback [28,29]. Well-developed biomaterials should be tolerated by the host immune system and non- antigenic surface receptors even after degradation [30,31]. More prolonged effects of injection and biocompatibility are the main desired outcomes in the development of future injectable biomaterials [32,33]. 1. Introduction Population-based studies among subjects over 60 years old or more reported up to 29% prevalence of vocal disorders, mainly from glottic insufficiency [1]. Incomplete closure of the vocal fold, namely glottic insufficiency, results in a breathy voice and risk of aspiration [2]. These symptoms are commonly caused by unilateral vocal fold paralysis or paresis and are mainly subsequent to surgery. The recurrent laryngeal nerve that supplies most intrinsic laryngeal muscles is at risk in surgeries of the thyroid gland, neck, trachea and esophagus [3]. Other risk factors include poor regeneration due to senescence, smoking and systemic disease [4]. Young recurrent laryngeal nerve (RLN) tissue appeared more elastic to strain, while adolescent RLN tissue was stiffer and tended to break with strain [5]. In treating glottic insufficiency, vocal fold injection is preferred as it is more cost-effective and time-saving [6,7]. Currently available biomaterials for vocal fold injection include bovine and porcine gelatin, carboxymethylcellulose, calcium hydroxylapatite (CaHA), autologous fat, collagen-based and hyaluronic acid (HA)-based hydrogels [8]. Vocal fold injection is also commonly performed concomitantly with nonselective laryngeal reinnervation [9]. Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). In developing a suitable biomaterial for vocal fold augmentation, the biochemical properties of the vocal fold need to be respected. This is because the intervention has the https://www.mdpi.com/journal/polymers Polymers 2021, 13, 2619. https://doi.org/10.3390/polym13162619 2 of 21 Polymers 2021, 13, 2619 2 of 21 potential to interrupt the microenvironment of the vocal fold, which eventually affects the quality of voice production [10]. Vocal folds are two bands of complex tissue that serve multiple roles, including respiration, voice production and airway protection [11]. The complex tissue consists of superficial and deep layers separated by the lamina propria [12]. Additionally, the lamina propria is further divided into three parts: (1) superficial, (2) inter- mediate and (3) deep layers [13]. The myoelastic-aerodynamic theory explains the unique characteristics of the vocal fold and the neuromuscular control that permits phonation [14]. The superomedial aspect of the superficial layer of the vocal fold is softer compared to its inferomedial surface [15]. The viscoelasticity of the vocal fold is primarily determined by the composition of the extracellular matrix (ECM) [16]. 1. Introduction Before further investigation up to in vivo and clinical study, the optimization stage of biomaterials is performed. However, the parameters to be assessed during preliminary study are not clear. Therefore, the myriad applications of biomaterials in glottic insufficiency research have been chosen for discussion in this review. A literature search was performed through electronic databases to identify characterization of biomaterials and in vitro studies performed on the application of biomaterials in acute and chronic glottic insufficiency. The objective of this review is to describe the outcome measures used to study the various physicomechanical characteristics of biomaterials developed for the vocal fold. Additionally, the review will provide insight on which aspects should be focused on in future studies. 3 of 21 Polymers 2021, 13, 2619 2.1. Search Strategy A systematic review of the literature was performed to determine relevant studies reporting the characterization of biomaterials and in vitro studies to test their applicability as vocal fold injections for the glottic insufficiency condition. The systematic review was structured based on PRISMA guidelines to ensure the quality and transparency of this review [34]. A total of four databases includes Scopus (Elsevier, Amsterdam, NH, The Netherlands), ISI Web of Science (WoS) (Clarivate Analytics, Philadephia, PA, USA), PubMed (National left for Biotechnology Information, NCBI, Bethesda, MD, USA) and Google Scholar (Mountain View, CA, USA) were used to search relevant articles within the last eleven years (from January 2010 to March 2021). The article searching process was guided by the focus question formulated using the PICO strategy whereby population (P) was laboratory study on biomaterials for vocal fold injection; intervention (I) was outcome measure used to characterize the biomaterials; comparison (C) with other biomaterials was not applicable; and outcome (O) was physicomechanical or cellular characteristics of the biomaterials studied. The searching process was performed by two independent reviewers. g p p y p The searching method was performed by two sets of keyword combinations: (1) bio- material* (to obtain biomaterial or biomaterials) or material* (to obtain material or materi- als) or regenerative therap*(to obtain regenerative therapy or regenerative therapies) or hyaluronic acid* (to obtain hyaluronic acid or hyaluronic acids) and (2) vocal fold injection* (to obtain vocal fold injection or vocal fold injections) or glottic insufficienc* (to obtain glottic insufficiency or glottic insufficiencies) or vocal fold medialization* (to obtain vocal fold medialization or vocal fold medializations) or vocal fold augmentation* (to obtain vocal fold augmentation or vocal fold augmentations). The search strategy was performed for all databases following summary in Table 1. Table 1. Search strategy for all databases. (*: to obtain both singular and plural forms of the search criterion). No. Terms 1 Biomaterial* 2 Material* 3 Regenerative therap* 4 Hyaluronic acid* 5 Vocal fold injection* 6 Glottic insufficienc* 7 Vocal fold medialization* 8 Vocal fold augmentation* 9 Or/1–4 10 Or/5–8 11 And/9 & 10 12 Line 11: Restrict to period: January 2010 to March 2021 Table 1. Search strategy for all databases. (*: to obtain both singular and plural forms of the search criterion). 2.3. Exclusion Criteria 2.3. Exclusion Criteria The exclusion criteria included all secondary literature and any original articles solely involving in vivo and clinical stage study, articles written or submitted in languages other than English and studies focused on developing biomaterials using biological elements such as cells, growth factors, genes and tissue components derived from animals. 2.4. Data Extraction and Management Articles were screened in three phases to fulfill part of this systematic review. The first step included screening of titles to remove titles that did not match the inclusion criteria. The second step included abstract screening of the remaining papers to further remove inappropriate articles based on the inclusion criteria. The last step included removing any papers that did not meet the inclusion criteria after full-text reading by two independent reviewers. This review could not be published on PROSPERO because it included in vitro studies. 2.2. Inclusion Criteria Due to limited resources for translation, only English articles were included. Original research articles discussing the effects of biomaterials used in injection laryngoplasty with the main priority of glottic insufficiency applications were chosen. The studies that involved different types of biomaterials were included in this review. Studies on the cells involved during healing in glottic insufficiency including fibroblasts, endothelial cells and macrophages were also included. 4 of 21 Polymers 2021, 13, 2619 2.5. Quality Assessment The review was conducted in a methodological approach using the critical appraisal instrument for systematic reviews [35]. The primary and secondary reviewers discussed each item in the appraisal instrument for each study included in this review. All studies included were considered acceptable to the aims of this review in terms of the specific study characteristics. A prior discussion between the independent reviewers was performed to determine what constitutes acceptable levels of information to allocate a positive appraisal compared with negative, or “unclear” responses. We utilized an appraisal instrument consisting of 11 questions where each question was answered with “yes”, “no” or “unclear”. 3.1. Searching Result 3.1. Searching Result 3.1. Searching Result Total of 6240 articles were identified as potentially relevant. The first screening removed a total of 6089 articles which were non-original articles, not written or submitted in English, were duplicates or had a title or abstract that did not fit the inclusion criteria. From the remaining 151 articles, reviewers read the full text and 136 articles were removed as the articles did not fulfill the inclusion criteria. After selection, total of 15 articles were chosen for reviewing. A flow chart of the article selection process is shown in Figure 1. Figure 1. PRISMA flow diagram. Figure 1. PRISMA flow diagram. 5 of 21 Polymers 2021, 13, 2619 3.2. Study Characteristics 3.2. Study Characteristics Among the selected articles, all articles included parameter in characterizing physi- comechanical properties of hydrogel. Total of 5 out of 15 studies involved cellular response study. Type of cells used for included in vitro study was listed in 3.5. Total of 7 out of 15 studies involved animal study but the data was not included as per exclusion criteria mentioned in 2.3. With that, the data were summarized into three different aspects includ- ing rheological properties, other characterization parameters such as pore size, particle size, injection force, swelling ratio, drug release test, morphology and gelation time and cellular response. All of the studies were published between January 2010 and March 2021. In general, ten studies aimed to develop new formulation of biomaterials [36–45]; three studies focused in improving or characterizing current biomaterials [46–48]; one study investigated the effect of the biomaterials toward inflammation [49]; three studies intended to improve fabrication methods in order to produce better biomaterials [36,46,50]. The bio- materials studied in the included articles were carbomer hydrogel, micronized dermal graft tissue, crosslinked HA, HA with gelatine hydrogel, CaHA, carboxymethylcellulose (CMC), bovine collagen, micronized alloderm (Cymetra) (Lifecell Corp, Branchburg, NJ, USA), HA gel, carboxylic and hydroxylic multi-walled functionalized carbon, unequal particle sized middle viscosity and low viscosity HA, Rofilan (Laborata es Filorga, Lisbonne, Paris, France),Radiesse (Merz, Franksville, WI, USA),Restylane (Galderma Laboratories, Fort Worth, TX, USA), dextran beads in HA microsphere (MP), polyethylene glycol-diamine (PEG) microparticles, gelatine methacrylate MP, HA methacrylate, semi-IPN MP, glycol chitosan hydrogel, pluronic F127 with collagen, HA with poly(ethylene glycol) diacry- late (PEGDA) crosslinkers, silk protein based in HA suspension, resilin-like-polypeptide hydrogel, PEG30 hydrogel and polydimethylsiloxane (PDMS) with polydopamine (PDA). 3.3. Rheological Properties The most frequent characterization of biomaterials for vocal fold injection is rheo- logical measurement; 14 out of 15 articles quantified this measurement with different rheometers and parameters. The outcome measures used include elastic shear modulus (G′), loss shear modulus (G′′), loss tangent (ξ), dynamic viscosity (η′), Young modulus (E′), strain sweep and shear storage modulus. The proportional relationship between G′ and G′′ with frequencies was investigated in most of the studies. Larger values of G′ compared to G′′ show that the biomaterials possess more elastic behavior than viscous properties. Two studies tested viscoelasticity of the biomaterials at high frequencies, up to 2000 Hz and 4000 Hz, whereas in other studies the tested range was 0.1 Hz to 250 Hz. Some of the studies tested in the range of 0.1 to 10 Hz because of the limitations of the instrument settings. Results of G′ and G′′ are dependent on the range of frequency, for instance Kazemirad et al. revealed that the outcome patterns of high and low frequency were consistent but with a greater magnitude in lower frequency range [40]. The strain (γ) used by the studies ranged from 0.01% to 2% but only one study applied up to 1000% to determine the limit of the linear viscoelastic regime [42]. The phonation threshold pressure (PTP) quantifies the minimum lung pressure needed to generate the desired voice. It is one of the aerodynamic measurements for the vocal fold. This measurement was used by a single study [36] in this review. The results are summarized in Table 2. Polymers 2021, 13, 2619 6 of 21 Table 2. Rheological study. Author, Year Type of Biomaterials Study Measure Outcome Summary of Results Conclusion 1. Klemuk et al., 2010 [36] 1. Carbomer hydrogel 2. Micronized dermal graft tissue 3. Crosslinked HA hydrogel 4. All biomaterials had stiffer properties compared to earlier studies, hence suggested for deep injection into the vocal fold but not into lamina propria. 3.3. Rheological Properties HA and gelatin crosslinked hydrogel (a) Rheology measurement by rotational (for 0.1 to 100 Hz) and piezoelectric rheometer (up to 2000 Hz): shear elastic (G′) and viscous moduli (G′′) (linear) (b) Pressure threshold projection (PTP) vocal fold length and frequency: (i) For males: 15.8 mm and 125 Hz (ii) For females: 10.63 mm, 200 Hz Shear elastic (G′) Mean values: 100 to 10,000 Pa Viscous moduli (G′′) Mean values: 10 to 5000 Pa Loss tangent (G′′/G′) in 100 to 1000 Hz Hylan B, Extracel and Cbmr: 0.08 to 0.66 (widest range) PTP value relative to nominal PTP value (0.283 kPa) Sample 2 had highest value (3× to 21×) and sample 4 had lowest value (0.01× to 0.05×) Crosslinked HA hydrogel, HA and gelatin crosslinked hydrogel and carbomer hydrogel are suitable for voice production. 2. Mahboubi, Mohraz & Verma 2016 [46] 1. CaHA 2. CMC (a) Viscosity modulus (η) by rotational rheometer (b) Shear elastic (G′) and loss moduli (G′′) with frequency sweeps at 0.01% strain and 0.1 to 200 Hz by oscillatory rheometer (linear) Viscosity CaHA (43,100 Pa.s) was 10 times more viscous than CMC (4540 Pa.s). Heating and shearing G′′ for CaHA reduced by 52% Heating and shearing potentially reduces viscosity of CaHA. 3. Kimura, Mau & W Chan 2010 [47] 1. 3% bovine collagen (atelocollagen) 2. micronized Alloderm 3. CaHA 4. 2.4% crosslinked HA gel (a) Elastic shear modulus (G′) tested with 0.3 to 0.5 mm gap size, 1 to 2% strain and 1 to 250 Hz. (b) Dynamic viscosity (n′) by custom build, controlled strain, linear simple shear rheometer system Elastic shear modulus (G′) Atelocollagen performed the nearest value (about 1000 Pa) to the vocal fold superficial layer′s value. Dynamic viscosity (η′) Atelocollagen performed the nearest value (about 0.7 Pa.s) to the vocal fold superficial layer′s value at around 135 Hz. All biomaterials had stiffer properties compared to earlier studies, hence suggested for deep injection into the vocal fold but not into lamina propria. 4. Ravanbakhsh et al., 2019 [37] 1. Carboxylic (COOH) multi-walled functionalized carbon nanotube (CNTs) 2. Hydroxylic (OH) multi-walled functionalized CNTs Storage modulus tested at 0.1 to 10 Hz and 1000 µm gap size, <5% shear strain by rotational rheometer (linear) Storage modulus* - Increased with higher CNT concentration - OH-CNT had higher storage modulus than COOH-CNT Mechanical strength of hydrogel was not influenced by the concentration of CNT. Heating and shearing potentially reduces viscosity of CaHA. 3.3. Rheological Properties Crosslinked HA hydrogel, HA and gelatin crosslinked hydrogel and carbomer hydrogel are suitable for voice production. Viscosity CaHA (43,100 Pa.s) was 10 times more viscous than CMC (4540 Pa.s). Heating and shearing G′′ for CaHA reduced by 52% 7 of 21 Polymers 2021, 13, 2619 Table 2. Cont. Author, Year Type of Biomaterials Study Measure Outcome Summary of Results Conclusion 5. Kim et al., 2015 [38] 1. Commercial HA 2. Unequal particle-sized middle viscosity HA (3,000,000 cP) 3. Unequal particle-sized low viscosity HA (30,000 cP) Elasticity at 0.02 Hz (not specified) Elasticity Commercial HA: 200 to 400 Pa Mid HA: 300 Pa Low HA: 3 Pa Unequal particle-size HA showed better outcomes than commercial HA in vivo. 6. Choi et al., 2012 [48] 1. Rofilan (non animal stabilized biomaterial) 2. Restylane (double crosslinked 3. Dextran beads in HA (dextran microspheres) (a) Shear viscosity (η) (b) Mean elastic modulus (G′) (c) Mean viscous modulus (G′′) at frequency of 0.1 to 10 Hz with strain controlled rheometer (linear) Steady state viscosity (η) Restylane had the highest (19.138 Pa·s) value. Mean elastic modulus (G′) Reviderm had the highest (464.1 Pa·s) value. Mean viscous modulus (G′′) Reviderm had the highest (167.8 Pa·s) value. All HA-based hydrogels had similar shear viscosities and the values were higher than reported human vocal fold but in vivo study showed that HA-based hydrogels were compatible with viscoelasticity of rabbit vocal fold. 7. Chan et al., 2014 [50] 1. PEG microparticles (MP) 2. Gelatin methacrylate MP 3. HA-methacrylate (HAMA) MP 4. Semi-IPN MP of HAMA & gelatine Shear storage modulus (G′) and shear loss modulus (G′′) at 0.6% strain by rotational rheometer (linear). Viscoelasticity for PEG-DA:PEG When the ratio of PEG-DA:PEG increased 50 to 100%, G′ increased from 523 Pa to 1599 a; G′′ increased from 38 Pa to 111 Pa Photopolymerization method was able to synthesize soft MP with varying stiffness which was independent of its size. 8. Coburn et al., 2020 [49] Glycol-chitosan hydrogel with different crosslinker concentrations: 0.005%, 0.01% and 0.02% Mechanical characterization at 0.1 to 100 rad/s by rotational rheometer (linear) Storage modulus (G′) and loss modulus (G′′) 0.005%: around 50 and 18 Pa 0.01%: around 340 and 17 Pa 0.02%: around 740 and 15 Pa G′ value > G′′: showing elastic property Hydrogel with higher stiffness potentially caused inflammation but delayed expression of IL-10 at 72 h caused higher macrophage apoptosis. 9. 3.3. Rheological Properties Fu et al., 2015 [39] Pluronic F127 with collagen of 1%, 2% and 3% (a) Storage modulus (b) Loss modulus Rheology measurement at 1.0 rad/s and 0.5% strain by rotational rheometer (linear) Elastic modulus (G′) at 1.0 rad/s Pluronic F127 with highest collagen (3%) exhibited lowest G′ (94.0 kPa). Viscous modulus (G′′) at 10 to 100 rad/s* Pluronic F127 with collagen did not reduce sharply compared to without collagen. Pluronic F127 with collagen enhanced the drug release time and favoured cell growth. Table 2. Cont. (a) Storage modulus (b) Loss modulus Rheology measurement at 1.0 rad/s and 0.5% strain by rotational rheometer (linear) Polymers 2021, 13, 2619 8 of 21 Table 2. Cont. Author, Year Type of Biomaterials Study Measure Outcome Summary of Results Conclusion . Kazemirad, Heris & Mongeau 16 [40] 1. Sample 1 to 3: 0.50%HA + crosslinker PEGDA of 0.25%, 0.5% & 1.0% 2. Sample 4 to 5: 0.45%HA + 0.05% gelatin (Ge) of 0.1% and 0.2% (a) Shear storage (G′) (b) Loss moduli (G′′) at frequency up to 4000 Hz (linear) Shear storage (G′) & Loss moduli (G′′) Sample 4 (G′: 19.61 Pa; G′′: 5.00 Pa) and 5 (G′: 12.24 Pa; G′′: 8.50 Pa) were comparable to viscoelasticity with human vocal fold. With optimized concentration of HA, Ge and crosslinker, the hydrogel showed comparable viscoelasticity. . Brown et al., 2019 [41] Silk protein-based in HA suspension Mechanical properties at 0.1 to 10.0 Hz and 1% strain by dynamic rotation shear rheometer (linear) Mechanical properties - Silk suspension increased stiffness less rapid (5× lesser) than CaHA-CMC - Injection of silk suspension (1.5 times) yield lesser stiffness in vocal fold than CaHA-CMC (4.0 times) Silk-HA had similar viscoelasticity properties with porcine vocal fold. . Li et al., 2018 [42] Chemically crosslinked resilin-like-polypeptide (RLP) hydrogel: 1. Sample 1: 10 wt% 2. Sample 2: 15 wt% (a) Shear storage modulus at 0.1 to 100 rad/s (b) Storage moduli (G′) and loss moduli (G′′) by stress controlled rheometer (c) strain sweep test of 0.01% to 1000% (linear) Shear storage modulus Sample 1 and 2 increased rapidly until 1000 Pa and 2000 Pa respectively Storage moduli (G′) and loss moduli (G′′) G′ was higher than G′′ for 100 to 200 fold. Strain sweep Sample 1: 265% Sample 2: 245% High resistance to break. Rheological properties of the hydrogels were in the range of native vocal fold tissue. . 3.3. Rheological Properties Pruett et al., 2020 [44] Fabrication of microporous annealed particle (MAP) by water-in-oil emulsion Young’s modulus (linear), compare with vocalis muscle Young’s modulus 1.9 wt% MAP showed with porcine vocal fold’s muscle comparable (~15,000 Pa). MAP gel exhibited similar rheological properties with porcine vocal fold tissue. . Karajanagi et al., 2011 [45] PEG30 hydrogel Elastic shear properties (G′) from 1 to 10 Hz with 0.6% strain by rotational rheometer (linear) Viscoelasticity* PEG30 showed softer hydrogel compared to value reported in literature review. PEG30 demonstrated optimal physical properties for vocal fold injection. Remarks: Result with * indicated no reported value. Table 2. Cont. Rheological properties of the hydrogels were in the range of native vocal fold tissue. Polymers 2021, 13, 2619 9 of 21 3.4. Other Characterization Parameters 3.4. Other Characterization Parameters 3.4. Other Characterization Parameters Other than the mechanical properties of the biomaterials, different features were tested to further support the feasibility of these biomaterials for vocal fold injection. A total of seven different tests were carried out. The most frequent tests include particle and pore size quantification [37,38,41,43,50]. Injection force was only measured by two studies in this review [41,50]. Swelling ratio [37,38] and drug release tests [39,50] were performed in two studies, while morphology and gelation time were only carried out by single study [37]. The results are summarized in Table 3. Polymers 2021, 13, 2619 10 of 21 Table 3. Other characterization parameters. Author, Year Type of Biomaterials Study Measure Outcome Summary of Results Conclusion . Ravanbakhsh et al., 2019 [37] 1. Carboxylic (COOH) multi-walled functionalized CNTs 2. Hydroxylic (OH) multi-walled functionalized CNTs (a) Morphology (b) Pore size (c) Swelling ratio (d) Gelation time Pore size Diameter of CNTs: 45 ± 5 nm Increased by 33% with increased concentration of COOT-CNT but not significant in OH-CNT. Swelling ratio Increased by 5% with increased COOT-CNT concentration. OH-CNT had no effect on this property. Gelation time* Increased starting 750 µg/mL of CNT COOH-CNT hydrogel showed larger pore size which might enhance cell migration. 2. Kim et al., 2015 [38] 1. Commercial HA (Restylane) 2. Unequal particle-sized middle viscosity HA 3. Unequal particle-sized low viscosity HA (a) Particle size (b) Swelling ratio Particle size Restylane: 200 µm Mid HA: 300 to 500 µm Low HA: No size Swelling ratio Restylane: 100 to 200% Mid HA: 130% Low HA: 200% Unequal particle-size HA showed better outcomes than Restylane® in vivo. 3. Chan et al., 2014 [50] 1. PEG MP 2. Gelatin methacrylate MP 3. HA-methacrylate (HAMA) MP 4. Semi-IPN MP of HAMA & gelatin (a) Particle size (b) Drug release test Ability to inject Can be injected through 22 gauge needle Particle size (D90) Range from 136 µm to 162 µm MP produced had uniform particle distribution with ~1.5 polydispersity (PDI). Increased stirring speed up to 600 rpm or surfactant reduced the size from 515 to 140 µm. Drug release test* Drug encapsulation and release in PEG NS/MP was lower than from NS alone. Higher stirring speed and surfactant concentration reduced size of MP and drug release time. Table 3. Other characterization parameters. COOH-CNT hydrogel showed larger pore size which might enhance cell migration. Remarks: result with * indicates no reported value. 3.4. Other Characterization Parameters Unequal particle-size HA showed better outcomes than Restylane® in vivo. Higher stirring speed and surfactant concentration reduced size of MP and drug release time. 11 of 21 Polymers 2021, 13, 2619 Table 3. Cont. Author, Year Type of Biomaterials Study Measure Outcome Summary of Results Conclusion 4. Fu et al., 2015 [39] 1. Pluronic F127 with collagen of 1%, 2% and 3% (a) Morphology (b) Drug release test Pore size With increased concentration of collagen incorporated in Pluronic F127, pore size was increased (from 5–20 µm to 20–40 µm). Drug release Collagen incorporated in Pluronic F127 reduced drug (ofloxacin) release (43.6% to 48.1%). Pluronic F127 with collagen enhanced the drug release time and favoured cell growth. 5. Brown et al., 2019 [41] Silk protein-based in HA suspension (a) Pore size (b) Injection force through 24 G long needle and 50 cm catheter with 1.05 mm inner diameter at 13 mm/min speed Pore size Diameter ranging 10 to 100 um and had ability to return into original shape after compression. Injection force Silk protein (34.9 N) needed less force than CaHA-CMC (51.4 N) as control. Particle size of silk-HA allowed macrophage passage, tissue adherence and was biocompatible. 6. Chung et al., 2017 [43] PDMScoated with PDA (a) Particle size (b) Morphology Particle size 79.23 µm ± 2.23 with 2.81% coefficient of variation. (less than 5% showed highly uniform size distribution) Morphology PDMS microsphere with PDA had a rougher surface while without PDA had a smoother surface. PDMS was injectable, non-absorbable and showed better cell adherence. Remarks: result with * indicates no reported value. Table 3. Cont. Pluronic F127 with collagen enhanced the drug release time and favoured cell growth. Particle size of silk-HA allowed macrophage passage, tissue adherence and was biocompatible. PDMS was injectable, non-absorbable and showed better cell adherence. 12 of 21 Polymers 2021, 13, 2619 12 of 21 3.5. Cellular Response To further identify suitable biomaterials, in vitro studies must include evaluations to elucidate the cellular response when integrated with the biomaterials. In vitro outcomes measured in this review included cell adhesion [43], cell viability/compatibility [37,39,50], cell phenotyping [49] and production of cytokines [49]. Among the types of cell used were human vocal fold fibroblasts (HVFF), NIH/3T3 cells, macrophages, vocal fold fi- broblasts (VFF), Hacat cells and mouse NIH-3T3 embryonic fibroblasts. Ravanbakhsh and co-researchers suggested a cell viability threshold of 70% [37]. However, Fu and co- researchers compared cell viability between the sets and control to quantify the cytotoxicity level of the biomaterials [39]. An interesting in vitro study by Coburn and co-researchers quantified the response of macrophages when cultivated with hydrogel and vocal fold fibroblasts [49]. The results are summarized in Table 4. 13 of 21 Polymers 2021, 13, 2619 Table 4. In vitro study. Author, Year Type of Biomaterials Study Measure Outcome Summary of Results Conclusion nbakhsh et al., ] 1. Carboxylic (COOH) multi-walled functionalized CNTs 2. Hydroxylic (OH) multi-walled functionalized CNTs Cell viability of HVFF Cell viability 1. COOH-CNT up to 750 ug/mL; 2. OH-CNT up to 1250 ug/mL as the cytotoxicity level increased after this threshold. COOH-CNT had higher cytotoxicity than OH-CNT et al., 2014 [50] 1. PEG MP 2. Gelatin methacrylate MP 3. HA-methacrylate (HAMA) MP 4. Semi-IPN MP of HAMA & gelatin Cytocompatibility test on NIH/3T3 cells Cytocompatibility test 0.1 to 50 mg/mL PEG50 culture resulted in cell viability of 80%. Hydrogel produced by photopolymerization was cytocompatible. rn et al., 2020 [49] Glycol-chitosan hydrogel with concentration: 1. 0.005% 2. 0.01% 3. 0.02% (a) Production of cytokines by macrophage (b) Macrophage viability (c) Macrophage phenotyping: -CD11b (+) CD33/CD80:proinflammatory CD33/CD206:anti-inflammatory Production of cytokines TNF-α and IL-10 increased in hydrogel culture and with increased stiffness of hydrogel. Cell viability Macrophage viability was reduced in hydrogel culture. Cell phenotyping More CD33/CD206 (anti-inflammatory) expressing macrophage in macrophage+ VFF+hydrogel than macrophage+hydrogel. Hydrogel with higher stiffness potentially caused inflammation but delayed expression of IL-10 at 72 h caused higher macrophage apoptosis. al., 2015 [39] Pluronic F127 with collagen of 1%, 2% and 3% Cell viability (Hacat cells) Cell viability Collagen incorporated in Pluronic F127 improved cell adhesion and viability. Pluronic F127 loaded with collagen improved cell adhesion and viability. 4. Discussion Even with the recent advances in regenerative therapy, no treatment is able to re- constitute a paralyzed vocal fold. Therefore, researchers have widely studied alternative biomaterials to reconstruct the physical properties of the vocal fold [51]. Since the viscoelas- ticity of the vocal fold is closely related to the efficiency of phonation, it is a primary concern when developing injectable biomaterials for vocal fold augmentation. Furthermore, studies showed that different stiffnesses of hydrogel would have different impacts on microenvi- ronmental responses such as cell adhesion and proliferation [52,53]. Therefore, the rheology study of injectable biomaterial is vital to understand its deformation (elasticity) and flow of matter (viscosity) [54]. Up to date, no reference study is able to quantify the viscoelasticity of human vocal folds precisely. This is because the viscoelasticity of the vocal fold is influenced by many factors such as age, gender, hydration level, disease status such as laryngeal nerve paralysis, mass lesions and fibrosis [55,56]. There are two ways to quantify the viscoelasticity of the vocal fold: linear and non-linear measurement. Linear measurement has been used widely and it is characterized by shear rheology which mainly is divided into two types: (1) rotational rheometry and (2) linear skin rheometry (LSR) [57]. Studies suggested that rotational rheometry generates more consistent results than LSR with 1% strain. Most of the studies in this review used linear methods to quantify viscoelasticity. Across the studies, various frequencies and strain rates were used, hence direct comparisons between the results were hard to perform. Torsional wave experiment (TWE) was suggested to quantify the linear behavior of viscoelasticity as it can overcome sample inertia at higher frequencies [58]. It is recommended to include phonation frequency by humans as conducted in the study by Kazemirad et al. [59]. The tested frequencies were in the range of 110 Hz to 260 Hz and 220 to 440 Hz for males and females, respectively. The current literature review did not provide a consistent range for the viscoelasticity value of the native vocal fold. For instance, Goodyer et al. suggested a value for males of 246 Pa to 3536 Pa and for females of 286 Pa to 3332 Pa by using the simple shear model method [55]. 3.5. Cellular Response g et al., 2017 [43] PDMS PDA Cell adhesion test (mouse NIH-3T3 embryonic fibroblast) Cell adhesion test PDMS microsphere with PDA had more cells attached on its surface. PDMS with PDA demonstrated better cell adherence. Table 4. In vitro study. 14 of 21 Polymers 2021, 13, 2619 14 of 21 4. Discussion However, another study has refuted this [15], suggesting the viscoelasticity of the human vocal fold superficial layer was 5.0 kPa (ranging from 4.7 to 5.4 kPa) for the superior medial and 7.0 kPa (ranging from 6.7 to 7.3 kPa) for the inferior medial surface. Recently, the inaccuracy of linear measurement was raised, and non-linear measurement was proposed [60]. This study demonstrated the non-linearity properties of the human vocal fold cover and ligament at a high strain of 0.5 (50%) with frequencies of 175 Hz and 125 Hz [60]. Tissues in this biological system, which consists of different compositions with distinct densities and topologies, appear to be the main obstacle in developing a suitable biomaterial for the vocal fold [61]. Therefore, this review prompts the need to provide significant values of vocal fold viscoelasticity across reported studies by statistical justification. Moreover, most of the studies tested the mechanical properties of biomaterials using linear measurement, which may not reflect their similarities with the native vocal fold. Inconsistency of testing parameters across studies highlights the insufficiency of the benchmark and established guidelines in developing a suitable biomaterial with desirable viscoelastic properties. p p Even though injectable biomaterials for vocal fold augmentation possess desired viscoelasticity, inflammation is a main concern as foreign body reaction could lead to serious complications such as airway edema [62]. Moreover, rare hypersensitivity cases occurred after injection of bovine collagen which can lead to more severe onset symptoms and require medical attention for a longer period [63]. Not to mention that a previously well-known injectable biomaterial, Teflon (Du Pont, Wilmington, DE, USA), resulted in granuloma formation [64]. Granuloma formation is closely associated with chronic inflammatory response [65]. HA is widely used nowadays, but an unusual allergy response has been observed [66]. Therefore, preliminary data on cell immune response is much needed when evaluating a biomaterial in an in vitro study. The vocal fold consists of fibroblasts which have been proven to be closely associated with inflammatory response [67]. Inflammation Polymers 2021, 13, 2619 15 of 21 15 of 21 in vocal fold is one of the pathological factors leading to vocal fold scarring [68]. As biomaterials are injected into the biological system, immune cells such as leukocytes detect them as foreign particles. The different chemistry and exterior characteristics of hosts can trigger an immune response [69]. 4. Discussion During this immune response, pro-inflammatory cytokines such as TNF-α, IL-6, IL-8, IL-1β and MCP-1 will be liberated whereas anti- inflammatory cytokines such as IL-10 and IL-12 play crucial roles in quantifying the efficiency of eliminating harmful materials while providing protection to host [67,70]. During wound repair in the vocal fold, increased pro-inflammatory cytokines IL-1β and IL-6 by neutrophils and macrophages promote fibrosis. However, the anti-inflammatory cytokine, IL-10 could have the potential to dampen the inflammation [71]. Nevertheless, this review shows that only a single study has explained inflammatory responses when developing biomaterials [49]. This test is suggested to be included for future research to elucidate molecular mechanisms of inflammation when a novel biomaterial is developed for tissue regeneration. Both pro- and anti-inflammatory responses should be quantified to ensure the balanced inflammatory response after injection of biomaterial. Apart from the above-mentioned tests, biomaterials with no migration and low resorp- tion are keys to determine practicality for injection application in the clinic [72]. Injection of HA was observed to have low complication rates between 3 and 5%, mainly from inflammatory reactions [66,73]. This response might be due to foreign body reaction or con- tamination during the injection process. Biodegradation is explained when disintegration of biomaterial occurs in the biological system [74]. Clinical measurement of biodegradation can be achieved by resorption rate of the biomaterial [75]. Current commercial biomaterials are divided into two categories, short term and long term injectates [76]. Bovine-based gelatin and collagen products, human-based collagen, HA and carboxymethylcellulose have temporary effects whereas calcium hydroxyapatite (CaHA), Teflon (Du Pont, Wilm- ington, DE, USA), autologous fat and polydimethylsiloxane possess longer augmentation effects. Occasionally, clinicians opt for temporary augmentation aiming for natural recov- ery and reducing the need for medialization laryngoplasty [77]. Temporary augmentation is also recommended during the wait of reinnervation period [78,79]. However, clinical studies have suggested 15% to 20% over injection of short-term biomaterial to counter resorption, especially of water-based gels [80]. Biodegradation can be quantified by using hydrolysis by enzymes such as lysozyme and collagenase in certain natural materials such as chitosan, gelatin and alginate [81–83]. Nevertheless, none of the reviewed articles include biodegradation tests. Hence, this review suggests a degradation test as prolonged degradation rates of biomaterials could positively influence local cellular activities [84]. Further investigation of the composition after degradation should be carried out to study the cytotoxicity effect [85]. 4. Discussion Accordingly, the end-products after degradation should be elucidated to provide evidence of background study during the initial stage of biomaterials development, specifically during in vitro studies. This could assist in providing strong evidence for future investigation such as in vivo and clinical studies. g Other characterization could be carried out depending on the specific requirements of hydrogel. The time taken for the hydrogel to polymerize should be optimized and 20 min was recommended by Ravanbaksh et al. [37]. Short gelation time could prevent destabilized gel washout from the desired location. On the other hand, it could result in insufficient injection time for clinicians [85,86]. A previous study reported that swelling ratio influenced the regulation of chondrocyte [87]. Thomas et al. conducted a swelling ratio test to determine the stability of the biomaterial to remain its original state when immersed in excess fluid as a simulation of the biological environment [53]. The porosity of biomaterials influenced the effectiveness of substances’ migration and mechanical properties. Therefore, fine-tuning between porosity and mechanical properties is needed to obtain effective biomaterials [88]. Homogeneous distribution of pore size has been shown to reduce cell interaction with the scaffold [89]. Among the biomaterials included in this review, some had been studied in clinical stages including micronized alloderm (Cymetra) (Lifecell Corp, Branchburg, NJ, USA) Polymers 2021, 13, 2619 16 of 21 16 of 21 HA, CMC, collagen, Rofilan (Laborata es Filorga, Lisbonne, Paris, France), Radiesse (Merz, Franksville, WI, USA) and Restylane (Galderma Laboratories, Fort Worth, TX, USA) [27,29,66,90–94]. It is vita l to refer to the outcome of the clinical studies, so that future study can address the suggested drawbacks of these biomaterials. The drawbacks included: (1) inconvenient preparation steps and the need for over-injection for Cymetra (Lifecell Corp, Branchburg, NJ, USA) [90]; (2) inflammatory reaction and a lack of long- lasting effect in application of HA [29,66,94]. CMC and collagen had similar issues, making them suitable only for short term augmentation [91,92] and lastly (3) Rofilan (Laborata es Filorga, Lisbonne, Paris, France) was reported to show no improvement in voice acous- tic analysis such as noise to harmonic ratio [93]. With that, this review suggests future study ought to include parameters that can address the limitations of these current bio- materials mainly with respect to longevity, inflammatory properties and viscoelasticity of biomaterials. The findings from this review are limited by potential bias. 4. Discussion In this study, only in vitro study was chosen as an inclusion criterion, leading to narrower results. Justification of this criterion is that this study aims to illuminate the importance of the initial stage of biomaterial development. Secondly, due to lack of facility to translate foreign languages, non-English literatures were excluded from this study. In addition, grey literature articles were also not evaluated in this work. We have, however, attempted to exclude duplicate ar- ticles in this review. To enhance the outcome of this review, statistical analysis is suggested for future evaluation. However, in vitro study should be a strong molecular support when exploring a higher level of studies. Abbreviations CaHA Calcium Hydroxypatite CMC Carboxymethylcellulose CNTs Carbon nanotube COOH Carboxylic COX2 Cyclooxygenase ECM Extracellular matrix HA Hyaluronic acid HAMA HA-methacrylate MP HVFF Human vocal fold fibroblast IL-1β Interleukin-1 beta IFN-γ Interferon-gamma LSR Linear skin rheometry MAP Microporous annealed particle MAPK Mitogen-activated protein kinase MCP-1 Monocyte chemoattractant protein-1 MP Microparticles NF-kB Necrosis factor kappa beta OH Hydroxylic PDA Polydopamine PDMS Poly(dimethysiloxane) microspheres PEG Polyethylene glycol-diamine PEGDA Poly(ethylene glycol) diacrylate PTP Phonation threshold pressure RLN Recurrent laryngeal nerve RLP Resilin-like-polypeptide TGF-β Transforming growth factor-beta TNF-α Tumor necrosis factor-alpha TWE Torsional wave experiment 5. Conclusions In conclusion, there is a lack of benchmarks to standardize the evaluation of novel biomaterials for vocal fold injection. After summarizing the studies included in this review and comparing the study outcome measures used with available clinical outcomes, it is suggested to prioritize characterization of the viscoelasticity (to improve voice outcomes), inflammatory response (to reduce side effects) and biodegradation (to improve longevity) profiles of biomaterials. Even though results generated by in vitro studies may not be con- sistent with outcomes seen in in vivo and clinical studies, it should provide a fundamental insight to consider the suitability of biomaterials for further study. If the outcomes of both in vitro and in vivo studies support each other, it could strengthen conviction and provide strong evidence for pre-clinical studies. Author Contributions: Conceptualization, N.W.-C., M.M.B., M.B.F., Y.L. and M.A.; methodology, N.W.-C., M.A. and M.B.F.; validation, M.M.B., M.B.F., Y.L. and M.A.; formal analysis, N.W.-C.; investigation, N.W.-C., M.A. and Y.L.; data curation, N.W.-C., M.A. and Y.L.; writing—original draft preparation, N.W.-C.; writing—review and editing, M.M.B., M.B.F., Y.L. and M.A.; visualization, N.W.- C., M.M.B., M.B.F., Y.L. and M.A; supervision, M.M.B., M.B.F., Y.L. and M.A.; project administration, M.B.F. and M.A.; funding acquisition, Y.L. and M.A. All authors have read and agreed to the published version of the manuscript. Funding: This research was funded by Minister of Higher Education (MOHE) Fundamental Research Grant Scheme (FGRS), grant number FRGS/1/2020/SKK06/UKM/01/1. Institutional Review Board Statement: The study was conducted according to the ethical guidelines underpinned by right-based theories, whereby it adheres to the principles of beneficence, non- maleficence, justice, honesty and gratitude. The study was approved by the Institutional Review Board (or Ethics Committee) of UNIVERSITI KEBANGSAAN MALAYSIA (protocol code FF-2020-818 on 3 February 2020). Informed Consent Statement: Informed consent was not necessary since this study included only secondary data, with no identifiable subjects. Data Availability Statement: Data sharing is not applicable to this article as no new data were created or analyzed in this study. 17 of 21 Polymers 2021, 13, 2619 17 of 21 Acknowledgments: We would like to thank the Otorhinolaryngology Head and Neck Surgery department, Tissue Engineering Centre and Faculty of Medicine UKM for providing resources to complete this review. This review was not be published on PROSPERO because it included in vitro studies. 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Graph Theoretical Analysis of Functional Brain Networks: Test-Retest Evaluation on Short- and Long-Term Resting-State Functional MRI Data
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Abstract 7102090) and the Scientific Research Foundation for the Returned Overseas Chinese Scholars (State Education Ministry). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: yong.he@bnu.edu.cn Abstract Graph-based computational network analysis has proven a powerful tool to quantitatively characterize functional architectures of the brain. However, the test-retest (TRT) reliability of graph metrics of functional networks has not been systematically examined. Here, we investigated TRT reliability of topological metrics of functional brain networks derived from resting-state functional magnetic resonance imaging data. Specifically, we evaluated both short-term (,1 hour apart) and long-term (.5 months apart) TRT reliability for 12 global and 6 local nodal network metrics. We found that reliability of global network metrics was overall low, threshold-sensitive and dependent on several factors of scanning time interval (TI, long-term.short-term), network membership (NM, networks excluding negative correlations.networks including negative correlations) and network type (NT, binarized networks.weighted networks). The dependence was modulated by another factor of node definition (ND) strategy. The local nodal reliability exhibited large variability across nodal metrics and a spatially heterogeneous distribution. Nodal degree was the most reliable metric and varied the least across the factors above. Hub regions in association and limbic/paralimbic cortices showed moderate TRT reliability. Importantly, nodal reliability was robust to above-mentioned four factors. Simulation analysis revealed that global network metrics were extremely sensitive (but varying degrees) to noise in functional connectivity and weighted networks generated numerically more reliable results in compared with binarized networks. For nodal network metrics, they showed high resistance to noise in functional connectivity and no NT related differences were found in the resistance. These findings provide important implications on how to choose reliable analytical schemes and network metrics of interest. Citation: Wang J-H, Zuo X-N, Gohel S, Milham MP, Biswal BB, et al. (2011) Graph Theoretical Analysis of Functional Brain Networks: Test-Retest Evaluation on Short- and Long-Term Resting-State Functional MRI Data. PLoS ONE 6(7): e21976. doi:10.1371/journal.pone.0021976 Editor: Marcus Kaiser, Newcastle University, United Kingdom Received February 25, 2011; Accepted June 14, 2011; Published July 19, 2011 ng et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits tion, and reproduction in any medium, provided the original author and source are credited. pyright:  2011 Wang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution L restricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by the Natural Science Foundation of China (Grant Nos. 81030028 and 30870667), Beijing Natural Science Foundation (Grant No. Graph Theoretical Analysis of Functional Brain Networks: Test-Retest Evaluation on Short- and Long-Term Resting- State Functional MRI Data ian Zuo2,3, Suril Gohel4, Michael P. Milham3, Bharat B. Biswal4, Yong He1* 1 State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China, 2 Laboratory for Functional Connectome and Development, Key Laboratory of Behavioral Science, Institute of Psychology, Chinese Academy of Sciences, Beijing, China, 3 Phyllis Green and Randolph Co¯wen Institute for Pediatric Neuroscience, New York University Langone Medical Center, New York, New York, United States of America, 4 Department of Radiology, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America Citation: Wang J-H, Zuo X-N, Gohel S, Milham MP, Biswal BB, et al. (2011) Graph Theoretical Analysis of Functional Brain Networks: Test-Retest Evaluation on Short- and Long-Term Resting-State Functional MRI Data. PLoS ONE 6(7): e21976. doi:10.1371/journal.pone.0021976 Introduction Abbreviation Full name Explanation TI Scanning time interval Short-term: ,1 hour apart Long-term: .5 months apart NM Network membership Network (+): only positive correlations Network (+/-): both positive and negative correlations NT Network type Binarized: binarized network Weighted: weighted network ND Node definition S-: Structural ROIs F-: Functional ROIs S-AAL Structural Anatomical Automatic Labeling atlas This atlas includes 90 regions S-HOA Structural Harvard-Oxford atlas This atlas includes 112 regions F-DOS Functional ROIs from ref (40) This set of ROIs includes 160 regions doi:10.1371/journal.pone.0021976.t001 doi:10.1371/journal.pone.0021976.t001 fMRI data during an executive task and demonstrated excellent reproducibility for both small-world properties and network efficiency metrics. Despite these progresses, however, the TRT reliability of network metrics derived from resting-state fMRI (R- fMRI) dataset has not been well documented so far. interregional functional connectivity is dynamic in time (from seconds to minutes) and frequency domains [18] and can be modulated by the levels of current conscious awareness [19,20,21,22], emotional state [23] and cognitive demand prior to resting-state scanning [24,25,26]. Using R-fMRI, Shehzad et al. [27] have demonstrated modest to good TRT reliability for some specific functional connections. However, these states or experi- ments related alterations in functional connectivity may further interact with the global network topology [28]. To our best knowledge, there are no studies to systematically examine the R–fMRI is a promising tool to non-invasively map intrinsic functional connectivity patterns of the human brain in vivo [2,14,15,16] and has been extensively used to investigate inherent brain network topological organization (for a review, see [17]). Of note, several previous R-fMRI studies suggest that the strength of Table 2. Brief descriptions of complex network metrics examined in the present study. Introduction While graph theoretical approaches provide valuable insights into normal brain architecture and pathological mechanism for brain disorders, the test-retest reliability has not been systemati- cally investigated. Reliable measures are fundamental to infer trustworthy conclusions and to serve as potential clinical biomarkers. In response to the demand, several groups examined the TRT reliability/reproducibility of graph network metrics. In anatomical world, Vaessen et al. [10] assessed the reproducibility of anatomical brain networks derived from DTI data and reported high inter-scan reproducibility of network metrics across sampling schemes (e.g., number of gradient directions and gradient amplitude). Bassett et al. [11] demonstrated high reproducibility and low variability of graph metrics for both DTI and diffusion spectrum imaging data derived networks. As for functional imaging arena, Deuker et al. [12] investigated the TRT reliability of functional brain networks using MEG data and reported high reliability during a working memory task but relatively low under resting condition for network metrics. More recently, Telesford et al. [13] constructed functional brain networks using baseline The human brain is a highly complex system represented as a structurally interconnected network by a dense of cortico-cortical axonal pathways (i.e., structural connectome, [1]) and a functionally synchronized network by external or intrinsic coherent neural activity (i.e., functional connectome, [2]). Mapping the brain connectome and highlighting the underlying organizational princi- ples are fundamental for our understanding of the brain architecture. Recent studies have manifested that human brain connectome networks can be constructed using neuroimaging (e.g., functional MRI (fMRI) and diffusion tensor imaging (DTI)) or electrophysiological (e.g., electroencephalography (EEG) and mag- netoencephalography (MEG)) data and further investigated by graph theoretical approaches. These brain networks have consis- tently demonstrated many non-trivial topological properties, such as small-worldness, modularity and highly connected hubs (for reviews, see [3,4,5,6,7]), and exhibited distinct alterations associated with different neurocognitive disorders (for reviews, see [8,9]). PLoS ONE | www.plosone.or PLoS ONE | www.plosone.org 1 July 2011 | Volume 6 | Issue 7 | e21976 Reliability of Brain Functional Networks Table 1. Brief descriptions of several specific acronyms used in the present study. Table 1. Brief descriptions of several specific acronyms used in the present study. Note that the formulas listed here are only for binarized networks. For details for weighted networks, see Text S1. 1First-order network metrics which are dependent on only one graph property. 2Second-order network metrics which are dependent on more than one property or are defined as rations of one property. doi:10.1371/journal.pone.0021976.t002 Introduction Parameter Character Descriptions Regional nodal parameters 1Degree ki The number of connections linked directly to a node 1Efficiency ei How efficient an index node communicates with the other nodes 2Betweenness bi The influences of an index node over information flow between other nodes 1Clustering coefficient ci The extent of interconnectivity among the neighbors of an index node 2Participant coefficient pi The ability of an index node in keeping the communication between its own module and the other modules 2Normalized pi pnor i The normalizedpi after correcting for the effects of number of modules Global network parameters 1Clustering coefficient Cp The extent of local clustering or cliquishness of a network 1Characteristic path length Lp The extent of overall routing efficiency of a network 2Gamma c The deviation of Cp of a network from those of surrogate random networks 2Lambda l The deviation of Lp of a network from those of surrogate random networks 2Sigma s The small-worldness indicating the extent of a network between randomness and order 1Local efficiency Eloc How efficient of information propagation over a node’s direct neighbors 1Global efficiency Eglob How efficient of information propagation through the whole network 2Assortativity r The tendency of nodes to link those nodes with similar number of edges 2Hierarchy b How likely it is that all nodes oscillate with the same wave pattern 1Synchronization S How likely that all nodes fluctuate in the same wave pattern 2Modularity Q The extent that nodes can be divided several subsets with dense connections within them but sparse between them Note that the formulas listed here are only for binarized networks. For details for weighted networks, see Text S1. 1First-order network metrics which are dependent on only one graph property. 2Second-order network metrics which are dependent on more than one property or are defined as rations of one property. doi:10.1371/journal.pone.0021976.t002 Table 2. Brief descriptions of complex network metrics examined in the present study. Note that the formulas listed here are only for binarized networks. For details for weighted networks, see Text S1. 1First-order network metrics which are dependent on only one graph property. 2Second-order network metrics which are dependent on more than one property or are defined as rations of one property. doi:10.1371/journal.pone.0021976.t002 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 2 Reliability of Brain Functional Networks TRT reliability of network topological metrics derived from R- fMRI data. Introduction Accordingly, systematic and direct work is clearly warranted. functional ROIs based node definition); (2) network membership (NM, i.e., inclusion or exclusion negative correlations); and (3) network type (NT, i.e., binarized or weighted networks). Table 1 lists those acronyms specific to the current study. In the current study, we implemented a comprehensive estimation of TRT reliability for both global network properties and regional nodal characteristics of intrinsic functional brain networks constructed using a public TRT R-fMRI dataset (http:// www.nitrc.org/projects/trt). This dataset allows us to examine both short-term (,1 hour apart) and long-term (.5 months apart) network reliability. Moreover, given numerous discrepancies in the analytical strategies of existing brain network studies (e.g., how to define network nodes or how to deal with negative correlations/ connections), we further evaluated the effects of three factors on network reliability. They are: (1) network node definition (ND, i.e, structural regions of interest (ROIs) based node definition or Reliability of Brain Functional Networks Reliability of Brain Functional Networks Subjects We used a TRT R-fMRI dataset of 25 participants (mean age 30.7 6 8.8, 9 males) that is publicly available at NITRC (http:// www.nitrc.org/projects/trt). The dataset has been used to examine TRT reliability of seed-based resting-state functional connectivity (RSFC) [27], independent component analysis and dual regression [29], amplitude of low-frequency fluctuations [30] and functional homotopy [31]. Figure 1. Spatial similarity and TRT reliability patterns of S-AAL-based RSFC. Mean Pearson correlation matrices (a), consistency of overall patterns between mean matrices (b) and TRT reliability of individual connections as well as the relationship between short-term and long-term reliability (c) are illustrated. The mean correlation matrices exhibited high similarity from both visual inspection (a) and quantitative spatial correlation analyses (b). Further TRT reliability analyses revealed a portion of connections exhibiting fair to excellent reliability (c, also see Fig. 2). Moreover, short- term reliability was significantly (p,0.05) correlated with long-term reliability among connections (c). Functional connections linking inter- hemisphere homotopic regions, as highlighted by plus signs (+), showed high connectivity strength and many of them exhibited high reliability. TRT, test-retest; RSFC, resting-state functional connectivity; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas. Of note, the structural ROIs were listed as in Table S1. doi:10.1371/journal.pone.0021976.g001 Figure 1. Spatial similarity and TRT reliability patterns of S-AAL-based RSFC. Mean Pearson correlation matrices (a), consistency of overall patterns between mean matrices (b) and TRT reliability of individual connections as well as the relationship between short-term and long-term reliability (c) are illustrated. The mean correlation matrices exhibited high similarity from both visual inspection (a) and quantitative spatial correlation analyses (b). Further TRT reliability analyses revealed a portion of connections exhibiting fair to excellent reliability (c, also see Fig. 2). Moreover, short- term reliability was significantly (p,0.05) correlated with long-term reliability among connections (c). Functional connections linking inter- hemisphere homotopic regions, as highlighted by plus signs (+), showed high connectivity strength and many of them exhibited high reliability. TRT, test-retest; RSFC, resting-state functional connectivity; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas. Of note, the structural ROIs were listed as in Table S1. doi:10.1371/journal.pone.0021976.g001 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 3 Data acquisition q Three resting-state scans were obtained for each participant using a Siemens Allegra 3.0-Tesla scanner. Each scan consisted of 197 contiguous EPI functional volumes (time repetition (TR) = 2000 ms; time echo (TE) = 25 ms; flip angle (FA) = 90u, number of slices = 39, matrix = 64664; field of view (FOV) = 192 mm; acquisition voxel size = 36363 mm3). Scans 2 and 3 were conducted in a single-scan session, 45 minutes apart, and were 5–16 months (mean 1164) after scan 1. All individuals were asked to relax and remain still with eyes open during the scan. Additionally, a high-resolution T1-weighted magnetization pre- pared gradient echo sequence was also obtained (MPRAGE, TR = 2500 ms; TE = 4.35 ms; inversion time = 900 ms; FA = 8u; number of slices = 176; FOV = 256 mm). Data preprocessing was performed using SPM5 package (http://www.fil.ion.ucl.ac.uk/spm). First, all images were correct- ed for intra-volume acquisition time offsets between slices using the Sinc interpolation and inter-volume geometrical displacement due to head movement using six-parameter (rigid body) transforma- tion. Then all functional images were normalized into the Montreal Neurological Institute space using an optimum 12- parameter affine transformation and nonlinear deformations, and then resampled to 3-mm isotropic voxels. Finally, the normalized images were further temporally band-pass filtered (0.01–0.1 Hz) to reduce the effects of low-frequency drift and high-frequency physiological noise. Notably, for the extraction of mean nodal time courses of functional defined ROIs, spatial smoothing with 6-mm Figure 2. TRT reliability distribution of RSFC. Both short-term and long-term TRT reliability exhibit approximatively normal distribution for all ROI sets. The mean reliability was about 0.28 (short-term) and 0.24 (long-term) for both structural ROIs-based RSFC while relatively low values were observed for functional ROIs-based RSFC. Green dots indicate the critical values used in the present study to grade reliability. RSFC, resting-state functional connectivity; TRT, test-retest. doi:10.1371/journal.pone.0021976.g002 Figure 2. TRT reliability distribution of RSFC. Both short-term and long-term TRT reliability exhibit approximatively normal distribution for all ROI sets. The mean reliability was about 0.28 (short-term) and 0.24 (long-term) for both structural ROIs-based RSFC while relatively low values were observed for functional ROIs-based RSFC. Green dots indicate the critical values used in the present study to grade reliability. RSFC, resting-state functional connectivity; TRT, test-retest. Data acquisition doi:10.1371/journal.pone.0021976.g002 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 4 Reliability of Brain Functional Networks full width at half maximum (FWHM) Gaussian kernel was performed before band-pass filtering (see below for node definition). full width at half maximum (FWHM) Gaussian kernel was performed before band-pass filtering (see below for node definition). across different node definitions. Specifically, to obtain structurally defined ROIs, a prior Anatomical Automatic Labeling atlas (AAL) [37] and Harvard-Oxford atlas (HOA) [38,39] were separately used to divide the whole brain into different number of regions. These two structural atlases parcellated the whole brain into 45 and 56 regions in each hemisphere and were termed as S-AAL and S-HOA, respectively. To obtain functionally defined ROIs, 160 spheres (radius = 5 mm) were generated around the peak coordinates previously identified form meta-analytic studies of multiple brain functions [40,41] and were termed as F-DOS. These ROIs are comprised of discrete spherical ROIs and not completely cover the cerebral cortex and cerebellum (Fig. S1). All Functional connectivity matrix and network construction Node definition (ND). A network (i.e., graph) is comprised of nodes and edges connecting nodes. In the current study, nodes represent ROIs and edges represent RSFC between ROIs. Given the accumulating evidence of effects of node definition on network topology [32,33,34,35,36], two strategies of defining ROIs (i.e., anatomical and functional ROIs) were employed to provide a comprehensive assessment of TRT reliability of brain networks Figure 3. Relationship between RSFC and TRT reliability. Scatter plots of mean connectivity strength against corresponding ICC values are depicted to show the relationship for both S-AAL (a) and F-DOS (b) based correlation matrices. The trend lines were obtained by linear least-square fit. Significant (p,0.05) positive correlations were found between positive RSFC and their corresponding ICC values for both ROIs sets and for both short-term and long-term scanning. In addition, significant negative correlations were also found for negative RSFC with their corresponding ICC values but only for F-DOS-based correlation matrices. These findings suggest higher reliability for stronger RSFC. Functional connections linking inter- hemisphere homotopic regions are highlighted by plus signs (+) for S-AAL but not for F-DOS because of the absence of direct correspondence. RSFC, resting-state functional connectivity; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g003 Figure 3. Relationship between RSFC and TRT reliability. Data acquisition Scatter plots of mean connectivity strength against corresponding ICC values are depicted to show the relationship for both S-AAL (a) and F-DOS (b) based correlation matrices. The trend lines were obtained by linear least-square Figure 3. Relationship between RSFC and TRT reliability. Scatter plots of mean connectivity strength against corresponding ICC values are depicted to show the relationship for both S-AAL (a) and F-DOS (b) based correlation matrices. The trend lines were obtained by linear least-square fit. Significant (p,0.05) positive correlations were found between positive RSFC and their corresponding ICC values for both ROIs sets and for both short-term and long-term scanning. In addition, significant negative correlations were also found for negative RSFC with their corresponding ICC values but only for F-DOS-based correlation matrices. These findings suggest higher reliability for stronger RSFC. Functional connections linking inter- hemisphere homotopic regions are highlighted by plus signs (+) for S-AAL but not for F-DOS because of the absence of direct correspondence. RSFC, resting-state functional connectivity; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g003 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 5 Reliability of Brain Functional Networks consisting of Pearson correlation coefficients between each pair of ROIs were therefore generated. consisting of Pearson correlation coefficients between each pair of ROIs were therefore generated. the ROIs are associated with five different kinds of functions of error-processing, default-mode, memory, language and sensori- motor. There were no any overlaps between ROIs. Names of the three sets of ROIs and their corresponding abbreviations are listed in Table S1, S2 and S3. Network type (NT). Individual correlation matrices Cij~ cij   derived above was converted into both a binarized network Edge definition. To measure inter-ROI RSFC, for each of the three sets of ROIs, a mean time series for each ROI was calculated by averaging the time series of all voxels within that ROI. Several potential nuisance signals associated with physiological processes were further removed. Specifically, we regressed out estimated head-motion profiles and global signal from each ROI’s mean time series [32,42]. The residuals were then used to estimate inter-ROI RSFC that were quantified by Pearson correlation coefficient. Reliability of Brain Functional Networks Sthr{max i,j ð Þ is a data-specific maximum of Sthr for ith subject at jth scans (note that scan2 and scan3 were used to determine the threshold range for short-term reliability estimation and scan1 and the average of scan2 and scan3 were used for long-term reliability estimation). Characterization of network topology over continuous sparsity levels allows us to trace the trajectory of TRT reliability of network properties over varying network structures and to identify specific threshold range of high reliability. the whole correlation matrices consisting of positive and negative connections and positive correlation matrices con- sisting of only positive connections (i.e., negative correlations were set to 0). Network metrics We explored two sets of network topological attributes: 1) regional nodal characteristics: degree ki, efficiency ei, between- ness bi, cluster coefficient ci, participant coefficient pi, and normalized participant coefficient pnor i ; 2) global network metrics: small-world parameters (clustering coefficient Cp, characteristic path length Lp, normalized clustering coefficient c, normalized characteristic path length l and small-worldness s), network efficiency (local efficiency Eloc and global efficiency Eglob), assortativity r, hierarchy b, synchronization S, modularity Q and the number of modules NM. All the computations of network metrics were performed using in-house custom MATLAB codes termed as GRETNA. Text S1 and Table 2 give detailed descriptions for above metrics. Reliability of Brain Functional Networks Reliability of Brain Functional Networks where rthr is a pre-defined correlation threshold. To determine rthr, sparsity measure, Sthr (defined as the ratio of the number of actual edges divided by the maximum possible number of edges in a network) was applied to each correlation matrix. Using the sparsity threshold, a subject-specific rthr was determined to threshold each correlation matrix such that the resulting networks have the same sparsity level (i.e., the same number of edges) across subjects and scans. Currently, there is no a definitive way to accurately determine threshold and previous studies construct brain networks either under a single threshold (e.g., [43,44]) or over a continuous threshold range (e.g., [45,46]) in terms of specific constraint conditions. Here, brain networks were constructed over the full range of sparsity, i.e., 0,Sthr,1 for the whole correlation matrices of both positive and negative correlations and 0,Sthr,min [Sthr{max i,j ð Þ] for only positive correlation matrices. Sthr{max i,j ð Þ is a data-specific maximum of Sthr for ith subject at jth scans (note that scan2 and scan3 were used to determine the threshold range for short-term reliability estimation and scan1 and the average of scan2 and scan3 were used for long-term reliability estimation). Characterization of network topology over continuous sparsity levels allows us to trace the trajectory of TRT reliability of network properties over varying network structures and to identify specific threshold range of high reliability. where rthr is a pre-defined correlation threshold. To determine rthr, sparsity measure, Sthr (defined as the ratio of the number of actual edges divided by the maximum possible number of edges in a network) was applied to each correlation matrix. Using the sparsity threshold, a subject-specific rthr was determined to threshold each correlation matrix such that the resulting networks have the same sparsity level (i.e., the same number of edges) across subjects and scans. Currently, there is no a definitive way to accurately determine threshold and previous studies construct brain networks either under a single threshold (e.g., [43,44]) or over a continuous threshold range (e.g., [45,46]) in terms of specific constraint conditions. Here, brain networks were constructed over the full range of sparsity, i.e., 0,Sthr,1 for the whole correlation matrices of both positive and negative correlations and 0,Sthr,min [Sthr{max i,j ð Þ] for only positive correlation matrices. Data acquisition For each subject at each scan, three correlation matrices (corresponding to three sets of ROIs) Aij~ aij   ~ 1, if cij  wrthr; 0, others ( ð1Þ ð1Þ and a weighted network Wij~ wij   ~ cij  , if cij  wrthr; 0, others ( ð2Þ ð2Þ Figure 4. Spatial similarity and TRT reliability patterns of F-DOS-based RSFC. Mean Pearson correlation matrices (a), consistency of overa patterns between mean matrices (b) and TRT reliability of individual connections as well as the relationship between short-term and long-term reliability (c) are illustrated. The mean correlation matrices exhibited high similarity from both visual inspection (a) and quantitative spatial correlatio analyses (b). Further TRT reliability analyses revealed many connections exhibiting fair to excellent reliability (c, also see Fig. 2). Moreover, a significan (p,0.05) correlation was found in the ICC matrices between short-term and long-term scans (c). No inter-hemisphere homotopic functiona connections were highlighted because of the absence of direct inter-hemisphere correspondence for these ROIs. TRT, test-retest; RSFC, resting-stat functional connectivity; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). Of note, the functional ROIs were listed as in Table S3. doi:10.1371/journal.pone.0021976.g004 Figure 4. Spatial similarity and TRT reliability patterns of F-DOS-based RSFC. Mean Pearson correlation matrices (a), consistency of overall patterns between mean matrices (b) and TRT reliability of individual connections as well as the relationship between short-term and long-term reliability (c) are illustrated. The mean correlation matrices exhibited high similarity from both visual inspection (a) and quantitative spatial correlation analyses (b). Further TRT reliability analyses revealed many connections exhibiting fair to excellent reliability (c, also see Fig. 2). Moreover, a significant (p,0.05) correlation was found in the ICC matrices between short-term and long-term scans (c). No inter-hemisphere homotopic functional connections were highlighted because of the absence of direct inter-hemisphere correspondence for these ROIs. TRT, test-retest; RSFC, resting-state functional connectivity; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). Of note, the functional ROIs were listed as in Table S3. doi:10.1371/journal.pone.0021976.g004 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 6 Test-retest reliability To investigate the TRT reliability of all graph metrics mentioned above, we used a common index of intraclass correlation [48]. For each global and nodal network measure derived under each combination of the three factors mentioned above, individual values were first merged into two 2562 matrices (rows corresponding to subjects and column corresponding to Network membership (NM). Given the disagreements in treating negative correlations in R-fMRI network studies (e.g., [46,47]), the thresholding procedure was performed on both Figure 5. TRT reliability of global network metrics as a function of sparsity threshold for S-AAL-based networks. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively. Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network anlysis; Weighted, weighted network analysis; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas. doi:10.1371/journal.pone.0021976.g005 Figure 5. TRT reliability of global network metrics as a function of sparsity threshold for S-AAL-based networks. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively. Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network anlysis; Weighted, weighted network analysis; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas. doi:10.1371/journal.pone.0021976.g005 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 7 7 Reliability of Brain Functional Networks Reliability of Brain Functional Networks scans), with one representing short-term intra-session across scans 2 and 3 and the other long-term inter-session between scan 1 and the average of scans 2 and 3. Additional long-term reliability estimation using scan 1 and scan 3 alone outputted similar results (Table S4). Therefore, long-term reliability results were reported based on scan 1 and the average of scan 2 and scan 3. Of note, the average was done on individual functional connectivity matrices rather than graph metrics between scan 2 and scan 3, followed by graph metric calculation. Using a one-way ANOVA on each of the two matrices, with random subject effects, we split the total sum of the squares into between-subject (MSb) and within-subject (MSw, i.e., residual error) sum of squares. Finally, ICC values were calculated according to the following equation where k is the number of repeated observations per subject [48]: ICC~ MSb{MSw MSbz k{1 ð ÞMSw ð3Þ ð3Þ Of note, the ICC derived from (3) has a relationship with the F- value derived from the one-way ANOVA as follows [49]: Of note, the ICC derived from (3) has a relationship with the F- value derived from the one-way ANOVA as follows [49]: ICC~ F{1 Fz k{1 ð Þ ð4Þ ð4Þ ICC is close to 1 for reliable measures that show low within-subject variance relative to between-subject variance and 0 (negative) otherwise. In the current study, reliability was recorded in terms of ICC is close to 1 for reliable measures that show low within-subject variance relative to between-subject variance and 0 (negative) otherwise. In the current study, reliability was recorded in terms of Figure 6. TRT reliability of summarized global network metrics (a) and metric-related differences in reliability (b). Areas under curves (AUCs) of each metrics were used to provide threshold-independent reliability estimation. Different metrics showed variable levels of reliability. Several of them were moderately reliable (e.g., lambda for S-AAL-based networks). Subsequent statistical analysis revealed significant differences in TRT reliability among the 12 global network metrics for S-AAL- but not for F-DOS-based networks. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively in (a). Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g006 Figure 6. TRT reliability of summarized global network metrics (a) and metric-related differences in reliability (b). Areas under curves (AUCs) of each metrics were used to provide threshold-independent reliability estimation. Different metrics showed variable levels of reliability. Several of them were moderately reliable (e.g., lambda for S-AAL-based networks). Subsequent statistical analysis revealed significant differences in TRT reliability among the 12 global network metrics for S-AAL- but not for F-DOS-based networks. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively in (a). Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10 1371/journal pone 0021976 g006 Figure 6. TRT reliability of summarized global network metrics (a) and metric-related differences in reliability (b). Areas under curves (AUCs) of each metrics were used to provide threshold-independent reliability estimation. Different metrics showed variable levels of reliability. Several of them were moderately reliable (e.g., lambda for S-AAL-based networks). Subsequent statistical analysis revealed significant differences in TRT reliability among the 12 global network metrics for S-AAL- but not for F-DOS-based networks. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively in (a). Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g006 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 8 Reliability of Brain Functional Networks transform) for each of the three TRT scans. Initial visual inspection suggested that mean RSFC matrices showed highly similar spatial patterns between different time points (Fig. 1a). Further quantitative spatial correlation analysis (Pearson correlation) confirmed the visual inspection, as revealed by high correlations in the mean correlation values between each pair among the three scans (Fig. 1b, scan1 vs. scan2: r = 0.961, p,102300; scan1 vs. scan3: r = 0.962, p,102300; scan2 vs. scan3: r = 0.966, p,102300). the criteria of [50,51], with an ICC value from 0 to 0.25 indicating poor; 0.25 to 0.4 indicating low; 0.4 to 0.6 indicating fair; 0.6 to 0.75 indicating good and 0.75 to 1.0 indicating excellent reliability. Since the network construction was done over a continuous range of sparsity threshold, ICC is a function of the threshold. To provide a threshold-independent reliability assess- ment, we also calculated the area under curve (AUC, i.e., the integral) for each network metric [52] that was used to compute a single ICC scalar for each network measure. Simulation analysis These findings indicate that reliability of functional connectivity was partly determined by their strength, whereas functional connectivity strength had limited predictive ability to their reliability since the small amount of variance in the functional connectivity reliability explained by their strength (R2,3%). Finally, we compared the consistency between ICC-based reliability and Pearson correlation coefficient-based similarity analysis (across subjects) for network metrics between scans, which was restricted to S-AAL- based networks. Reliability of RSFC. ICC-based TRT reliability analysis on individual functional connections demonstrated an approximate normal distribution of the ICC values for all 4005 (i.e., 90689/2) connections with a mean around 0.25 for both short-term and long-term scans (Fig. 2a). In terms of the category used in the present study, 1203 (,30.0%) functional connections exhibited fair to excellent reliability for short-term scans (fair: 1006, ,25.1%; good: 191, ,4.8%; excellent: 6, ,0.2%) and 914 connections (,22.8%) for long-term scans (fair: 796, ,19.9%; good: 114, ,2.9%; excellent: 4, ,0.1%). The majority of RSFC (up to 70% for both short- and long-term scans) showed low or poor reliability. Additionally, a significantly positive correlation (Pearson correlation, r = 0.266, p,10264) was found in the ICC values across connections between short-term and long-term scans (Fig 1c) Simulation analysis To investigate the effects of numerical changes in RSFC on network metric reliability, we performed simulation analyses as follows: individual functional connectivity matrices based on S- AAL were calculated using dataset of scan1 and their correspond- ing network metrics (both global and nodal metrics) were used as reference values. Then, for each correlation matrix, different levels of independent Gaussian noise were added and all network metrics were recomputed. The added Gaussian noise were zero mean and the variances varied across six equally spaced levels corresponding to 8.3%, 16.7%, 25.0%, 33.3%, 41.7% and 50.0% of actual functional connectivity variances for each subject. This procedure assures the same proportion of noise added to each correlation matrix. Of note, the procedure of noise addition was performed 5 times. Therefore, 25 (subjects) | 6 (noise levels) | 5 (random times) = 750 functional connectivity matrices were simulated in total. Finally, the TRT reliability of each metric was calculated between the reference values and those obtained from simulated functional networks under each level of noise and then averaged across 5 rounds of noise addition. ( g ) Relationship between connectivity and reliability. To explore the relationship between connectivity strength and reliability, linearly fitted lines were obtained separately for positive connections and negative connections with their corresponding ICC values. We found significantly positive correlations (Pearson correlation) between positive connections and their ICC values for both short-term (r = 0.135, p,1027) and long-term (r = 0.145, p,1028) scans (Fig. 3a). No significant correlations were found between negative correlations and their ICC values (p.0.3 for both short-term and long-term scans) (Fig. 3a). These findings indicate that reliability of functional connectivity was partly determined by their strength, whereas functional connectivity strength had limited predictive ability to their reliability since the small amount of variance in the functional connectivity reliability explained by their strength (R2,3%). Relationship between connectivity and reliability. To explore the relationship between connectivity strength and reliability, linearly fitted lines were obtained separately for positive connections and negative connections with their corresponding ICC values. We found significantly positive correlations (Pearson correlation) between positive connections and their ICC values for both short-term (r = 0.135, p,1027) and long-term (r = 0.145, p,1028) scans (Fig. 3a). No significant correlations were found between negative correlations and their ICC values (p.0.3 for both short-term and long-term scans) (Fig. 3a). TRT reliability of RSFC: S-AAL TRT reliability of RSFC: S-AAL Consistency of overall RSFC patterns. The mean RSFC matrices across subjects were calculated (after Fisher’s r-to-z Table 3. Summary of the main findings in the present study. Factors effecting network metric reliability Time interval Network type Network membership S-AAL Global metrics Long.Short (Binarized) N.S. Network (+).Network (+/-) Nodal metrics N.S. N.S. N.S. S-HOA Global metrics N.S. Binarized.Weighted N.S. Nodal metrics N.S. N.S. N.S. F-DOS Global metricsa N.S. N.S. N.S. Nodal metrics N.S. N.S. N.S. S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; S-HOA, structural ROIs from Harvard-Oxford atlas; F-DOS, functional ROIs from ref (40); Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; N.S., non-significant. aThere were no significant differences in reliability among global network metrics for F-DOS based networks while nodal network metrics for F-DOS and both global and nodal metrics for S-ALL and S-HOA based networks were significantly different. doi:10.1371/journal.pone.0021976.t003 Table 3. Summary of the main findings in the present study. Table 3. Summary of the main findings in the present study. Factors effecting network metric reliability S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; S-HOA, structural ROIs from Harvard-Oxford atlas; F-DOS, functional ROIs from ref (40); Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; N.S., non-significant. aThere were no significant differences in reliability among global network metrics for F-DOS based networks while nodal network metrics for F-DOS and both global and nodal metrics for S-ALL and S-HOA based networks were significantly different. doi:10.1371/journal.pone.0021976.t003 S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; S-HOA, structural ROIs from Harvard-Oxford atlas; F-DOS, functional ROIs from ref (40); Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; N.S., non-significant. aThere were no significant differences in reliability among global network metrics for F-DOS based networks while nodal network metrics for F-DOS and both global and nodal metrics for S-ALL and S-HOA based networks were significantly different. TRT reliability of network metrics: S-AAL TRT reliability of network metrics: S AAL Reliability of global network metrics. In the present study, individual networks were constructed at the same sparsity level by applying subject-specific correlation thresholds to individual correlation matrices (see Fig. S4 for the corresponding correlation thresholds under each sparsity level). Sparsity threshold ensures all resultant networks to have comparable topological structures of the same number of edges. Figure 5 shows the TRT reliability of 12 global network metrics over the whole sparisty range. Generally, most global network metrics exhibited poor to low reliability, irrespective of the factors of TI, NT and NM. For example, clustering coefficient Cp was found to uniformly exhibit poor reliability (ICC,0.25) under all conditions. Nonetheless, we noted that some global metrics (e.g., lambdal and assortativity r) exhibited modest long-term reliability when the networks were sparsely connected (sparsity,10%). Interestingly, we found that global network reliability appeared to depend on the factors of TI and NM but relatively insensitive to NT by qualitatively visual inspection. Specifically, long-term scans seemed to be associated with better reliability in compared with short-term scans and the exclusion of negative correlations enhanced network reliability (Fig. 5). These were reflected in both increased ICC values and the broadened threshold range of high ICC. Finally, a threshold- independent reliability scalar was obtained for each global network metric by using the AUC. Again, several specific global metrics (e.g., lambdal) demonstrated moderate long-term reliability under certain analytical schemes (Fig. 6a, left). Of note, we found that Relationship between connectivity and reliabiflity. Con- sistent with S-AAL, positive correlations were found between positive RSFC and their reliability for the S-HOA-based corre- lations (short-term: r = 0.166, p,10-17; long-term: r = 0.148, p,10213), indicating limited determination of functional con- fnectivity strength on their reliability (R2,3%). Additionally, a negative correlation was demonstrated between negative corre- lations and their reliability for long-term scans (r = 20.033, p = 0.048) (Fig. S3). TRT reliability of RSFC: S-AAL doi:10.1371/journal.pone.0021976.t003 S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; S-HOA, structural ROIs from Harvard-Oxford atlas; F-DOS, functional ROIs from ref (40); Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; N.S., non-significant. aThere were no significant differences in reliability among global network metrics for F-DOS based networks while nodal network metrics for F-DOS and both global and nodal metrics for S-ALL and S-HOA based networks were significantly different. doi:10.1371/journal.pone.0021976.t003 PLoS ONE | www.plosone.org 9 Reliability of Brain Functional Networks Figure 7. TRT reliability of nodal metrics for S-AAL-based networks. Nodal reliability varied across nodal attributes and spatial locations. The full names of region’s abbreviations were listed as in Table S1. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively. Network (+/-), networks constructed using absolute both positive and negative correlations; Figure 7. TRT reliability of nodal metrics for S-AAL-based networks. Nodal reliability varied across nodal attributes and spatial locations. The full names of region’s abbreviations were listed as in Table S1. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively. Network (+/-), networks constructed using absolute both positive and negative correlations; July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 10 Reliability of Brain Functional Networks Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas. doi:10 1371/journal pone 0021976 g007 Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas. doi:10.1371/journal.pone.0021976.g007 TRT reliability of RSFC: S-HOA excellent reliability. Of note, those reliable connections were mainly related with ROIs designated as default mode network according to previous study [40]. In addition, short-term reliability was found to positively correlate with long-term reliability across all connections (Fig. 4c, Pearson correlation, r = 0.337, p,10-300). excellent reliability. Of note, those reliable connections were mainly related with ROIs designated as default mode network according to previous study [40]. In addition, short-term reliability was found to positively correlate with long-term reliability across all connections (Fig. 4c, Pearson correlation, r = 0.337, p,10-300). Consistency of overall RSFC patterns. The mean S-HOA- based RSFC matrices across subjects also showed highly similar spatial patterns revealed by visual inspection (Fig. S2a) and quantitative spatial correlation analyses (Fig. S2b, r.0.95 between any two scans). Relationship between connectivity and reliability. In the case of functional ROIs based RSFC matrices, functional connectivity strength explained relatively more in comparison with structural ROIs based matrices but still low variance (R2,8%) in connectivity reliability (positive correlations and their reliability: r = 0.279, p,10-86 for short-term and r = 0.273, p,10-83 for long-term scans; negative correlations and their reliability: r = 20.098, p,10217 for short-term and r = 20.097, p,10217 for long-term scans) (Fig. 3b). Reliability of RSFC. Similar to S-AAL, approximate normal distributions were also found for the reliability of S-HOA-based RSFC which had comparable mean (, 0.25) (Fig. 2b). Also consistent with S-AAL, although there were quite a few connections showing fair to good to excellent reliability (1874, ,30.1% for short-term and 1356, ,21.8% for long-term scans), most connections were poorly reliable (4342, ,69.9% for short- term and 4860, ,78.2% for long-term scans). Finally, short-term reliability was found to positively correlate with long-term reliability across connections (Fig. S2c, Pearson correlation, r = 0.307, p,102135). TRT reliability of RSFC: F-DOS Furthermore, TI (F(1,11) = 8.176, p = 0.016) and NM (F(1,11) = 4.492, p = 0.058) showed significant or marginally significant main effects on global network reliability, respectively. In addition, a significant interaction was observed between TI and NT (F(1,11) = 5.317 , p = 0.042). NT and other interactions were not significant (p.0.05). Further post-hoc comparisons (paired t-tests) revealed that long-term scans outperformed short-term scans only assortativity rshowed moderated both short-term and long-term reliability for networks of positive correlations. Beyond the descriptive results mentioned above, we further performed statistical analyses to test the differences in reliability among 12 global metrics (one-way repeated-measure ANOVA) and the effects of TI, NM and NT on the reliability of global network metrics (three-factor repeated-measure ANOVA). Those AUC-based ICC values were used for the statistical analyses. The results showed that TRT reliability differed significantly Figure 9. Nodal TRT reliability of degree and its relationship with nodal degree centrality for S-AAL-based networks. (a) Nodal TRT reliability was mapped in anatomical space after average across scanning time interval, network type and network membership because of no effects of these factors on nodal reliability. (b) Nodal degree centrality (AUCs) was also mapped in anatomical space which was averaged across subjects and factors of scanning time interval, network type and network membership. Trend lines were further obtained by linear least-square fit to reveal the relationship between nodal degree centrality and their corresponding reliability after with (d) and without (c) correcting for the effects of regional size. Of note, the full names of region’s abbreviations were listed as in Table S1. TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; k, nodal degree; A, anterior; P, posterior; L, left; R, right. doi:10.1371/journal.pone.0021976.g009 Figure 9. Nodal TRT reliability of degree and its relationship with nodal degree centrality for S-AAL-based networks. (a) Nodal TRT reliability was mapped in anatomical space after average across scanning time interval, network type and network membership because of no effects of these factors on nodal reliability. (b) Nodal degree centrality (AUCs) was also mapped in anatomical space which was averaged across subjects and factors of scanning time interval, network type and network membership. Trend lines were further obtained by linear least-square fit to reveal the relationship between nodal degree centrality and their corresponding reliability after with (d) and without (c) correcting for the effects of regional size. TRT reliability of RSFC: F-DOS Consistency of overall RSFC patterns. Relative to structural ROIs-based RSFC matrices (both S-AAL and S- HOA), the similarity in the spatial patterns across scans decreased for the mean RSFC matrices derived on the basis of 160 functional ROIs but still remained high (Scan1 vs. Scan2: r = 0.896, p,102300; Scan1 vs. Scan3: r = 0.915, p,102300; Scan2 vs. Scan3: r = 0.902, p,102300) (Fig. 4a and b). Reliability of RSFC. Normal distributions were also found for TRT reliability of functional ROIs-based RSFC, however lower mean ICC values (,0.20) were obtained in this case in comparison with structural ROIs-based RSFC (,0.25) (Fig. 2c). Moreover, higher percentage of connections (up to ,80.0%) showed poor and low reliability for both short-term and long-term scanning procedure, with ,20.0% showing fair to good to Figure 8. Boxplot of mean nodal TRT reliability for S-AAL- (a) and F-DOS- (b) based networks. Significant differences were found in the mean nodal reliability among the six nodal metrics examined with nodal degree showing the highest ICC values and least variances for both ROIs sets. TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g008 Figure 8. Boxplot of mean nodal TRT reliability for S-AAL- (a) and F-DOS- (b) based networks. Significant differences were found in the mean nodal reliability among the six nodal metrics examined with nodal degree showing the highest ICC values and least variances for both ROIs sets. TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g008 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 11 Reliability of Brain Functional Networks (F(11,77) = 3.434, p = 0.001) among 12 global network metrics with lambda l showing the highest reliability (Fig. 6b, left). Furthermore, TI (F(1,11) = 8.176, p = 0.016) and NM (F(1,11) = 4.492, p = 0.058) showed significant or marginally significant main effects on global network reliability, respectively. In addition, a significant interaction was observed between TI and NT (F(1,11) = 5.317 , p = 0.042). NT and other interactions were not significant (p.0.05). Further post-hoc comparisons (paired t-tests) revealed that long-term scans outperformed short-term scans only (F(11,77) = 3.434, p = 0.001) among 12 global network metrics with lambda l showing the highest reliability (Fig. 6b, left). Reliability of Brain Functional Networks Reliability of Brain Functional Networks for binarized networks (t(23) = 5.100, p,1024) but not for weighted networks (t(23) = 1.333, p = 0.196) and excluding nega- tive correlations increased the reliability (t(47) = 3.228, p = 0.002) of global network metrics. See Table 3 for the summary of all statistical results. for binarized networks (t(23) = 5.100, p,1024) but not for weighted networks (t(23) = 1.333, p = 0.196) and excluding nega- tive correlations increased the reliability (t(47) = 3.228, p = 0.002) of global network metrics. See Table 3 for the summary of all statistical results. mapped nodal reliability of degree of all regions after averaging over factors of TI, NM and NT (Fig. 9a). This was because nodal degree showed higher reliability and less variance as compared to other nodal metrics and was robust to TI and NM as well as NT. As shown in Figure 9a, some association and limbic/paralimbic cortex regions [53] exhibited fair reliability that were predomi- nately located in bilateral parietal and occipital lobes, such as association cortex regions of the left angular gyrus (ANG), right paracentral lobule (PCL), right precuneus (PCUN), bilateral supramarginal gyrus (SMG), bilateral dorsolateral superior frontal gyrus (SFGdor), right medial superior frontal gyrus (SFGmed) and left superior occipital gyrus (SOG), and limbic/paralimbic regions of the bilateral hippocampus (HIP) and the left posterior cingulate gyrus. In addition, one primary cortex region of the left calcarine fissure (CAL) was also found to be fairly reliable. To test whether or not nodal reliability was related with nodal centrality, we also mapped the mean nodal degree over TI, NM and NT (Fig. 9b) and found visually different patterns between nodal degree and nodal reliability. The most reliable regions located on the posterior while the most connected regions on the anterior portions of the brain. Further quantitative correlation analysis revealed that only tiny variance (R2,7%) in nodal reliability could be explained by nodal degree centrality in both cases of with (r = 0.255, p = 0.015, Fig. 9c) and without (r = 0.263, p = 0.012, Fig. 9d) correction for regional nodal size. To test whether there exist a relationship between spatial location and nodal reliability, we compared nodal degree reliability between anterior (y.0) and posterior (y,0) regions. The results revealed that posterior regions were more Reliability of local nodal metrics. Nodal reliability was estimated based on AUCs. TRT reliability of RSFC: F-DOS Of note, the full names of region’s abbreviations were listed as in Table S1. TRT, test-retest; S-AAL, structural ROIs from Anatomical Automatic Labeling atlas; k, nodal degree; A, anterior; P, posterior; L, left; R, right. doi:10.1371/journal.pone.0021976.g009 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 12 Reliability of Brain Functional Networks We found that nodal reliability showed: (1) unconspicuous differences associated with factors of TI, NM and NT; (2) different patterns across nodal metrics; and (3) a spatially heterogeneous distribution over the whole brain (Fig. 7). First, nodal reliability patterns did not show remarkable differences associated with the factors of TI, NM and NT by visual inspection. To test whether or not there exist differences in the TRT reliability associated with these factors, three-factor repeated-measure ANOVA was further performed on the mean ICC values over all nodes. Results revealed that none of these three factors had significant main effects or interactions on the mean nodal reliability (p.0.05) (Table 3). Second, nodal reliability exhibited variable patterns across nodal attributes under each combination of the three factors. Further one-factor repeated-measure ANOVA on the mean nodal reliability over regions supported this finding that there was significant (F(5,35) = 6.578, p = 0.0002) differences among the six nodal metrics examined, with the highest ICC values and least variance for nodal degree (Fig. 8a). Finally, nodal reliability distributed non-uniformly over the brain, an observation irrespective of nodal metrics and factors of TI, NM and NT. To highlight those reliable regions, we selectively Figure 10. The similarity between inter-scan ICC-based reliability and inter-scan Pearson correlation coefficients for S-AAL-based networks. The reliability and correlation analyses revealed highly consistent results (r.0.9 under most conditions), ruling out the possibility of linear scaling biases of network metrics across test and retest scans that will lead to low TRT reliability. doi:10.1371/journal.pone.0021976.g010 Figure 10. The similarity between inter-scan ICC-based reliability and inter-scan Pearson correlation coefficients for S-AAL-based networks. The reliability and correlation analyses revealed highly consistent results (r.0.9 under most conditions), ruling out the possibility of linear scaling biases of network metrics across test and retest scans that will lead to low TRT reliability. doi:10.1371/journal.pone.0021976.g010 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 13 13 Reliability of Brain Functional Networks reliable than anterior regions even if nodal mean functional connectivity differences were corrected (t(87) = 2.801, p = 0.006). In addition, we also found dramatically different patterns across nodal metrics even for those most reliable regions except for the right PCL (Fig. S5a). 0.312, p = 0.601, repeated two-way ANOVA) in the resistance to noise between binarized and weighted network analyses (Fig. Reliability of Brain Functional Networks 12); 3) there were no differences in numerical stability against noise in functional connectivity (p.0.05 under each noise level) between the first-order and second-order network metrics (Table 2); 4) nodal network metrics were more numerically reliable than global network against noise in functional connectivity (p,1023 under each noise level). Of note, although sensitive to functional connectivity noise, the degree varied dramatically among global metrics. For instance, small-world parameters and network efficiency were extremely sensitive to even little noise in func- tional connectivity while assortativity, hierarchy, synchronization and modularity were relatively resistant to noise (Fig. 11). Consistency between ICC-based reliability analysis and Pearson correlation analysis. To test the possibility of linear scaling biases across test and retest scans which may result in low TRT reliability, we calculated the inter-scan Pearson correlation coefficient for each global network metric (AUC) across subjects for both short-term and long-term scans. Further scatter plots between ICC values and Pearson correlation coefficients revealed highly correlated patterns (r.0.9 under most conditions) (Fig. 10), suggesting consistent results revealed by the two measures. TRT reliability of network metrics: S-HOA Simulation results. By simulating functional connectivity matrices with different levels of noise, we found that: 1) for global network metrics, the TRT reliability was sensitive (F(5,55) = 23.303, p,10-11, repeated two-way ANOVA) to disturbances in functional connectivity values and weighted network analysis generated numerically more (F(1,11) = 5.183, p = 0.044, repeated two-way ANOVA) reliable results than binarized network analysis (Fig. 11); 2) for nodal network metrics, although sensitive to the levels of noise (F(5,25) = 7.762, p,1023, repeated two-way ANOVA), they were highly resistant to numerical changes in functional connectivity and there were no differences (F(1,5) = Reliability of global network metrics. Analogous to results from S-AAL-based networks, S-HOA-based networks also showed overall low (Fig. S6a) but metric- (Fig. S6b) and threshold- (Fig. S7) sensitive reliability. However, unlike the finding of modest long- term reliability of multiple global metrics for S-AAL-based networks (Fig. 5 and Fig. 6a, left), S-HOA-based networks were mainly related with moderate short-term reliability in multiple global metrics (except for lambda) (Fig. S6a and Fig. S7). Of note, synchronization S was found to repeatedly show overall moderate reliability (Fig. S6a). Subsequent statistical comparisons revealed Figure 11. TRT reliability of global network metrics as a function of noise in RSFC for S-AAL-based networks. Global network metrics were sensitive to disturbances of RSFC and weighted network analysis generated numerically more stable results in comparison with binarized network analysis. The highlighted black border marks are the average reliability across metrics for binarized (square) and weighted (circle) network analysis, respectively. Of note, the sensitivity varied dramatically among metrics. Small-world parameters and network efficiency were extremely sensitive to even little noise in functional connectivity while assortativity, hierarchy, synchronization and modularity were relatively resistant to noise. TRT, test-retest; RSFC, resting-state functional connectivity. doi:10.1371/journal.pone.0021976.g011 Figure 11. TRT reliability of global network metrics as a function of noise in RSFC for S-AAL-based networks. Global network metrics were sensitive to disturbances of RSFC and weighted network analysis generated numerically more stable results in comparison with binarized network analysis. The highlighted black border marks are the average reliability across metrics for binarized (square) and weighted (circle) network analysis, respectively. Of note, the sensitivity varied dramatically among metrics. Small-world parameters and network efficiency were extremely sensitive to even little noise in functional connectivity while assortativity, hierarchy, synchronization and modularity were relatively resistant to noise. TRT, test-retest; RSFC, resting-state functional connectivity. TRT reliability of network metrics: S-HOA doi:10.1371/journal.pone.0021976.g011 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 14 Reliability of Brain Functional Networks Figure 12. TRT reliability of nodal network metrics as a function of noise in RSFC for S-AAL-based networks. Nodal network metrics were sensitive to disturbances of RSFC and no differences were observed in the resistance to noise in functional connectivity between binarized and weighted network analysis. The highlighted black border marks are the average reliability across metrics for binarized (square) and weighted (circle) network analysis, respectively. Of note, although sensitive, nodal network metrics showed strong tolerance of disturbances in RSFC. TRT, test-retest; RSFC, resting-state functional connectivity. doi:10.1371/journal.pone.0021976.g012 Figure 12. TRT reliability of nodal network metrics as a function of noise in RSFC for S-AAL-based networks. Nodal network metrics were sensitive to disturbances of RSFC and no differences were observed in the resistance to noise in functional connectivity between binarized and weighted network analysis. The highlighted black border marks are the average reliability across metrics for binarized (square) and weighted (circle) network analysis, respectively. Of note, although sensitive, nodal network metrics showed strong tolerance of disturbances in RSFC. TRT, test-retest; RSFC, resting-state functional connectivity. doi:10.1371/journal.pone.0021976.g012 Figure 12. TRT reliability of nodal network metrics as a function of noise in RSFC for S-AAL-based networks. Nodal network metrics were sensitive to disturbances of RSFC and no differences were observed in the resistance to noise in functional connectivity between binarized and weighted network analysis. The highlighted black border marks are the average reliability across metrics for binarized (square) and weighted (circle) network analysis, respectively. Of note, although sensitive, nodal network metrics showed strong tolerance of disturbances in RSFC. TRT, test-retest; RSFC, resting-state functional connectivity. doi:10.1371/journal.pone.0021976.g012 that TRT reliability of global network metrics were modulated by NT factor (F(1,11) = 6.819, p = 0.024) with higher reliability observed for binarized networks (t(47) = 2.248, p = 0.029, paired t-test) (Table 3). characteristic path length Lp, normalized clustering coefficient c, normalized characteristic path length l and small-worldness s) were fairly reliable (predominantly for long-term reliability) for positive networks. The threshold-independent reliability was presented in the right panel of Figure 6a. Subsequent statistical analyses revealed that, in contrast with the measure-related differences in global network reliability observed for structural ROIs based-networks (Fig. 6b, left and Fig. S6b), there was no significant differences (F(11,77) = 1.298, p = 0.242) among global metrics (Fig. TRT reliability of network metrics: S-HOA 6b, right) for functional ROIs-based networks. Furthermore, unlike the sensitivity of global network reliability to experimental factor of TI and graph-based analytical strategies of NM and NT for structural ROIs-based networks, reliability of functional ROIs-based networks was robust against these factors (p.0.05) (Table 3). Reliability of local nodal metrics. Nodal reliability of S- HOA-based networks (Fig. S8) exhibited the same patterns as those for S-AAL-based networks of 1) factors independent (p.0.05 for all the factors of TI, NM and NT as well as all possible interactions) (Table 3), 2) metric-sensitive (F(5,35) = 12.098, p,1026, degree was the most reliable and least variable) (Fig. S9), and 3) spatial heterogeneous distribution over the brain (Fig. S10a). The most reliable regions were also mainly unimodal and heteromodal association cortex regions and limbic/paralimbic regions of temporal and parietal lobes that were not replicated by other nodal metrics (Fig. S5b). Also, nodal centrality (Fig. S10b) showed no significant relationship (R2,2%) with nodal reliability (Fig. S10c and d). Reliability of local nodal metrics. Figure 14 delineated the nodal reliability for functional ROIs-based networks. No significant (p.0.05) effects were observed for TI, NM and NT on mean nodal reliability (Table 3), consistent with findings from structural ROIs-based networks (both S-AAL and S-HOA). Also analogous to findings of structural ROIs-based networks, nodal degree was found to show the highest reliability and least variance in compared with others (F(5,35) = 3.041, p = 0.022) (Fig. 8b). After averaged over factors of TI, NM and NT, mean nodal TRT reliability of network metrics: F-DOS Reliability of global network metrics. In compared with structural ROIs-based networks, functional ROIs-based networks showed fair reliability in more global metrics over wider threshold range, especially for networks of positive correlations (Fig. 13). For example, small-world parameters (clustering coefficient Cp, PLoS ONE | www.plosone.org July 2011 | Volume 6 | Issue 7 | e21976 15 Reliability of Brain Functional Networks Figure 13. TRT reliability of global network metrics as a function of sparsity threshold for F-DOS-based networks. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively. Multiple network metrics showed modest reliability in certain threshold range. Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network anlysis; Weighted, weighted network analysis; TRT: test-retest; F- DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g013 Figure 13. TRT reliability of global network metrics as a function of sparsity threshold for F-DOS-based networks. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively. Multiple network metrics showed modest reliability in certain threshold range. Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network anlysis; Weighted, weighted network analysis; TRT: test-retest; F- DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g013 degree reliability showed that there were quite a few reliable regions distributed in bilateral temporal, parietal and the right frontal lobes (Fig. 15a). The nodal centrality pattern (Fig. 15b) can only explain a small fraction (R2,6%) of nodal reliability pattern (Fig. 15c and d). We also noted that the most reliable regions were predominantly located in the right hemisphere (Fig. 15a) and varied across nodal metrics (Fig. S5c). of R-fMRI based brain networks. Our findings suggested continued usage of graph theoretical approaches to explore brain networks and had potential relevance for guiding graph analytical schemes for R-fMRI to achieve reliable results. For global network metrics, we observed overall low TRT reliability. This observation was consistent with results reported in a previous MEG study [12]. Indeed, compared with task engagement, Deuker et al. (2009) found that resting state was related with significantly lower reliability of global network metrics. TRT reliability of network metrics: F-DOS This may be related to variable mental states of participants across scans which induce variations in RSFC [19,20,21,22,23,24,25]. Such discrepancies in RSFC especially in shortcuts or inter-module/component connections [54] may further affect the topological organization of the overall connec- tivity network [28]. To test the possibility, we examined the differences in RSFC strength between scans by paired t-tests. The results revealed that no connections showed significant differences (p,0.05, corrected) across scans, implying the temporal stability of RSFC [27,29,31]. Despite of non-significant differences, our simulation analysese indicated that global network metrics were extremely sensitive to numerical changes in RSFC, especially for small-world parameters and network efficiency. Another possible origin of low TRT reliability is due to low between-subject variance or low ability of global network metrics to differentiate subjects. With that said, the low TRT reliability of global metrics may suggest high consistency of global properties of intrinsic brain networks across subjects. Finally, the noise resulting from MRI PLoS ONE | www.plosone.org Discussion Structural ROIs were obtained mainly in terms of anatomical features of sulcal pattern (S-AAL) [37] or standard anatomical boundaries (S-HOA) [38,39] whereas functional ROIs were derived from previous meta-analyses of fMRI activation studies which carried specific functional informa- tion [40,41]. Furthermore, even for structural ROIs based networks, the modulations of TI, NM and NT differed across parcellations. Previous studies have demonstrated that network properties were sensitive to nodal definition based on parcellation strategies [32,36] and spatial scales [33,34,35]. Nevertheless, it’s hard to conclude which approach or which parcellation is better since all of them are valid and important approaches to uncover brain connectivity architecture from different perspectives [40,43,61,62]. Here, our results provide references for studying intrinsic brain networks, for example, binarized networks should be preferred for S-HOA-based intrinsic brain networks according to our results. data acquisition and coregistration inaccuracy may also influence network reliability, which should be elucidated in the future work. network reliability, which should be elucidated in the future work. Despite of the overall low TRT reliability, some global metrics showed relatively high reliability. For example, lambda showed moderate long-term reliability for structural both S-AAL and S- HOA-based networks. This may be due to the correction of absolute characteristic path length to referenced random networks which compensates for underlying differences of baseline net- works. Further statistical analyses revealed significant differences in TRT reliability among global metrics, suggesting an obvious heterogeneity among different global network metrics in reliably capturing intrinsic brain architecture. Moreover, the profiles of global network reliability presented threshold sensitive patterns indicating the importance of threshold selection for reliable results. These findings raise the question of how to determine threshold for brain network studies. A compromise strategy is to investigate brain networks over a continuum threshold range under the circumstance that no sufficient knowledge exists for prior threshold selection. Several factors were found to significantly affect the TRT reliability of global network metrics. First, inclusion of negative functional connectivity in brain networks tended to decrease TRT reliability of global network properties. Previous evidence has manifested that negative correlations showed greater population and state related variance in the spatial maps [55] and lower TRT reliability [27] relative to positive correlations. Consistent with these findings, our results suggest that negative connectivity should be treated with cautions for resting-state brain network studies, which may reduce the TRT reliability. Discussion In the present study, we examined the test-retest reliability of topological metrics of intrinsic connectivity networks derived from human brain R-fMRI data. First, we replicated previous findings that RSFC exhibited modest to high test-retest reliability [27]. Further reliability analyses of network metrics highlighted several main findings: 1) that global network metrics showed overall poor to low but threshold-sensitive reliability; 2) that local nodal metrics were fairly reliable for association and limbic/paralimbic cortex regions; 3) that reliability of network metrics (both global and local) differed significantly among the measures examined; 4) that reliability of global network metrics depended on multiple experiment and analytical factors while nodal reliability was robust to these factors; and 5) that weighted networks (compared to binarized networks) and nodal (compared to global) network metrics were numerically more reliable in the face of noise in functional connectivity. Taken together, we provided a systemat- ically quantitative TRT reliability evaluation of topological metrics PLoS ONE | www.plosone.org July 2011 | Volume 6 | Issue 7 | e21976 16 Reliability of Brain Functional Networks PLoS ONE | www.plosone.org July 2011 | Volume 6 | Issue 7 | e21976 July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 17 Reliability of Brain Functional Networks Reliability of Brain Functional Networks Figure 14. TRT reliability of nodal metrics for F-DOS-based networks. Nodal reliability varied across nodal attributes and spatial locations. The full names of region’s abbreviations were listed as in Table S3. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively. Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; TRT, test-retest; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010). doi:10.1371/journal.pone.0021976.g014 indicating a robust finding. Nevertheless, further work is needed to verify this finding and aid in our understanding of how network topology interacts with the scanning procedure of time interval. Finally, TRT reliability of global network metrics was modulated by strategies of network node definition. Specifically, reliability of only structural (S-AAL and S-HOA) rather than functional (F-DOS) ROIs-based networks depended on the factors of TI, NM and NT. The discrepancy may reflect different approaches of generating ROIs. Discussion It should be noted that the emergence of negative connectivity is related with the global signal regression, a currently controversial step in preprocessing R-fMRI data [56,57,58,59]. For local nodal metrics, nodal degree showed the highest reliability and least variance across factors of TI, NM and NT among the six nodal metrics. Using this metric, we found that some association cortex and limbic/paralimbic regions exhibited fair to good TRT reliability for S-AAL and S-HOA derived networks, such as precuneus, angular gyrus, superior forntal gurus, paracentral lobule, supramarginal gyrus, anterior cingulate gyrus, hippocampus and parahippocampal gyrus. Most of these regions have been identified to serve as structural or functional hubs/connectors in human brain networks [43,44,54,60, 63,64,65,66]. For F-DOS derived networks, more regions were modestly reliable, predominately located in the right frontal lobe and bilateral parietal and temporal lobes. Hubs are essential in supporting the performance of high cognitive functions of the human brain by integrating specialized brain regions into coordinated networks. Buckner and colleagues [64] demonstrated that the topography of human brain cortical hubs is highly similar across populations and robust against task states, therefore reflecting a stable property of brain functional architecture. Here, our results indicate that those reliable regions qualitatively tend to serve as hubs in intrinsic functional brain networks. Nonetheless, our quantitative analysis found that nodal reliability showed low correlations (although significant) with nodal centrality (R2,10%), suggesting limited predictive ability of nodal centrality on reliability. These findings imply that there may exist other factors affecting nodal reliability, such as the spatial locations of nodes or regions. Indeed, we found that posterior regions were more reliable than anterior regions even after correcting for the differences in functional connectivity across regions. This may reflect the nature of the brain in which the neural dynamics of spatially different brain regions are differently constrained in the resting-state. It would be an Second, binarized networks outperformed weighted networks in TRT reliability of global network metrics. This finding seemed counterintuitive. Indeed, weighted networks could characterize network topology more precisely and detect more subtle network topological changes than binarized networks due to the consider- ation of connectivity strength [60]. However, this is not necessary to mean better reliability for weighted networks since the possibility that weighted networks may introduce simultaneously extra noise or overly model individual specific details. All these may lead to more within-subject variance (i.e., variance across scans) and thus lower reliability. Discussion (a) Nodal TRT reliability was mapped in anatomical space after average across scanning time interval, network type and network membership because of no effects of these factors on nodal reliability. (b) Nodal degree centrality (AUCs) was also mapped in anatomical space which was averaged across subjects and factors of scanning time interval, network type and network membership. Trend lines were further obtained by linear least-square fit to reveal the relationship between nodal degree centrality and their corresponding reliability after with (d) and without (c) correcting for the effects of regional size. Of note, the full names of region’s abbreviations were listed as in Table S1. TRT, test-retest; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010); k, nodal degree; A, anterior; P, posterior; L, left; R, right. doi:10.1371/journal.pone.0021976.g015 Reliability of Brain Functional Networks Figure 15. Nodal TRT reliability of degree and its relationship with nodal degree centrality for F-DOS-based networks. (a) Nodal TRT reliability was mapped in anatomical space after average across scanning time interval, network type and network membership because of no effects of these factors on nodal reliability. (b) Nodal degree centrality (AUCs) was also mapped in anatomical space which was averaged across subjects and factors of scanning time interval, network type and network membership. Trend lines were further obtained by linear least-square fit to reveal the relationship between nodal degree centrality and their corresponding reliability after with (d) and without (c) correcting for the effects of regional size. Of note, the full names of region’s abbreviations were listed as in Table S1. TRT, test-retest; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010); k, nodal degree; A, anterior; P, posterior; L, left; R, right. doi:10 1371/journal pone 0021976 g015 Figure 15. Nodal TRT reliability of degree and its relationship with nodal degree centrality for F-DOS-based networks. (a) Nodal TRT reliability was mapped in anatomical space after average across scanning time interval, network type and network membership because of no effects of these factors on nodal reliability. (b) Nodal degree centrality (AUCs) was also mapped in anatomical space which was averaged across subjects and factors of scanning time interval, network type and network membership. Trend lines were further obtained by linear least-square fit to reveal the relationship between nodal degree centrality and their corresponding reliability after with (d) and without (c) correcting for the effects of regional size. Discussion Of note, our simulation results showed that weighted networks generated numerically more stable results against noise in functional connectivity in comparison to binarized networks. This suggests that the observed reliability derived from actual R-fMRI data were affected by various factors, not a single factor of numerical changes in functional connectivity. Third, long-term scans showed higher TRT reliability of global network metrics than short-term scans. This finding was contrast to previous findings that RSFC exhibited higher TRT reliability for short-term interval scans [27]. It may reflect the fact that the average of scan2 and scan3 in the current study can potentially improve the estimation of long-term reliability, i.e., reduce within- session noise [29,30]. To test this interpretation, we further calculated the long-term TRT reliability by using scan1 and scan3 and again found a long-term-larger-than-short-term pattern, Second, binarized networks outperformed weighted networks in TRT reliability of global network metrics. This finding seemed counterintuitive. Indeed, weighted networks could characterize network topology more precisely and detect more subtle network topological changes than binarized networks due to the consider- ation of connectivity strength [60]. However, this is not necessary to mean better reliability for weighted networks since the possibility that weighted networks may introduce simultaneously extra noise or overly model individual specific details. All these may lead to more within-subject variance (i.e., variance across scans) and thus lower reliability. Of note, our simulation results showed that weighted networks generated numerically more stable results against noise in functional connectivity in comparison to binarized networks. This suggests that the observed reliability derived from actual R-fMRI data were affected by various factors, not a single factor of numerical changes in functional connectivity. Third, long-term scans showed higher TRT reliability of global network metrics than short-term scans. This finding was contrast to previous findings that RSFC exhibited higher TRT reliability for short-term interval scans [27]. It may reflect the fact that the average of scan2 and scan3 in the current study can potentially improve the estimation of long-term reliability, i.e., reduce within- session noise [29,30]. To test this interpretation, we further calculated the long-term TRT reliability by using scan1 and scan3 and again found a long-term-larger-than-short-term pattern, July 2011 | Volume 6 | Issue 7 | e21976 PLoS ONE | www.plosone.org 18 Reliability of Brain Functional Networks Figure 15. Nodal TRT reliability of degree and its relationship with nodal degree centrality for F-DOS-based networks. Reliability of Brain Functional Networks Figure S3 Relationship between RSFC and TRT reliability for S-HOA-based correlation matrices. Scatter plots of mean connectivity strength against corresponding ICC values are depicted to show the relationship. The trend lines were obtained by linear least-square fit. Significant (p,0.05) positive correlations were found between positive RSFC and their corresponding ICC values for both short-term and long-term scanning. In addition, significant negative correlations were also found for negative RSFC with their corresponding ICC values but only for long-term scanning. These findings suggest higher reliability for stronger RSFC. Functional connections linking inter-hemisphere homo- topic regions are highlighted by plus signs (+). RSFC, resting-state functional connectivity; TRT, test-retest; S-HOA, structural ROIs from Harvard-Oxford atlas. (DOC) Figure S3 Relationship between RSFC and TRT reliability for S-HOA-based correlation matrices. Scatter plots of mean connectivity strength against corresponding ICC values are depicted to show the relationship. The trend lines were obtained by linear least-square fit. Significant (p,0.05) positive correlations were found between positive RSFC and their corresponding ICC values for both short-term and long-term scanning. In addition, significant negative correlations were also found for negative RSFC with their corresponding ICC values but only for long-term scanning. These findings suggest higher reliability for stronger RSFC. Functional connections linking inter-hemisphere homo- topic regions are highlighted by plus signs (+). RSFC, resting-state functional connectivity; TRT, test-retest; S-HOA, structural ROIs from Harvard-Oxford atlas. (DOC) Figure S4 The absolute correlation thresholds under each sparsity level for all the three sets of ROIs based networks. The correlation thresholds decrease with the increase of sparsity and are comparable across scans and across subjects for each set of ROIs-based networks. Of note, negative correlations were included. (DOC) In conclusion, we studied the TRT reliability of graph-based network metrics derived from resting-state fMRI data and the effects of several factors on the reliability. Based on our findings, we provide some methodological recommendations for resting- state fMRI community in dealing with brain connectome studies. First, negative correlations need to be excluded or considered with cautions for S-AAL-based brain network studies. Second, binarized networks should be preferred for S-HOA-based brain network studies as compared to weighted networks. Third, reliability of functional ROIs-based networks was robust against the three factors of scanning time, network membership and network type. Finally, nodal metrics (especially nodal degree) could produce more reliable results and are more resilient to functional connectivity disturbances, which should be popularized in future brain network studies. (DOC) Figure S6 TRT reliability of summarized global network metrics (a) and metric-related differences in reliability (b). The area under curve (AUC) of each metric was used to provide threshold-independent reliability estimation. Different metrics showed variable levels of reliability. Several of them were moderately reliable (e.g., lambda and synchronization). Subse- quent statistical analysis revealed significant differences in TRT reliability among the 12 global network metrics, with lambda showing relatively high reliability and low variance. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively in (a). Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; TRT, test-retest; S-HOA, structural ROIs from Harvard-Oxford atlas. (DOC) Discussion Of note, the full names of region’s abbreviations were listed as in Table S1. TRT, test-retest; F-DOS, functional ROIs from Dosenbach et al. (2006, 2010); k, nodal degree; A, anterior; P, posterior; L, left; R, right. doi:10.1371/journal.pone.0021976.g015 Nodal reliability was found to be robust against the factors of TI, NM and NT, regardless of different node definition strategies. Simulation analyses revealed that nodal metrics were highly tolerant of fluctuations in functional connectivity values and were numerically more stable than global network metrics in the face of connectivity noise. The reliable and robust features of nodal interesting question for future studies. Additionally, we noted that the most reliable regions appeared to predominately locate in the right hemisphere for F-DOS and S-HOA based networks. Hence, exploring brain functional asymmetry from the perspective of reliability may provide more insights into the brain’s functional architecture. interesting question for future studies. Additionally, we noted that the most reliable regions appeared to predominately locate in the right hemisphere for F-DOS and S-HOA based networks. Hence, exploring brain functional asymmetry from the perspective of reliability may provide more insights into the brain’s functional architecture. PLoS ONE | www.plosone.org July 2011 | Volume 6 | Issue 7 | e21976 19 Reliability of Brain Functional Networks Reliability of Brain Functional Networks metrics propose local nodal metrics as reliable candidates to reveal topological organization of intrinsic functional brain networks. Fig. 2). Moreover, a significant (p,0.05) correlation was found in the ICC matrices between short-term and long-term scans (c). Functional connections linking inter-hemisphere homotopic re- gions, as highlighted by plus signs (+), showed high connectivity strength and many of them exhibited high reliability. TRT, test- retest; RSFC, resting-state functional connectivity; S-HOA, structural ROIs from Harvard-Oxford atlas. Of note, the structural ROIs were listed in the order as in Table S2. (DOC) Fig. 2). Moreover, a significant (p,0.05) correlation was found in the ICC matrices between short-term and long-term scans (c). Functional connections linking inter-hemisphere homotopic re- gions, as highlighted by plus signs (+), showed high connectivity strength and many of them exhibited high reliability. TRT, test- retest; RSFC, resting-state functional connectivity; S-HOA, structural ROIs from Harvard-Oxford atlas. Of note, the structural ROIs were listed in the order as in Table S2. (DOC) There are several issues that remained to be addressed in future. First, the reliability analyses of graph-based network metrics were conducted after several R-fMRI preprocessing steps. To date, how different preprocessing strategies affect the TRT reliability of network metrics is rarely investigated. Specifically, in the current study, RSFC were obtained based on band-pass filtered data (0.01–0.1 Hz). Previous R-fMRI studies have demonstrated frequency specific features for RSFC [67,68,69] and network topology [43,46,70,71]. Accordingly, exploring the impacts of different preprocessing steps on TRT reliability, especially the filtering frequency bands, is an important topic to determine specific processing schemes for consistent, reliable results. Second, we limited our examination of TRT reliability to 12 global network properties and 6 nodal characteristics, which were widely used to characterize brain network architectures. However, there are still a lot of other network metrics, such as motif [72] and vulnerability [73] (for reviews, see [74,75]) whose TRT reliability need to be evaluated in future. Finally, using R-fMRI, we examined the TRT reliability of intrinsic functional brain networks. Previous studies have performed similar analyses of structural or functional brain networks using DTI, MEG, or fMRI data during resting state or cognitive task engagement [10,11,12,13]. Despite these advances, a systematic reliability evaluation using multimodal data from the same cohort of population is warranted to gain more insights into human brain’s structural and functional architectures. Reliability of Brain Functional Networks Nonetheless, we pointed out that further work is necessary to standardize the methodological framework on this burgeoning field. Figure S5 Ranks of reliable regions revealed by nodal degree over other nodal metrics. (a) S-AAL-based networks; (b), S-HOA- based networks; (c) F-DOS-based networks. The ranks of those most reliable regions in terms of nodal degree (regions with ICC.0.4 in Fig. 9a, Fig. S10a and Fig. 15a) changed dramatically over nodal metrics for all ROIs sets, indicating inconsistency for most reliable regions. The full names of region’s abbreviations were listed as in Table S1, S2 and S3. (DOC) References 1. Sporns O, Tononi G, Kotter R (2005) The human connectome: A structural description of the human brain. PLoS Comput Biol 1: e42. 1. Sporns O, Tononi G, Kotter R (2005) The human connectome: A structural description of the human brain. PLoS Comput Biol 1: e42. 15. Fox MD, Raichle ME (2007) Spontaneous fluctuations in brain activity observed with functional magnetic resonance imaging. Nat Rev Neurosci 8: 700–711. 16. Zhang D, Raichle ME (2010) Disease and the brain’s dark energy. Nat Rev Neurol 6: 15–28. 2. Biswal BB, Mennes M, Zuo XN, Gohel S, Kelly C, et al. (2010) Toward discovery science of human brain function. Proc Natl Acad Sci U S A 107: 4734–4739. 17. Wang J, Zuo XN, He Y (2010) Graph-based network analysis of resting-state functional MRI. Front Syst Neurosci 4: 16. 3. Bullmore E, Sporns O (2009) Complex brain networks: graph theoretical analysis of structural and functional systems. Nat Rev Neurosci 10: 186–198. 18. Chang C, Glover GH (2010) Time-frequency dynamics of 18. Chang C, Glover GH (2010) Time-frequency dynamics of resting-state connectivity measured with fMRI. Neuroimage 50: 81–98. 4. He Y, Evans A (2010) Graph theoretical modeling of brain connectivity. Curr Opin Neurol 23: 341–350. 19. Greicius MD, Kiviniemi V, Tervonen O, Vainionpaa V, Alahuhta S, et al. (2008) Persistent default-mode network connectivity during light sedation. Hum Brain Mapp 29: 839–847. 5. Guye M, Bettus G, Bartolomei F, Cozzone PJ (2010) Graph theoretical analysis of structural and functional connectivity MRI in normal and pathological brain networks. MAGMA. 20. Horovitz SG, Braun AR, Carr WS, Picchioni D, Balkin TJ, et al. (2009) Decoupling of the brain’s default mode network during deep sleep. Proc Natl Acad Sci U S A 106: 11376–11381. 6. Stam CJ, Reijneveld JC (2007) Graph theoretical analysis of complex networks in the brain. Nonlinear Biomed Phys 1: 3. 7. Bullmore ET, Bassett DS (2010) Brain Graphs: Graphical Models of the Human Brain Connectome. Annu Rev Clin Psychol. 21. Horovitz SG, Fukunaga M, de Zwart JA, van Gelderen P, Fulton SC, et al. (2008) Low frequency BOLD fluctuations during resting wakefulness and light sleep: a simultaneous EEG-fMRI study. Hum Brain Mapp 29: 671–682. 7. Bullmore ET, Bassett DS (2010) Brain Graphs: Brain Connectome. Annu Rev Clin Psychol. 8. He Y, Chen Z, Gong G, Evans A (2009) Neuronal networks in Alzheimer’s disease. Neuroscientist 15: 333–350. 22. Reliability of Brain Functional Networks time interval, network type and network membership. Trend lines were further obtained by linear least-square fit to reveal the relationship between nodal degree centrality and their corre- sponding reliability after with (d) and without (c) correcting for the effects of regional size. Of note, the full names of region’s abbreviations were listed as in Table S2. TRT, test-retest; S-HOA, structural ROIs from Harvard-Oxford atlas; k, nodal degree; A, anterior; P, posterior; L, left; R, right. (DOC) and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network anlysis; Weighted, weighted network analysis; TRT: test-retest; S-HOA, structural ROIs from Harvard-Oxford atlas. (DOC) Figure S8 TRT reliability of nodal metrics for S-HOA-based networks. Nodal reliability varied across nodal attributes and spatial locations. Moreover, removing negative correlations seemed to result in more regions showing higher reliability in more nodal attributes (predominantly for binarized networks). The full names of region’s abbreviations were listed as in Table S2. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively. Network (+/-), networks constructed using absolute both positive and negative correlations; Network (+), networks constructed using only positive correlations; Binarized, binarized network analysis; Weighted, weighted network analysis; TRT, test- retest; S-HOA, structural ROIs from Harvard-Oxford atlas. (DOC) Table S1 Regions of interest from S-AAL. (DOC) Table S2 Regions of interest from S-HOA. (DOC) Table S3 Regions of interest from F-DOS. (DOC) Table S4 Correlation coefficients between long-term reliability estimated by scan1 and the average of scan 2 and scan 3 and those estimated by scan 1 and scan 3 alone. (DOC) Figure S9 Boxplot of mean nodal TRT reliability for S-HOA- based networks. Significant differences were found in the mean nodal reliability among the six nodal metrics examined with nodal degree showing the highest ICC values and least variances. TRT, test-retest; S-HOA, structural ROIs from Harvard-Oxford atlas. (DOC) Text S1 Mathematical definitions of network metrics. (DOC) Acknowledgments We thank Mr. Jonathan Adelstein for his assistance in language editing. We thank Mr. Jonathan Adelstein for his assistance in language editing. Figure S10 Nodal TRT reliability of degree and its relationship with nodal degree centrality for S-HOA-based networks. (a) Nodal TRT reliability was mapped in anatomical space after average across scanning time interval, network type and network mem- bership because of no effects of these factors on nodal reliability. (b) Nodal degree centrality (AUCs) was also mapped in anatomical space which was averaged across subjects and factors of scanning Author Contributions Conceived and designed the experiments: YH. Performed the experiments: MPM. Analyzed the data: JHW XNZ. Contributed reagents/materials/ analysis tools: JHW XNZ SG MPM BBB YH. Wrote the paper: JHW XNZ YH. Conceived and designed the experiments: YH. Performed the experiments: MPM. Analyzed the data: JHW XNZ. Contributed reagents/materials/ analysis tools: JHW XNZ SG MPM BBB YH. Wrote the paper: JHW XNZ YH. Supporting Information Figure S1 Spatial locations of functionally defined ROIs. These ROIs broadly but not completely cover the cerebral cortex and cerebellum without any overlap between ROIs and were associated with five functions of error-processing, default-mode, memory, language and sensorimotor. A, anterior; P, posterior; L, left; R, right. Figure S2 Spatial similarity and TRT reliability patterns of S- HOA-based RSFC. Mean Pearson correlation matrices (a), consistency of overall patterns between mean matrices (b) and TRT reliability of individual connections as well as the relationship between short-term and long-term reliability (c) are illustrated. The mean correlation matrices exhibited high similarity from both visual inspection (a) and quantitative spatial correlation analyses (b). Further TRT reliability analyses revealed many connections exhibiting fair to excellent reliability (c, also see Figure S7 TRT reliability of global network metrics as a function of sparsity threshold for S-HOA-based networks. ICC values less than 0.25 were mapped to a single color of dark blue as well dark red color for ICC values greater than 0.75, respectively. Network (+/-), networks constructed using absolute both positive PLoS ONE | www.plosone.org July 2011 | Volume 6 | Issue 7 | e21976 20 Reliability of Brain Functional Networks Reliability of Brain Functional Networks Neuron 50: 799–812. 42. Fox MD, Snyder AZ, Vincent JL, Corbetta M, Van Essen DC, et al. (2005) The human brain is intrinsically organized into dynamic, anticorrelated functional networks. Proceedings of the National Academy of Sciences of the United States of America 102: 9673–9678. 66. 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PLoS ONE | www.plosone.org July 2011 | Volume 6 | Issue 7 | e21976 21 July 2011 | Volume 6 | Issue 7 | e21976 Reliability of Brain Functional Networks Costa LdF, Rodrigues FA, Travieso G, Boas PRV (2007) Characterization of complex networks: A survey of measurements. Advances in Physics 56: 167 - 242. y y 49. Stratford PW (1989) Confidence limits for your ICC. Phys Ther 69: 237–238. 50. Winer BJ (1971) Statistical principles in experimental design. New York: McGraw-Hill press. pp 283–293. 74. Rubinov M, Sporns O (2010) Complex network measures of brain connectivity: uses and interpretations. Neuroimage 52: 1059–1069. 51. Sampat MP, Whitman GJ, Stephens TW, Broemeling LD, Heger NA, et al. (2006) The reliability of measuring physical characteristics of spiculated masses on mammography. Br J Radiol 79 Spec No 2: S134–140. 75. Boccaletti S, Latora V, Moreno Y, Chavez M, Hwang DU (2006) Complex networks: Structure and dynamics. Physics Reports 424: 175–308. 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Implementation of SLAM, Navigation, Obstacle Avoidance, and Path Planning of a Robust Mobile Robot Using 2D Laser Scanner
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IMPLEMENTATION OF SLAM, NAVIGATION, OBSTACLE AVOIDANCE, AND PATH PLANNING OF A ROBUST MOBILE ROBOT USING 2D LASER SCANNER by Omid Karimpour A project presented to Ryerson University in partial fulfillment of the requirements for the degree of Master of Engineering in the program of Electrical and Computer Engineering ©Omid Karimpour, 2019 Author's Declaration I hereby declare that I am the sole author of this project. This is a true copy of the project, including any required final revisions, as accepted by my examiners. I authorize Ryerson University to lend this thesis to other institutions or individuals for the purpose of scholarly research. I further authorize Ryerson University to reproduce this thesis by photocopying or by other means, in total or in part, at the request of other institutions or individuals for the purpose of scholarly research. I understand that my thesis may be made electronically available to the public. I understand that my thesis may be made electronically available to the public. ii 2019 Over the last decade, navigation and Simultaneous Localization and Mapping (SLAM) have become key players in developing robust mobile robots. Several SLAM approaches utilizing camera, laser scan, sonar and fusion of sensors were developed and improved by a number of researchers. In this thesis, comparisons of these methods were evaluated, especially those offering low cost benefits, and low computation and memory consumption. The aim of this thesis was to select the most reliable and cost-efficient approach for indoor autonomous robotic applications. Currently, there are numerous studies that have optimized these SLAM methods; however, they still suffer from various complications such as scale drifting and excessive computation. This study performed different experiments to observe these challenges in real- world environments. A modified Pioneer robot was used to implement the selected SLAM system and furthermore, perform obstacle avoidance and path planning in indoor office environments. The results and tests show the reliable performance of Gmapping after tuning its parameter and set right configurations. iii Acknowledgements I’m thankful to many people for their continuing support of this work. Above all, I’d like to acknowledge my professor Dr. Alexander Ferworn, who always believed in my abilities and never hesitated with inspirational support. His trust made me believe in myself more than ever and gave the freedom to explore this field and pursue my passion. The collaboration and discussions throughout my time in Network-Centric Applied Research Team (NCART) Lab, paved the way for my future works. I’d like to acknowledge my friend Mohammadreza Mousaei, without his help and support I would never take this path, his uninterrupted guidance is notable during this work and my life. Last but not least, thank all lab mates. iv Dedication Dedicated to my parents who’ve supported me and trusted me, in academy and life. My mother, her infinite love and support can hardly be expressed by words. My father with spending all his life to provide us with a brighter future. My father with spending all his life to provide us with a brighter future. Table of Contents Table of Contents ABSTRACT . ................................................................................................................................................ III LIST OF FIGURES ................................................................................................................................... VIII GLOSSARY ................................................................................................................................................ X SECTION 1. INTRODUCTION ...................................................................................................................... 1 1.1. OVERVIEW OF THE PROJECT ........................................................................................................... 1 SECTION 2. LITERATURE REVIEW AND PREVIOUS WORKS................................................................ 4 2.1. SIMULTANEOUS LOCALIZATION AND MAPPING .................................................................................. 4 2.1.1. Introduction to SLAM................................................................................................................... 5 2.1.2. Vision-Based SLAM Algorithms .................................................................................................. 7 2.1.2.1. Semi-direct Visual Odometry (SVO).................................................................................................... 8 2.1.2.2. Dense Piecewise Planar Tracking and Mapping SLAM ...................................................................... 8 2.1.2.3. Large Scale Direct SLAM .................................................................................................................... 8 2.1.2.4. Direct Sparse Odometry ...................................................................................................................... 9 2.1.2.5. ORB SLAM ........................................................................................................................................ 10 2.1.2.6. Stereo Parallel Tracking and Mapping .............................................................................................. 10 2.1.3. LIDAR-based SLAM Algorithms ................................................................................................ 10 2.1.3.1. KartoSLAM ........................................................................................................................................ 11 2.1.3.2. Core SLAM ........................................................................................................................................ 12 2.1.3.3. Lago SLAM........................................................................................................................................ 12 2.1.3.4. Cartographer ..................................................................................................................................... 13 2.1.3.5. HectorSLAM ...................................................................................................................................... 13 2.1.3.6. Gmapping .......................................................................................................................................... 14 2.2. PRE-MAPPING ............................................................................................................................... 14 2.3. LOOP CLOSURE ............................................................................................................................ 16 SECTION 3. IMPLEMENTATION TECHNIQUES ...................................................................................... 17 SECTION 2. LITERATURE REVIEW AND PREVIOUS WORKS................................................................ 4 2.1. SIMULTANEOUS LOCALIZATION AND MAPPING .................................................................................. 4 2.1.1. Introduction to SLAM................................................................................................................... 5 2.1.2. Vision-Based SLAM Algorithms .................................................................................................. 7 2.1.2.1. Semi-direct Visual Odometry (SVO).................................................................................................... 8 2.1.2.2. Dense Piecewise Planar Tracking and Mapping SLAM ...................................................................... 8 2.1.2.3. Large Scale Direct SLAM .................................................................................................................... 8 2.1.2.4. Direct Sparse Odometry ...................................................................................................................... 9 2.1.2.5. ORB SLAM ........................................................................................................................................ 10 2.1.2.6. Stereo Parallel Tracking and Mapping .............................................................................................. 10 2.1.3. LIDAR-based SLAM Algorithms ................................................................................................ 10 2.1.3.1. KartoSLAM ........................................................................................................................................ 11 2.1.3.2. Core SLAM ........................................................................................................................................ 12 2.1.3.3. Lago SLAM........................................................................................................................................ 12 2.1.3.4. Cartographer ..................................................................................................................................... 13 2.1.3.5. HectorSLAM ...................................................................................................................................... 13 2.1.3.6. Gmapping .......................................................................................................................................... 14 2.2. PRE-MAPPING ............................................................................................................................... 14 2.3. LOOP CLOSURE ............................................................................................................................ 16 SECTION 3. IMPLEMENTATION TECHNIQUES ...................................................................................... 17 3.1. HARDWARE SYSTEM ..................................................................................................................... 18 vi 3.2. SOFTWARE SYSTEM ...................................................................................................................... 22 3.2.1. ROS ........................................................................................................................................... 23 3.2.2. RPLIDAR Setup on ROS .......................................................................................................... 25 3.2.3. Pioneer 2DX Setup on ROS ..................................................................................................... 27 3.2.4. SLAM ......................................................................................................................................... 28 3.2.5. Localization ............................................................................................................................... 31 3.2.6. Navigation Stack ....................................................................................................................... 32 SECTION 4. CONDUCTED TESTS AND RESULTS ................................................................................. 33 4.1. CHALLENGES AND OBSERVATIONS................................................................................................. 37 4.1.1. Small and Narrow Obstacles and Different Surfaces ............................................................... 38 4.1.2. Glass Detection Challenge ....................................................................................................... 39 4.1.3. Stairs Detection and Mapping Challenge ................................................................................. 41 4.1.4. Loop Closure Challenge............................................................................................................ 44 4.1.5. Disaster Area’s Pre-mapping Practical Objection ..................................................................... 44 4.1.6. Dynamic Environments ............................................................................................................. 45 4.2. SENSOR FUSION ........................................................................................................................... 45 SECTION 5. CONCLUSION AND FUTURE WORK .................................................................................. 47 5.1. FUTURE WORK ................................................................................................................................... 47 APPENDICES ............................................................................................................................................. 49 REFERENCES ............................................................................................................................................ 59 vii List of Figures Figure 1: Table and glass manual adjustment of the map prior to the localization ...................... 15 Figure 2: Pioneer 2DX physical dimensions [24] ......................................................................... 18 Figure 3: Robot set up using pioneer 2DX, laptop and serial port [24] ........................................ 19 Figure 4: Supposed to be a RPDIDAR photo ............................................................................... 20 Figure 5: RPLIDAR dimensions [25] ........................................................................................... 21 Figure 6: Regulator DE-SWADJ .................................................................................................. 22 Figure 7: System overview ........................................................................................................... 24 Figure 8: Visualization of ROS a) Performing Gmapping in real world b) Performing Gmapping using Gazebo simulation ............................................................................................................... 25 Figure 9: RPLIDAR placement .................................................................................................... 26 Figure 10: 2nd floor of engineering building’s map (Large loop) ................................................. 30 Figure 11: NCART lab’s map (Small loop) .................................................................................. 30 Figure 12: Initial localization process in NCART lab .................................................................. 31 Figure 13: Path being plan by this system in NCART Lab .......................................................... 32 Figure 14:: NCART map with velocity of 1 m/s ...................................................................... 35 Figure 15: NCART map with velocity of 1.5 m/s ...................................................................... 35 Figure 16: NCART map with velocity of 2 m/s ....................................................................... 35 Figure 17: NCART map with velocity of 3 m/s ....................................................................... 35 Figure 18: Loop closure test in 2nd floor Engineering building Ryerson University (The break on top of the map shows he mismatch h) ........................................................................................... 35 Figure 19: NCART loop closure test (Small loop) ....................................................................... 36 viii Figure 20: Bumpy areas were substituted with books, metal and wood plates ............................ 39 Figure 21: Glass detection test in front of the glass ...................................................................... 40 Figure 22: The top part shows glass scans and how they fail to detect the glass ......................... 41 Figure 23: Stairs in engineering building...................................................................................... 42 Figure 24: Mapping stairs using Gmapping as the robot is going up ........................................... 43 Figure 25: Mapping stairs using Gmapping as the robot is going down ...................................... 43 ix Glossary x Autonomous Mobile Robot ActiveMedia Robotics Interface for Applications Dense Piecewise Planar Tracking & Mapping Direct Sparse Odometry Laser Scanner Large Scale Monocular Network Centric Applied Research Team Personal Computer Particle Filter Rao-Blackwellized particle filter Root Mean Square Error Robot Operating System Real-Time Appearance-Based Mapping Extended Kalman Filter Simultaneous Localization & Mapping Stereo Parallel Tracking and Mapping Sparse Pose Adjustment Semi-direct Visual Odometry Unmanned Aerial Vehicle Unmanned Ground Vehicle Robot Model Description Urban Search and Rescue AMR: ARIA: DPP-TAM: DSO: LIDAR: LSM: NCART: PC: PF: RBPF: RMSE: ROS: RTAB-Map: SKF: SLAM: SP-TAM: SPA: SVO: UAV: UGV: URDF: USAR: AMR: ARIA: DPP-TAM: DSO: LIDAR: LSM: NCART: PC: PF: RBPF: RMSE: ROS: RTAB-Map: SKF: SLAM: SP-TAM: SPA: SVO: UAV: UGV: URDF: USAR: Autonomous Mobile Robot ROS: x Section 1. Introduction Over the past decades, mobile robot applications have been a source of attention. There are several major areas of interests such as mapping of indoor and outdoor environments, localizing the robot in a pre-mapped environment, and performing both tasks simultaneously which is called Simultaneous Localization and Mapping (SLAM) [1]. Nowadays, there is a dramatic increase in mobile robotic research where new algorithms are being proposed to address SLAM and navigation challenges. Moreover, many investigations and experience have improved these algorithms to reduce the amount of redundant data processing resulted in more efficient computation and the ability to utilize multi-sensors. Recent studies in the Robot Operating System (ROS), SLAM, Navigation stacks, layered Costmap, obstacle avoidance, and other optimization techniques, make it possible to process more data with limited processing power and memory. These findings improve the overall result by developing other approaches such as utilizing sensor fusion. It is important however, not to assume that these techniques will work in all cases. 1.1. Overview of the Project The objective of this project is to determine a robust and reliable SLAM system that could perform in an indoor environment utilizing low-cost sensors and processing power. First and foremost a survey of various SLAM systems was conducted. We avoided approaches that rely on highly accurate sensors and high computation hardware as they come at a high cost. These methods often utilize more than one type of sensor. We outlined the advantages and disadvantages of popular vision and Light Imaging Detection and Ranging (LIDAR)-based algorithms and among 1 them, Gmapping provided the most reliable result. Gmapping SLAM algorithm has been implemented on a customized Pioneer 2dx platform to perform SLAM, obstacle avoidance, and path planning using Navigation Stack. Thereafter, we investigated several optimization methods such as Layered Costmap. This method enhanced the map by layering different features and landmarks especially in dynamic areas. This dynamic layer is unstable and causes a constant change in the robot navigation. The Layered Costmap also sets other layers such as sensor fusion, sonar and LIDAR to provide faster and reliable navigation. We dedicate part of the second section explaining the limitations and challenges of layered Costmap in different mobile robot applications. In general, different layers of the Costmap are configured to contain selected landmarks. These layers are being established so that the algorithm could detect different areas with their corresponding features. This allows the navigation to plan out the fastest path by making adjustments such as avoiding dynamic areas. These navigation decisions are being made by a path planner; therefore, an accurate scan measurement is critical. Another navigation challenge that can occur is detecting glass in new office buildings. Low-cost laser scanners such as RPLIDAR are not able to fully recognize glass resulting in a misguided path. Currently, there is only a few studies on this complication which has been reviewed in the literature review section, particularly pre- mapping which offers a low-cost solution. Other challenges to the navigation system that are briefly outlined are freer zone likelihood, and personal space. In the Implementation and Conducted Tests and Results sections we disclose our experiments where a detailed step-by-step implementation of SLAM, Navigation Stack, Obstacle avoidance, Path planning and other methodologies using RPLIDAR, and Pioneer mobile robot are 2 2 discussed. Some experiments on avoiding stairs, mapping stairs and practical glass detection. 1.1. Overview of the Project Thereafter, we proposed some possible solutions to resolve mentioned challenges such as stairs detection. Overall in this study, we utilized the ROS, and all configurations, transforms, and Launch files have been added to the system and discussed in detail. The implementations of this project are performed by the ROS Kinetic and C++ Programming language. RVIZ package has been used for visualization of the robot model, movement and other ROS visualizations. All simulations have been performed in Gazebo (9.0.0). 3 Section 2. Literature Review and Previous Works The Robot Operating System is the most popular robotics framework used in robotic research and development around the world. ROS provides a platform which focuses on collaborative and rapid software development in the robotic field. The addition of libraries, packages, and tools to the ROS have simplified roboticists endeavors to build robust robot platforms such as autonomous mobile robot (AMR) [2]. All non-trivial mobile robots are expected to move effectively in a specified environment, localize themselves within some form of mapped representation of the environment, and would typically use the maps to avoid obstacles. Having a map such as this and being able to improve this map is essential for continuous operation in the environment. To make competent decisions about where to move, a path planner is added to the system. The path is being chosen based on the map that has been generated. As localization and mapping are extremely important to mobile robot applications, this section provides an overview of various SLAM systems. 2.1. Simultaneous Localization and Mapping Many AMRs localize themselves with respect to an internal map. The map is devised by various means and is derived through the interpretation of sensor data. This map is never complete and is constantly being augmented and corrected as new sensor data is being measured simultaneously. This concept is a classic example of the “chicken and egg” problem, where the robot does not know where it is, so it attempts to localize itself on a map it creates or tries to build a map so it can determine its location within it. This apparent paradox can be explained through an example. Imagine you are on vacation and parked your car to reach a tourist destination by walking. You know that you eventually have to come back to where you parked. At first, you might start collecting information such as landmarks to remind yourself later where your car is. A café, restaurant, street number and other features or landmarks are some of the parts of a map you build inside your mind and is intended to remind you of the path you have taken and would lead you back to your car. SLAM schemes use a similar approach with the expectation that the location of the robot is accurate in the map since critical mobility functions such as successful obstacle avoidance, path planning and exploration are dependent on the accuracy of SLAM. From this point, several SLAM algorithms have been proposed, but established SLAM algorithms have been thoroughly investigated and will be discussed here. Among all these SLAM algorithms, Gmapping, Hector SLAM and cartographer are found to be more robust and accurate. The objective of all SLAM systems is to read the sensor measurements, send series of controls during a period of time to compute the pose estimation of the Robot, and map the environment simultaneously. These arguments are usually probabilistic, based on a given map, sensor measurements, controls, and the pose. The algorithm calculates the belief which is the knowledge of the robot from its state in the environment. The most general algorithm to calculate the robot’s state is the Bayes filter [3]. 2.1.1. Introduction to SLAM While there is a plethora of SLAM systems that are used for indoor and outdoor mobile robot applications, this project is focused on indoor environments. Furthermore, this section will discuss the number of SLAM systems that exist in ROS. The state-of-the-art algorithms and ease 5 of implementation are some of ROS strengths. This section discusses the advantages and disadvantages of several SLAM systems and how it relates to the proposed system. The proposed system is a LIDAR-based SLAM system. Further details of this selection are presented in the next section along with the technical approach. A survey of other works that used this approach will be explained here. In contrast, we also discussed visual SLAM systems and why they are unsuitable for the proposed system. We also expanded some of the experiments conducted by Maksim Filipenko and Ilya Afanasyev in some of these vision-based and LIDAR-based SLAM methods [4]. While there are a vast variety of sensors, camera and LIDAR-based approaches, this thesis examined monocular, stereo camera, and laser scanners because they are commonly used for this type of system. A technique that combines these sensor data from different sources is called sensor fusion which results in less uncertainty and more dependable data. Undoubtedly, the idea of sensor fusion was impossible up until the last decade due to processing and memory limitations. However, several algorithms and developments have contributed to making sensor fusion possible. One of these developments have utilized sensor fusion to accurately map a glass office environment without pre-mapping or adding extra adjustments. Explicit discussion in the sensor fusion utilizing LIDAR, sonar/advanced sonar [5] and cameras; tuning SLAM parameters [6]; and their effects on SLAM accuracy, have been conducted in the next section to search for an optimal solution for indoor AMR applications and their challenges. These Approaches are discussed in the following two different sections: vision-based SLAM algorithms and LIDAR-based SLAM Algorithms including the challenges of these approaches. Overall performance of vision-based SLAM systems depends on the computation resource. The focus of this project is on a limited hardware; therefore, visual SLAM approaches are not an optimal choice. However, we will go through these vision-based methods only to analyze their performances in different environments. A discussion on the comparison of LIDAR-based SLAM performances shows that mapping Cartographer, and Hector SLAM provide more accurate results compared to KartoSLAM, Core SLAM, and Lago SLAM algorithms. 2.1.1. Introduction to SLAM However, issues with these approaches are that Cartographer suffers from the blurry effects, Hector SLAM does not provide an accurate result when low rate laser scans are available and Gmapping increases computation and has other challenges such as depletion problem. For the purpose of this project, Gmapping is preferred over other LIDAR systems as an adaptive resampling technique. This technique has been developed by [7] to optimize Gmapping performance. 2.1.2. Vision-Based SLAM Algorithms 7 Vision-based SLAM algorithms are based on either monocular or stereo cameras. Monocular-based approaches require extra modules in order to perform the scale recovery. As the distance between features and the camera cannot be measured in real scale, recovery of these scales is necessary to eliminate this drift of scale. In contrast, stereo cameras achieve reliable results over monocular algorithms as they perform flawlessly without the scale recovery. However, they suffer from the same problem when the distance between the camera and feature is high. Both of these methods could be used as an additional source for pose estimation and mapping. Approaches such as Semi-Direct Visual Odometry (SVO) and Dense Piecewise Planar Tracking and Mapping (DPPTAM) suffer from losing track of robot turns when there is a lack of features in the environment. Other monocular approaches such as Large Scale Direct (LSD) SLAM, Direct Sparse Odometry (DSO) and ORB SLAM are accurate enough if the scale recovery is being used as an additional module. ORB SLAM is the most stable and robust algorithm among other visual SLAMs. We will briefly discuss each of these SLAM approaches and point their advantages and disadvantages. SLAMs. We will briefly discuss each of these SLAM approaches and point their advantages and disadvantages. 2.1.2.2. Dense Piecewise Planar Tracking and Mapping SLAM DDPTAM method is a direct system for pose estimation and uses a similar approach as SVO, but with more accuracy. This direct monocular SLAM algorithm was developed in [9] and resulted in an advanced algorithm containing an uncluttered output with fewer errors in a variety of conditions. There were several comparisons between this method and other monocular methods and overall, higher accuracy and lower processing time was the result of DDPTAM. It is important to mention, that this method is not robust enough and fails on tracking all robot turns. 2.1.2.1. Semi-direct Visual Odometry (SVO) SVO is a popular monocular algorithm which provides a decent accuracy and speed with limited computation in most applications. In [8, 9], this approach has been developed by analyzing the intensity of each pixel using a probabilistic mapping method. This method includes more dependable points than any other monocular approach. This dependable point has been tested by Maksim Filipenko and Ilya Afanasyev [4] in areas and environments without access to GPS. The result is a high frame-rate motion estimation which increases the accuracy and robustness of this method and therefore, makes a great addition for mapping and pose estimation. 2.1.2.3. Large Scale Direct SLAM LSD is another monocular SLAM algorithm which was proposed by [10] and uses a similar approach to the last two methods. However, the advantage of this method is that it provides an accurate pose estimation compared to other methods. The result of this featureless monocular 8 algorithm is a real-time output that filters over a large number of pixelwise stereo comparisons. LSD is a direct tracking method that contemplates the depth value and it is also less susceptible to noise. Some of the novelties of this approach include its ability to detect scale-drift and incorporate noise on the estimated depth using its probabilistic approach. This system also provides a loop closure option to perform flawlessly when any drift error occurs, however, the system has problems with identifying the robot’s initial pose shift and has a poor ROS integration [4]. 2.1.2.6. Stereo Parallel Tracking and Mapping The Stereo Parallel Tracking and Mapping (SP-TAM) SLAM is a real-time and feature- based approach suitable for both indoor, and outdoor environments. It also includes a loop closure with a large range of dynamic areas. This method avoids the boost mapping problem in monocular methods by dividing the tasks into two parts. The first part is the tracking that deals with the camera pose and the second part is mapping that updates a submap with a lower frequency [14]. Overall this method is reliable and robust but has inaccurate localization. 2.1.2.5. ORB SLAM The ORB is a powerful SLAM algorithm, suitable for different environments. Reliable loop closure and robust initializations are other advantages of this feature-based method. Findings from ORB SLAM [13] show that the system produces robust and real-time results because it uses a novel strategy of creating sparse point cloud as the map. This approach has an accurate pose estimation and creates a 3D sparse map [4]. Automatic initialization, bundle adjustment and depth estimation are a number of optimizations that result in a more robust approach. This method is mostly being used in indoor robotics applications and the map is a good approximation of the real world. The only disadvantage of this approach is that scale recovery is not solved which result in a weak trajectory approximation [13]. 2.1.2.4. Direct Sparse Odometry DSO SLAM algorithm is a monocular visual odometry. The main features of this method are calibration, motion bias and shutter effect. In [11], a comparison was conducted on both feature-based and semi-supervised methods. It was found that photometric calibration results in an improvement of direct methods. Moreover, feature-based methods have a large performance bias on certain movements compared to direct methods, whereas direct and semi-direct methods are more sensitive to rolling shutter effect. Therefore, feature-based methods need a higher resolution in order to perform accurately. DSO, like many monocular SLAM systems, has a robust pose tracking, however, it suffers from the lack of a loop closure resulting in a noisy map. The dependency of this method to scale recovery is also a general criticism of this technique [4]. The next two methods are based on Stereo SLAM algorithms. The major advantages of stereo compared to monocular is eliminating the scale recovery step, using the collected databases to process them offline, and delivers an accurate state estimation [12]. 9 2.1.3. LIDAR-based SLAM Algorithms LIDAR measures the duration from sending a laser scan to receiving the reflection to detect the distance and objects around it. LIDARs are not only robust against interference, but also are independent from ambient lights. Some of these SLAM algorithms are more dependent to an 10 accurate LIDAR measurement than others. Among SLAM algorithms that we studied, Gmapping, Hector SLAM, and Cartographer are more robust and reliable than Lago, Karto and CoreSLAM. These algorithms will be outlined in detailed in the sections below. Some of the general comparisons between these algorithms is that Lago SLAM has the highest CPU usage. Another comparison is that Karto results are more accurate than Lago SLAM and are less affected by noise in the real world. However, Karto SLAM provides a less reliable map compared to Gmapping, Hector SLAM and Cartographer. On the other hand, Core SLAM is a simple Particle Filter (PF) approach that requires more particles which lead to a more complex computation. PFs are a set of Monte Carlo algorithms used to solve the filtering problem by estimating the posterior density of the state variable based on given sensor observations [3]. Between the three most robust and reliable algorithms, Cartographer suffers from blurry effects in some cases whereas Hector SLAM only uses scan matching and does not use the odometry data which could be a disadvantage in some environments. Scan matching is a technique that finds the robot’s pose by comparing its positions from two different scans. Relying on only scan matching increases the complexity of computation, and therefore the CPU load. As the industry tries to optimize the cost, keeping the CPU loads low is critical. Gmapping approach is less complex than Hector SLAM and therefore, result in less computation. It also remains a robust and accurate approach among many studies since it utilizes both scan matching and odometry to minimize the use of particles. 2.1.3.2. Core SLAM Core SLAM is based on tiny SLAM algorithm and has been designed to have less computation compared to other approaches [16]. Core SLAM calculates the distance with a variety of sensor measurements and matches these scans with the map to find the optimized pose. Each particle is being assigned a specific weight based on the final pose decision. The lowest weight particle is the least accurate estimation and is being removed. The highest weight particle is the most accurate pose estimation and is the robot’s pose. Finally, an optimization technique maps the obstacles using points around each obstacle [16]. This approach has a more complex computation and is not desirable for projects with limited resources such as this thesis. 2.1.3.1. KartoSLAM The Karto SLAM algorithm is a graph-based SLAM method that was developed by Karto Robotics [15]. Overall, graph-based SLAMs require a loop closure improvement method to be 11 more accurate on large scales. Also, they generate higher efficiency when a higher number of landmarks is being used which evidently requires higher computation and memory usage. Karto SLAM is not suitable for our project not only because adding the loop closure improvement to this method would increase the computation, but also there are other approaches such as Gmapping that would provide a better result with the same CPU load. 2.1.3.4. Cartographer The cartographer approach focuses on the backpack mapping platform, enhancing the loop closure in real time, as well as, other improvements such as branch and bound [18]. This system was developed recently in 2016 and it represents the closest fitting from the 2D LIDAR map to the real world. The tests from [19] show that the difference between trajectories of Cartographer and Hector SLAM are less than 3cm in the root mean square error (RMSE) which means they both demonstrate a similar result. Cartographer also uses pose estimation continuously and includes real-time loop closure. The only downside of Cartographer is the blurry effect which was evaluated by Anton et al. [20] based on analyzing the following metrics: number of corners in a map, enclosed areas, and the proportion of occupied and free cells. 2.1.3.3. Lago SLAM Lago SLAM requires an initial guess of the robot’s pose [17] similar to any other graph- based SLAM methods. Lago SLAM solves a local convex approximation in each step. Then, updates the graph until it reaches a minimum local cost function. This method can take advantage of any optimizer. The results of this method, even after using optimizers, are not as accurate as Karto SLAM and it is more affected by noise than other systems [4]. 12 2.1.3.6. Gmapping Rao-Blackwellized particle filter (RBPF) base methods effectively proposed a solution to the SLAM problem by using PF and creating a grid-based map [7]. Gmapping, a RBPT-based SLAM approach, is an efficient indoor AMR algorithm that is also being utilized particularly in the Search and Rescue (SAR) field. In this method, landmarks are constantly being captured in order to estimate the robot’s pose. Low efficiency in capturing landmarks could result in poor mapping and high efficiency landmark capturing results in lags due to low processing speed. In the study [6], the researchers tuned Gmapping parameters to optimize the number of landmarks with respect to the processing power. However, one of the disadvantages of this algorithm is that a high number of particles are required to achieve an accurate result. Gmapping uses a set of particles to approximate the probability distortion in order to solve the SLAM [7]. An improvement approach called adaptive resampling technique [21], was created to deal with these high volumes of particles. Considering both present and past movements of the robot, the author came up with a distribution accuracy computation to limit the required particles. 2.1.3.5. HectorSLAM Hector SLAM is a flexible and scalable SLAM system, superior in its class, which provides pose estimation with full 6 degrees of freedom [19]. It utilizes limited computation resources resulting in a reduction in both the cost and weight of the robot. Hector SLAM uses an occupancy grid map in order to represent an arbitrary environment, the LIDAR scans are being transformed into a local frame to be stable in event of scanning across 6 degrees of freedom motion. The scans are being converted to the point cloud of LIDAR scan endpoints. These point clouds need to be processed to perform down-sampling. The endpoints are being sorted within the threshold of the intended scan to limit the processing and memory [19]. Compared to Gmapping, this approach has been successful in small case scenarios with unstructured environments such as most disaster areas, however, it is not suitable for large loop closures as it only relies on scan matching. Therefore, Hector mapping is a desirable solution for applications that can’t rely on accurate 13 odometry. As long as high rate scans are being used, Hector SLAM is a reliable and accurate approach. odometry. As long as high rate scans are being used, Hector SLAM is a reliable and accurate approach. 2.2. Pre-mapping In USAR applications, having the floor map, stairs and exits of a building prior to the disaster could help the rescue team outline the areas with more probability of possible survivors. However, glass doors/windows and stairs pose great challenges and may require manual adjustments to modify these areas on the map. This process of mapping is called pre-mapping [22], which serves an important role in better understanding a disaster area. In [22], LIDAR was used to outline this 14 idea, although they faced several problems such as floor plan distortion by a catastrophic event. We will review some of these challenges in more detail in “Problem and Solution” section. It is important to note that current SLAM methods present some shortages such as failing to detect slim objects, glasses, and obstacles that are out of the sensor’s range. A low-cost solution to this issue is to manually adjust the map. The evidence in support of this could be found in some of the tests that we performed on mapping the environment prior to localization shown in Figure 1. These tests result in a better understanding of certain obstacles which are not easily detectable by most sensors and SLAM algorithms. Figure 1: Table and glass manual adjustment of the map prior to the localization Figure 1: Table and glass manual adjustment of the map prior to the localization In one particular study [22], a classroom with narrow tables has been chosen to test the Gmapping. The first test involved an ideal classroom with wider objects and walls that were completely covered by cardboard. This allowed them to evaluate the robot’s Gmapping 15 performance in an ideal environment. For the second test, a similar classroom with narrower spaces and smaller objects resulted in a lack of data as expected. A third and final test was performed in a dynamic classroom with elements from the first two tests. A major evaluation was conducted after all experiments with respect to different SLAM methods in an effort to find the optimal SLAM method. The results were compiled in [22] and their work has proposed pre-mapping as a reliable solution for lack of reliable results in such environments. 2.3. Loop Closure For each SLAM algorithm test, mapping a large loop is an essential part of the process. Without a loop closure optimization, most of these approaches fail to close this loop because of unreliable sensor measurements. In [23], an improved loop closure method was presented and implemented by utilizing a low-cost LIDAR similar to the scanner used in this project. Gmapping with RPLIDAR does not provide an optimal result in small indoor environments since many landmarks need to be captured. Since RPLIDAR measurements are reliable on large scales but not accurate enough on small scales, the loop closure improvement is still an attractive idea in both small and large loop corrections. Loop closure consists of two areas of improvement which are loop correction and loop detection. There are several optimizations in the loop correction, however, loop detection still remains a major challenge. Gmapping registers several different laser measurements including when a robot moves to a certain distance, change direction or in specific time periods, which are all hard to control. To control these registrations, a study developed a Kalman filter-based loop closure improvement method was developed to register the laser scans only when the robot moves to a specific distance [23]. This method assumes that the robot detects the loop accurately, and when the robot revisits the starting point, the loop correction procedure starts and changes the map to result in the closure of the loop. 16 Section 3. Implementation Techniques In this section, a detailed explanation of implementation techniques and the objective behind hardware and software used will be outlined. The types of hardware components reviewed are the Pioneer 2DX, motor controller, RPLIDAR, batteries, host computer and connections. An overview of software will include the ROS, ARIA client program, RPlLIDAR, Gazebo simulation, SLAM system, costmaps, obstacle avoidance and path planning. In this project, Gmapping has been utilized and tested in variety of environments such as offices and rough surface environments. The tests and experiments showed that Gmapping is robust and reliable in such environments. Evidence that supports this finding can be found in the “Conducted Test and Results” section. Since all tests are being performed in the ROS platform, the first step is to interact with Pioneer 2DX using a host computer and Serial-USB port. A connection is established between ARIA and ROS using ROSARIA package and then the system is tested by publishing a velocity command through a ROS topic. Secondly, establish the connection between Rplidar and host computer using Micro USB-USB port. In this host computer the RPLIDAR ROS package and RVIZ simulator is being used to send the scans’ measurements to RVIZ. Before testing the system in the real world, simulations of the EKF and Gmapping SLAMs were run to compare the results and establish a baseline by referencing this map as an ideal map. This system was then tested in a real-world environment by using both small and large loop closure to compare the results. This test was conducted several times at different velocities and scanned frequencies to find the optimal set up for our environment. After generating a map with an optimal set up, it was saved and used in the next step so that the robot can localize itself 17 on this map and perform obstacle avoidance and path planning. In this section, hardware and software components and their implementations are reviewed. on this map and perform obstacle avoidance and path planning. In this section, hardware and software components and their implementations are reviewed. 3.1. Hardware System Pioneer 2DX: This mobile robot has been chosen as the base because the dimensions were ideal compared to other available platforms. In consideration that a host computer has been used in this project, there was no minimum requirement of computation component. Also, the weight of this robot was decreased by applying some modifications which will be discuss in this section. The client-server architecture for this robot was originally developed by Kurt Konolige, Ph.D. Pioneer 2 DX. An ActiveMedia’s robot base has a three-wheel mobile platform including two powered wheels and one caser wheel which allows it to freely rotate. To run this robot, it is essential to either use the onboard microcontroller or host computer with a client server software. ARIA client server was selected because ROS packages for this client server is available and it was suggested by the manufacturer. Physical dimensions of this robot are shown in Figure 4. 18 Figure 2: Pioneer 2DX physical dimensions [24] Figure 2: Pioneer 2DX physical dimensions [24] Figure 2: Pioneer 2DX physical dimensions [24] 18 Several expansion power and I/O ports are available for additional sensors and accessories. RS-232 serial port, digital I/O, A/D ports and other controllers are accessible for clients to communicate with this base and made this robot an ideal choice for our project. Moreover, the motor-power board supplies both 12 and 5 VDC for external accessories. The Pioneer 2DX microcontroller has a 20 MHz Siemens 88C166 with 32k ROM and dynamic RAM, and other I/O ports. A serial port is available on the consul to connect this microcontroller to the client computer (Host) for data exchange [24]. Figure 3: Robot set up using pioneer 2DX, laptop and serial port [24] Figure 3: Robot set up using pioneer 2DX, laptop and serial port [24] The first step before using this base is performing a self-test by pressing the MOTORS button twice after start-up. The self-test consists of two tests which are Motors Test and Sonars test. Motors test start by engaging the left and right drive wheel separately by forward and backward 19 movement. Lastly, it tests each sonar sensor range and connection separately. To confirm the data, distance measurements were retrieved. This self-test was performed to ensure the drivers, motor- power board and connections were working properly. 3.1. Hardware System Figure 4: Supposed to be a RPDIDAR photo Figure 4: Supposed to be a RPDIDAR photo Figure 4: Supposed to be a RPDIDAR photo 20 RPLIDAR: The RPLIDAR A1M8 was used in this project as this sensor has a reliable scan measurement compared to other LIDARs with similar price range. Other models such as RPLIDAR A3M1 has a more reliable scan but is susceptible to noise. However, as the industry tries to keep the cost low. A1M8 provides a comparable result in our test environments to its costly competitors. To process the distance and angle between object and RPLIDAR, the object is 20 sampled by reflecting a laser signal from the object. This distance is being captured more than 2000 times per second. In terms of hardware, a LIDAR typically consists of a range scanner system and a motor system. These two systems are powered separately and that’s why a regulator has been used to power the RPLIDAR motor system separately. This 360 scanner uses TTL serial port to communicate with the server and power the range scanner. Figure 4 shows the regulator DE- SWADJ that was used to power the RPLIDAR’s motor system. The dimensions of this sensor are shown in Figure 5 [25]. Figure 5: RPLIDAR dimensions [25] Figure 5: RPLIDAR dimensions [25] 21 Regulator: As mentioned a DE-SWADJ regulator has been used to power the RPLIDAR motor separately. This regulator plays an important role as it allows the ability to adjust the speed of the RPLIDAR’s motor and therefore scans using this module. Figure 6: Regulator DE-SWADJ Figure 6: Regulator DE-SWADJ Power Supply: A LiPo battery replaced the old batteries of this robot to lower the weight from 9KG to 7.5KG. This battery is a DXF Li-polymer with 32SP cells, 11.1V Voltage, Capacity of 7000 mAh, Discharge of 35C and weight of 595g. 3.2. Software System The types of software discussed in this section are the ROS configuration full software overview and configuring Pioneer and RPLIDAR with ROS. Detailed instructions of the SLAM, navigation, Costmap, obstacle avoidance and other implementations will be thoroughly explained. 22 3.2.1. ROS ROS [15] is a Linux based software framework that uses packages, nodes, topics, messages and services to operate a robot. A node receives sensor measurements and passes it to other nodes in order to process data. The information that moves from node to node is called a message. These messages travel through a portal called a topic. A Publisher is publishing data to this topic and subscriber is subscribing to this topic to receive these messages. The package consists of all related nodes and is essential for building a control system for any robot through ROS. In this thesis, ROS Kinetic was installed and the ROS environment was configured. To create, build, and modify Catkin packages, a directory called Workspace was used. The ROS workspace was created using the commands in A.2. The command in A.3 was added to the bashrc file so that it could automatically occur every time the terminal is opened as only one catkin workspace was created for this thesis. 23 Figure 7: System overview Figure 7: System overview The Figure 7 shows all connections of the ROS systems including all transforms. In the figure 8, one could find the visualization of our system computation graph in ROS which consist of the robot, simulation, LIDAR and other components. 24 Figure 8: Visualization of ROS a) Performing Gmapping in real world b) Performing Gmapping using Gazebo simulation Figure 8: Visualization of ROS a) Performing Gmapping in real world b) Performing Gmapping using Gazebo simulation 3.2.2. RPLIDAR Setup on ROS RPLIDAR A1M8 is a 360 2D LIDAR that was used in this thesis. This LIDAR has been placed centred on top of the robot with a height of 245 mm as shown in Figure 9. A plastic plate was used to fix this laser scanner on top of the chassis. Maximum scanning frequency of this LIDAR with 360 points samples is 5.5 Hz. During testing, the nominal speed of this laser scanner was maintained at 35-40% of its max speed which is the optimal speed for this environment. A USB connection was used to transfer the data to the LIDAR and a power supply of 5-10V was required for the regulator to supply power for RPLIDAR motor’s system. It is important to keep in mind that changing the value of this regulator affects our scanning speed. For any further information, please refer to the RPLIDAR A1M8 data sheet [25]. 25 Important factors need to be considered when setting up the LIDAR on the robot. If the LIDAR is set too low, it would affect the mapping as well as localization since it is unable to capture enough landmarks. On the other hand, setting this laser scanner too high could result in not detecting the obstacles that the robot is supposed to avoid. After conducting different height tests, we placed the RPLIDAR at the centre of the robot with a height of 245 mm. This gave an optimal navigation by easily identifying most obstacles in our test environment (2nd floor of Ryerson Engineering Building) Figure 9: RPLIDAR placement Figure 9: RPLIDAR placement Figure 9: RPLIDAR placement Figure 9: RPLIDAR placement Powering RPLIDAR with only an USB is not sufficient for long distances and therefore, this laser scanner needs a separate port for its power consumption. A regulator was added to not only control the RPLIDAR motor speed, but also was a separate power source for this motor 26 system. The motor speed directly affected the map as the number of landmarks captured were changing respectfully. system. The motor speed directly affected the map as the number of landmarks captured were changing respectfully. 3.2.3. Pioneer 2DX Setup on ROS In order to setup the Pioneer 2DX, an interface that connects to the ActiveMedia controller was required. This interface is called ActiveMedia Robotics Interface (ARIA) and is an open source software based on C++. Any low-level details such as commands and serial communication could be accessible through ARIA. The ARIA package was installed on the Linux Ubuntu 16.04, using the commands in A.1. At this point, ARIA and ROS are installed and ROSARIA package is required to communicate between the ARIA library and ROS. This platform automatically updates the ARIA version and provides both control and position estimations by using ROS nodes to connect to this library. The ROSARIA package has been retrieved to our catkin workspace and the package was built using commands in A.5. This process had only needed to be completed once. However, roscore must always be running so that the ROS nodes can communicate in their network. At last, the ROS nodes are implemented as shown in Appendix A.6. The robot was connected to a host via serial to a USB port. In such case, the command was modified in order to connect via USB0. After getting a connection to the robot using ROSARIA, the pose estimation was echoed as the ARIA publishes the odometry data. This information is being published in RosAria/pose topic every 100 ms. This frequency is by default and is adjustable. Two other parameters that refer to the port and frame of the robot are base_link_frame, port. They are set to dev/ttyUSB0 and base_link by default. 27 In the first test, different velocities were observed on the robot in order to test the velocity commands in A.9. This velocity state is being published to the ARIA using /RosAria/cmd_vel. This command needs to be published every 100 ms in order to maintain this velocity. If the robot does not receive the cmd_vel message for 600 ms, timeout will occur, and the robot stops for safety reasons. In order to eliminate this, the command needs to be modified to publish a more frequent velocity greater than 600 ms. Overall, all commands are shown in the Appendix including the laser scanner in RVIZ, the connection of the base_link to laser_frame and launching the pioneer 2DX robot model description (URDF). 3.2.4. SLAM SLAM algorithms are developing rapidly and high demands for smaller and lighter robots have challenged researchers to simplify their methods and decrease the computation parts. The rapid development in indoor 2D SLAM applications has been heavily studied, which led to several improvements such as [7] by Grisetti et al. These approaches improved the RBPT by considering both the recent observation of the robot and updating its motion model. The number of particles decreased using the scan matching technique (lower computation) after reducing the resampling step frequency. Gmapping SLAM algorithm has been used in this project which is one of the most studied algorithms with several optimization methods. A thorough implementation and evaluation study of Gmapping was conducted by Abdelrasoul et al. which proposed an optimization technique that involved tuning its parameters [6]. To lower computation, they modified the number of particles and resampled the threshold. This created a reliable map with less CPU load and memory requirements. Our work supports these findings and will be further discussed in the “Conducted 28 Tests and Results” section where implementing this method resulted in low memory usage. This involved conducting different speeds of the robot using Gmapping SLAM using low-cost 2D LIDAR which resulted in different maps with different speeds. Tests and Results” section where implementing this method resulted in low memory usage. This involved conducting different speeds of the robot using Gmapping SLAM using low-cost 2D LIDAR which resulted in different maps with different speeds. In this test, the scan measurements from RPLIDAR and odometry of the Pioneer are used by SLAM Gmapping to create a map using the Rao-Blackwellized particle filter base [Gmapping] approach. Firstly, the test was conducted using Gazebo and RVIZ simulation, and thereafter, the robot was tested in a small and large loop in a real-world environment. After the Gmapping process, the map is saved into PGM and YAML files. These two files are respectfully an image of the map (PGM) and a description of this map (YAML). This saved map is used later on to navigate and localize the robot. The instructions for the simulation and practical tests are found in the Appendix A.8, A.10 and A.11. Figure 11 and 12 also shows the final map of the NCART lab and a loop closure of the 2nd floor, Engineering building, Ryerson University. 3.2.4. SLAM The visualization of the system computation graph of both simulation and real tests are shown in Figure 11 and 12. 29 Figure 10: 2nd floor of engineering building’s map (Large loop) Figure 10: 2nd floor of engineering building’s map (Large loop) Figure 11: NCART lab’s map (Small loop) Figure 11: NCART lab’s map (Small loop) 30 3.2.5. Localization A localization algorithm uses odometry data, LIDAR scans, and a saved map to visualize the map and location of the robot. To deal with different states of localization, launch files are written and configured. Launch and configurations files are critical for the robot localization and can be found in Appendix A.13 and A.14. During localization, the map is retrieved from the saved map using a Map Server. Thereafter, AMCL is used to localize the robot in the map which also requires an initial guess by the user. In Figure 13, the location of the robot is identified and shown. As the robot moves, the algorithm captures more landmarks which increases the certainty of localization. 31 Figure 12: Initial localization process in NCART lab Figure 12: Initial localization process in NCART lab 31 3.2.6. Navigation Stack After mapping and localizing the robot, navigation is the main objective of an AMR. A move base package from the navigation stack [26] was used where this package provides a velocity command and uses localization data to navigate the robot in the environment. The details of this approach are mentioned in [26]. RVIZ tools were then configured and provided a destination for the robot to plan a safe path, accordingly. Two launch files were set up to launch all necessary transform connections such as roscore, ROSARIA, RPLIDAR, map server and RVIZ. The YAML file was used and saved from the SLAM section. For further details, the commands, configurations and launch files are found in Appendix A.13 and A.14. Figure 14 shows the planned path by this system after manually setting a goal for the robot to reach by avoiding obstacles on its way. Figure 13: Path being plan by this system in NCART Lab Figure 13: Path being plan by this system in NCART Lab 32 Section 4. Conducted Tests and Results The tests in this section focus on providing an optimized robot set up and reveal the challenges faced and potential solutions. The goal is to simplify some of these challenges by creating a more reliable map and pose estimation. Some of these findings address the challenges faced by past studies and gives future studies the foundation to further explore in this field. The “Challenges and Observation” section offers an in-depth discussion on results of these tests. Robot speed’s modification: Mapping the environment is one of the main tasks which is performed by capturing a sufficient number of landmarks from the environment. One factor that could affect this process is the speed of the robot. To evaluate the effects speed has on mapping, an experiment was conducted in the NCART lab at Ryerson University where changes in the velocity of the robot were evaluated and SLAM was performed with each of these speeds. Additionally, this experiment involved loop closure, analyzing the SLAM accuracy and tuning parameters. The robot speed and direction were controlled using the command line in Appendix A.9. We started off with 1 m/s and increased this speed by 0.5m/s steps to reach 3 m/s. Figures 15- 18 shows that loop closure was completed on all scenarios. It was expected that there would be a less reliable map when the speed was increased. However, the difference between these maps created by various speeds were not significantly noticeable and it was concluded that the performance of Gmapping is independent to various speeds of Pioneer 2DX. 33 Figure 14:: NCART map with velocity of 1 m/s Figure 15: NCART map with velocity of 1.5 m/s Figure 16: NCART map with velocity of 2 m/s Figure 17: NCART map with velocity of 3 m/s Figure 15: NCART map with velocity of 1.5 m/s Figure 15: NCART map with velocity of 1.5 m/s Figure 14:: NCART map with velocity of 1 m/s Figure 15: NCART map with velocity of 1.5 m/s Figure 16: NCART map with velocity of 2 m/s Figure 17: NCART map with velocity of 3 m/s Figure 16: NCART map with velocity of 2 m/s Figure 17: NCART map with velocity of 3 m/s Figure 17: NCART map with velocity of 3 m/s Altering the LIDAR heights: Setting the LIDAR sensor at an appropriate height is critical as it changes the range of obstacles and landmarks that is being captured. Section 4. Conducted Tests and Results This height could be set differently depending on the environment and its landmarks. For the purpose of this thesis, most of the obstacles the robot needs to avoid on the second floor of the Ryerson Engineering building are either not dependent to height such as doors and walls, or has obstacles that are the same height as the robot. Obstacles such as tables are not necessarily an obstacle for the robot if it can find a better path using the space under the table. Therefore, the LIDAR was installed at the center and top of the Pioneer with height of 245 mm which was shown in Figure 9. This setup allows the 34 robot to easily navigate the lab and office areas including passing under the table, if there is a possible path. robot to easily navigate the lab and office areas including passing under the table, if there is a possible path. Long and short loop closure test: Firstly, the loop closure has been tested in the NCART lab, which is a small area compared to the Ryerson Engineering building 2nd floor. Thereafter, the robot was tested in a larger loop on the 2nd floor. During this test, it was discovered that the Gmapping could fail to detect this loop. In this case, the final map is not reliable as the loop correction depends on the loop detection to happen. We hope to optimize the loop closure process of Gmapping by manually adjusting the map in our future work. Figure 18: Loop closure test in 2nd floor Engineering building Ryerson University (The break on top of the map shows the drift) Figure 18: Loop closure test in 2nd floor Engineering building Ryerson University (The break on top of the map shows the drift) Figure 18: Loop closure test in 2nd floor Engineering building Ryerson University (The break on top of the map shows the drift) 35 Figure 19: NCART loop closure test (Small loop) Figure 19: NCART loop closure test (Small loop) Stairs mapping: A robust mobile robot should be able to autonomously navigate through a building and move to other floors either using elevator or stairs. In case of using the stairs, the robot should be able to detect these stairs. To evaluate stair navigation, LIDAR was used for mapping and these results are discussed in the “Challenges and Observation” section. Section 4. Conducted Tests and Results Destroyed environment vs flat surface: During navigation, there may be some cases where an AMR is required to navigate through different types of surfaces. These surfaces could be a simulation of toys in a house, stack of papers on the ground of an office floor, or maybe a damaged area after an explosion. As one can see, different applications are required for the robot to move in various situations. We tested some of these less flat areas in our application. We extended this section in the “challenges and observations” subsection. RPLIDAR speed’s modification: Not only does the speed and height of the robot could influence the scans, but also RPLIDAR’s frequency directly affects the number of landmarks that 36 are being captured at a given period of time. Therefore, we dedicated a section on the overview of RPLIDAR power and nominal speed. The implementations of this project were performed by utilizing Robot Operating System (ROS Kinetic) and C++ Programming language. RVIZ package has been used for visualization of the robot model, movement and other ROS visualizations. All simulations of have been performed in Gazebo (9.0.0). 4.1. Challenges and Observations An AMR could face several challenges such as not detecting certain obstacles (tables or glasses) due to the height of the sensors or their capabilities. There were a few optimizations that aimed to solve these challenges. Particularly, AMR applications have been perfected in the past decade. Being able to process the data with less computation and memory requirements is one among many optimizations that are possible. Studies have advanced these approaches and have paved the way to achieve more accurate results in areas such as localization, mapping, and path planning. However, problems still remain with these approaches. In practice, mapping an indoor environment with glass walls and stairs is one among many. The goal of this thesis is to investigate the challenges during the mapping of glass environments and based on the findings, provide potential solutions. One of the many solutions to this challenge had utilized the advantages of sensor fusion and has been outlined in the introduction of sensor fusion. During the investigation of real-world challenges, another critical challenge especially in the exploration of real buildings is detecting and mapping stairs. This particular situation has brought us to investigate several approaches. For instance, in uneven and unpredictable terrain, locating and mapping uneven terrain is problematic and extremely important as seconds could change the lives of people in planning a 37 path to a trapped victim in a damaged building. The rescue team would need to be highly accurate on their calculations beforehand. Supporting evidence on this matter can be found in situations where the rescue team does not have access to a floorplan. Therefore, an AMR may be required to map the uneven terrain and the rest of the environment. However, Robots utilizing 2D LIDAR are not capable of fully mapping stairs and other similar features. Altogether, AMR applications suffer from limitless number of challenges which requires many optimizations and developments; however, only some significant challenges have been outlined in this section. 4.1.1. Small and Narrow Obstacles and Different Surfaces After conducting tests at the NCART lab, small and narrow obstacles were mainly observed such as narrow tables and chairs. These types of obstacles are not detectable by the LIDAR and result in a less accurate map. During the navigation process, the robot uses the map to plan its path through these tables which evidently resulted in the robot crashing. In addition to these narrow obstacles, small objects that are not detectable by the sensors create a bumpy surface. To overcome this issue, these bumpy areas were substituted with books, metal and wood plates as shown in Figure 21. In this type of situation, the robot either has to detect these obstacles and change its path, or pass these gravel-like surfaces which requires different robot bases. Changing the base of the robot is not only costly, but also not effective enough as it creates other challenges such as requiring wider paths to choose from. Subsequently, detecting these obstacles become essential for the navigation process. It would be beneficial to use fusion sensors such as camera and laser scanner as it is a cost-effective approach and will be discussed more in the “Future Works” section. 38 Figure 20: Bumpy areas were substituted with books, metal and wood plates Figure 20: Bumpy areas were substituted with books, metal and wood plates 4.1.2. Glass Detection Challenge Glass detection is one of the well-known challenges that hasn’t been extensively studied by researches until recently. However, there have been several attempts as mentioned to solve this challenge. Despite some expensive sensors that are able to detect glass, other approaches use at least two sensors, which require more processing power and memory. In this thesis, several tests were conducted in glass areas to investigate this problem further. These tests involved using a RPLIDAR that is not able to detect glass surfaces due to the reflection beam is either coming back from the wall behind the glass or no reflection is being detected at all. Sensor fusion could be a solution to this issue according to studies of T. Chang et al. in [27], which used both advanced sonar and LIDAR. Despite their high computation, these methods certainly provide a solution 39 model to this current high-profile challenge. Sonar sensors are not the best choice in terms of mapping as the sensor measurements are not reliable and accurate, however they are being used as an additional sensor since they could detect glass surface. Using LIDAR and sonar together not only could be more accurate, but also is able to detect these surfaces. When sonar sensor measurements provide a significant difference from the LIDAR measurements, the surface is most likely a glass because LIDAR is not detecting it. Figure 21 shows the LIDAR scan measurements against glass surface. We will discuss these methods further in depth in the “Fusion Sensors” section. Figure 21: Glass detection test in front of the glass Figure 21: Glass detection test in front of the glass 40 Figure 22: The top part shows glass scans and how they fail to detect the glass Figure 22: The top part shows glass scans and how they fail to detect the glass Figure 22: The top part shows glass scans and how they fail to detect the glass 4.1.3. Stairs Detection and Mapping Challenge One of the main challenges in robot navigation is stair detection and mapping. An advantage to having these maps is that it could be helpful for a SAR team to use after incidents such as bombing and certain tasks that require a immediate response in limited time manner. The number and height of stairs could be captured and mapped by using either Unmanned Ground Vehicle (UGV) or Unmanned Aerial Vehicle (UAV). In this section, we tried to show how this attempt failed for 2D laser scanners going up the stairs and what are the next steps to solve this challenge utilizing low-cost sensors. 41 Figure number 24 and 25 are demonstrating the stairs maps which has been gathered by Gmapping and RPLIDAR A1M8. Figure 24 shows the map after the robot climbed up the stairs 41 and Figure 25 illustrates the map after the robot climbed down the stairs. Evidently, these maps are not practicable as the scan measurements are stacked on top of each other to create a meaningless map. Based on these tests and mentioned challenges, 3D LIDAR is preferable for such applications. Also, separate Costmap layer could be assigned to maps of the stairs in order to improve the behaviour of the robot. and Figure 25 illustrates the map after the robot climbed down the stairs. Evidently, these maps are not practicable as the scan measurements are stacked on top of each other to create a meaningless map. Based on these tests and mentioned challenges, 3D LIDAR is preferable for such applications. Also, separate Costmap layer could be assigned to maps of the stairs in order to improve the behaviour of the robot. To provide a more stable platform for the robot to go up and down the stairs, the robot was centered on top of a wooden board. Certainly, an alternative platform such as a tracked robot is more practical for future works. 4.1.4. Loop Closure Challenge Several studies have attempted to optimize the loop closure in a number of approaches such as Gmapping. Some of these studies have led to the development of new loop closure methods and others have added optimizations on current approaches. However, most of these studies only focused on the loop correction and relied on an accurate loop detection. In this thesis, mismatches on the loop detection were observed when the robot was required to close a longer loop. It was the Gmapping loop detection that failed to detect the loop in a long loop in 2nd floor Ryerson Engineering building. This detection is more challenging when there are similar features and landmarks in environments such as office and dynamic areas. 4.1.3. Stairs Detection and Mapping Challenge Figure 23: Stairs in engineering building Figure 23: Stairs in engineering building 42 Figure 24: Mapping stairs using Gmapping as the robot is going up Figure 24: Mapping stairs using Gmapping as the robot is going up Figure 24: Mapping stairs using Gmapping as the robot is going up Figure 25: Mapping stairs using Gmapping as the robot is going down Figure 25: Mapping stairs using Gmapping as the robot is going down Figure 25: Mapping stairs using Gmapping as the robot is going down 43 4.1.6. Dynamic Environments AMRs face dynamic areas on a day-to-day basis as most applications require robots to robustly navigate in such environments like in houses or offices. In the literature review section, we discussed how indoor navigation and SLAM demand a robust navigation in dynamic areas. It is also noteworthy to mention that the boundary of each person is their privacy and should be set so that the robot does not get too close to a person. To address this issue, these boundaries need to be adaptable as the environment changes. In any case, detecting a dynamic object from a static obstacle is critical to meet these expectations. These dynamic areas could be saved in a separate Costmap layer to simplify robot’s navigation. This argument has been supported by evidence from Layered Costmap for Context-Sensitive Navigation in [28]. In this study, the robot could avoid driving to close to people by navigating through paths with less dynamic areas. It was suggested that it is more reliable to choose a path with less hazard to lower the chance of collision by assigning a Costmap to caution zones. It is our intent to implement and improve this layer in our future work. 4.1.5. Disaster Area’s Pre-mapping Practical Objection Pre-mapping an indoor office or public environment are necessary, in some cases. One particular pre-mapping approach that is common among studies is mapping these environments for emergency rescue teams to use in future natural disasters such as an earthquake. This approach is called Disaster Areas Pre-mapping and has found to be helpful for the USAR team to approximate the location of survivors [22]. It is critical to emphasize that currently, the number of places which have been mapped are few which make this approach more theoretical than practical. Pre-mapping an indoor office or public environment are necessary, in some cases. One particular pre-mapping approach that is common among studies is mapping these environments for emergency rescue teams to use in future natural disasters such as an earthquake. This approach is called Disaster Areas Pre-mapping and has found to be helpful for the USAR team to approximate the location of survivors [22]. It is critical to emphasize that currently, the number of places which have been mapped are few which make this approach more theoretical than practical. There is also the problem of the chaotic effects of forces capable of producing a disaster. For example, a severe earthquake or bomb blast might cause of multi-story structure to collapse and deform in ways that make any pre-mapping irrelevant. Locating the critical part of a building such as stairs, and hallways is almost impossible in the case of a severe destruction. Disaster Area’s Pre-mapping still remains a popular approach among current studies and we hope to provide recommendations that addresses this issue based on improved and more complete simulations. There is also the problem of the chaotic effects of forces capable of producing a disaster. For example, a severe earthquake or bomb blast might cause of multi-story structure to collapse and deform in ways that make any pre-mapping irrelevant. Locating the critical part of a building such as stairs, and hallways is almost impossible in the case of a severe destruction. Disaster Area’s Pre-mapping still remains a popular approach among current studies and we hope to provide recommendations that addresses this issue based on improved and more complete simulations. 44 4.2. Sensor Fusion Having considered sensor fusion, it is also reasonable to look at limitations of single-sensor- based applications. Main sensors that are being used in indoor AMR applications are LIDAR, camera and sonar. As we already compared vision-based and LIDAR-based advantages and disadvantages, we will briefly go through sonar and LIDAR sensors and sensor fusion using these two sensors. 45 Sonar Sensor: This sensor is being used in a number of indoor robotic applications and is one of the most useful and cost-efficient sensors compared to other methods. This sensor is able to detect any transparent surface such as glass, which is commonly used in most offices and indoor environments. However, high range of errors and the low-resolution readings of this sensor makes it unreliable compared to other alternatives such as LIDAR and camera. LIDAR Sensor: Laser scans can provide a high resolution and highly accurate detection. This accurate scan data is the main reason LIDAR is dramatically being used in indoor mapping, localization and navigation. However, transparent surfaces such as glass are not fully detectable by LIDAR. Therefore, it is not suggested to use these sensors without pre-mapping and further map adjustment. These two sensors can complement each other where sonar results are unreliable but able to detect transparent areas. LIDAR scans are reliable, despite not being able to detect transparent areas. To compensate for this lack of detection, [27] developed an algorithm using both sensors. This algorithm compares both measurements of sonar and LIDAR, and if there is a significant difference between these measurements, the algorithm assumes it detects a glass object if LIDAR did not detect an obstacle, but sonar did. Although, significant errors in sonar sensors, especially in edge situations, could dramatically affect the accuracy of this solution [27]. Using sensor fusion in our future work could eliminate the number of failures that we faced in our tests and could potentially result in a more accurate navigation in such indoor environments. 46 Section 5. Conclusion and Future Work In this thesis, the advantages and disadvantages of different LIDAR and vision-based SLAM systems were investigated and compared. The main conclusion derived was that vision- based SLAM approaches suffered from scale drifting, lost track of the robot and relied on a high computation in comparison to LIDAR-based approaches. However, LIDAR-based SLAMs are preferable as it met our requirement of limited hardware for this project. Among these LIDAR- based approaches, Gmapping provides a reliable and cost-efficient result. This finding was based on the modified mobile robot used to evaluate Gmapping performance in a typical office environment. Different experiments were conducted by launching the robot in various closed-loop trajectories. Simulation of a dynamic office environment with a bumpy area, and glass detection areas are some of these experiments that required manual map adjustments. Sensor measurements such as LIDAR were collected to perform Gmapping SLAM, and AMCL Navigation. This study shows the reliability of Gmapping in indoor office environments. A.1. Installations and setups sudo dpkg -i libaria_2.9.1+ubuntu16_i368.deb A.3. bashrc modification . ~/catkin_ws/devel/setup.bash A.2. ROS workspace mkdir -p ~/catkin_ws/src cd ~/catkin_ws/src catkin_init_workspace cd ~/catkin_ws cd ~/catkin_ws catkin_make 5.1. Future Work In this thesis we explored several different techniques for exploring closed loop navigation and traversal. We examined solutions for dealing with glass (windows) in offices and stairs. The main challenges encountered during testing were discussed and gave us insights to the shortcomings of dealing with static real-world environments. We assume that any AMR should be able to navigate in any typical office environment that generally consists of stairs, glass walls, bumpy areas and large closed loops. Based on our findings, we suggest the manual adjustment of obstacles in the map as most low-cost sensors are not capable of accurately detecting some of these obstacles, dynamic areas, and bumpy areas. However, the true definition of indoor autonomous 47 mobile robot requires a robot to autonomously navigate in any indoor environment without human interaction. As this is beyond the scope of this thesis, we hope more realistic solutions will be developed over time. Our work suggests that this will inevitably involve sensor fusion and areas additional forms of maps used for specific purposes (unstructured area maps for example). 48 A.4. Launching RPLIDAR roslaunch rplidar_ros view_rplidar.launch Appendices A.1. Installations and setups A.7. Echo the pose using ARIA library rostopic echo /RosAria/pose A.6. Launch ARIA using ROSARIA rosrun rosaria RosAria _port:=/dev/ttyUSB1 A.8. gmapping Gazebo simulation roslaunch p3dx_gazebo gazebo.launch roslaunch p3dx_description rviz.launch roslaunch Rplidar_ros view Rplidar.launch rosrun gmapping slam_gmapping scan:=/p3dx/laser/scan rosrun tf static_transform_publisher 0 0 0.1 0 0 0 odom base_link 100 rqt_graph rqt_graph #different terminal Rosrun teleop_twist_keyboard teleop_twist_keyboard.py And add a display with a map to the RVIZ, then set it to the topic /map. A.5. ROSARIA cd ~/catkin_ws/src git clone https://github.com/amor-ros-pkg/rosaria.git make -j4 make -j4 catkin_make 49 roscore A.6. Launch ARIA using ROSARIA A.9. Publishing Velocity through ROSARIA A.9. Publishing Velocity through ROSARIA 50 The code below was used to move the robot forward The code below was used to move the robot forward rostopic pub /RosAria/cmd_vel geometry_msgs/Twist -r 3 -- '[0.1, 0.0, 0.0]' '[ 0.0, 0.0, 0.0]' A.10. Gmapping using RPLIDAR A.10. Gmapping using RPLIDAR roscore roslaunch rplidar_ros view_rplidar.launch (rosrun rplidar_ros rplidarNode) rostopic echo scan dmesg | grep tty rosrun rosaria RosAria _port:=/dev/ttyUSB1 roslaunch p3dx_description rviz.launch rosrun tf static_transform_publisher 0 0 0.1 0 0 0 base_link laser_frame 100 rostopic echo scan dmesg | grep tty rosrun rosaria RosAria _port:=/dev/ttyUSB1 roslaunch p3dx_description rviz.launch rosrun tf static_transform_publisher 0 0 0.1 0 0 0 base_link laser_frame 100 A.11. Saving the map after SLAM Rosrun rosaria RosAria port:/dev/ttyUSB0 Transforms? Rosrun mapping slam gmapping Rosrun mapping slam gmapping Rosrun map server map saver -f mymap A.12. Localization 51 rosrun rviz rviz 52 A.13. Move Base Launch File <launch> <master auto="start"/> <!-- Run the map server --> <node name="map_server" pkg="map_server" type="map_server" args="$(fin d my_map_package)/my_map4.pgm 4000 X 4000"/> <!--- Run AMCL --> <include file="$(find amcl)/examples/amcl_omni.launch" /> <node pkg="move_base" type="move_base" respawn="false" name="move_base " output="screen"> <remap from="/odom" to="/pose" /> <remap from="cmd_vel" to="/RosAria/cmd_vel"/> <rosparam file="$(find p3dx_2dnav)/costmap_common_params.yaml" command ="load" ns="global_costmap" /> <rosparam file="$(find p3dx_2dnav)/costmap_common_params.yaml" command ="load" ns="local_costmap" /> <rosparam file="$(find p3dx_2dnav)/local_costmap_params.yaml" command= "load" /> <rosparam file="$(find p3dx_2dnav)/global_costmap_params.yaml" command ="load" /> <rosparam file="$(find p3dx_2dnav)/base_local_planner_params.yaml" com mand="load" /> A.13. Move Base Launch File A.13. Move Base Launch File <rosparam file="$(find p3dx_2dnav)/base_local_planner_params.yaml" com mand="load" /> 52 </node> </launch> A.14. Configuration Files <launch> <!-- Launch rplidar --> <node pkg="rplidar_ros" type="rplidarNode" name="rplidarNode" output="screen" > <param name="serial_port" type="string" value="/dev/ttyUSB0"/> <param name="serial_baudrate" type="int" value="115200"/><!--A1 /A2 --> <!--param name="serial_baudrate" type="int" value="256000"--><! --A3 --> <param name="frame_id" type="string" value="laser"/> <param name="inverted" type="bool" value="false"/> <param name="angle_compensate" type="bool" value="true"/> </node> <!-- Connect to Pioneer --> <node pkg = "rosaria" type = "RosAria" name = "RosAria"> <param name="port" value="/dev/ttyUSB1" type="string"/> </node> <!-- Launch p3dx description --> </node> </launch> A.14. Configuration Files <launch> <!-- Launch rplidar --> <node pkg="rplidar_ros" type="rplidarNode" name="rplidarNode" output="screen" > <param name="serial_port" type="string" value="/dev/ttyUSB0"/> <param name="serial_baudrate" type="int" value="115200"/><!--A1 /A2 --> <!--param name="serial_baudrate" type="int" value="256000"--><! --A3 --> <param name="frame_id" type="string" value="laser"/> <param name="inverted" type="bool" value="false"/> <param name="angle_compensate" type="bool" value="true"/> </node> <!-- Connect to Pioneer --> <node pkg = "rosaria" type = "RosAria" name = "RosAria"> <param name="port" value="/dev/ttyUSB1" type="string"/> </node> <!-- Launch p3dx description --> A.14. Configuration Files <!-- Launch rplidar --> <param name="frame_id" </node> <!-- Connect to Pioneer --> <param name="port" value="/dev/ttyUSB1" type="string"/> </node> <!-- Launch p3dx description --> 53 <arg name="model" default="$(find p3dx_description)/urdf/pioneer3dx.xml"/> <arg name="gui" default="False" /> <param name="robot_description" textfile="$(arg model)" /> <param name="use_gui" value="$(arg gui)"/> <param name="use_gui" value="$(arg gui)"/> <param name="use_gui" value="$(arg gui)"/> <node name="joint_state_publisher" pkg="joint_state_publisher" type="joint_st ate_publisher" ></node> <node name="robot_state_publisher" pkg="robot_state_publisher" type="state_pu blisher" /> <node name="rviz" pkg="rviz" type="rviz" args="-d $(find urdf_tutorial)/urdf. rviz" /> <!-- transfor configurations --> <node pkg="tf" type="static_transform_publisher" name="link1_broadcaster" arg s="0 0 0.2659 0 0 0 base_link laser_frame 100"/> <node pkg="tf" type="static_transform_publisher" name="link2_broadcaster" arg s="0 0 0.1 0 0 0 map odom 100"/> <node pkg="tf" type="static_transform_publisher" name="link3_broadcaster" arg s="0 0 0.2659 0 0 0 base_link laser 100"/> </launch> 54 55 A.15. Navigation Launch File <launch> <!-- Launch rplidar --> <node pkg="rplidar_ros" type="rplidarNode" name="rplidarNode" output="screen" > <param name="serial_port" type="string" value="/dev/ttyUSB0"/> <param name="serial_baudrate" type="int" value="115200"/><!--A1 /A2 --> <!--param name="serial_baudrate" type="int" value="256000"--><! --A3 --> <param name="frame_id" type="string" value="laser"/> <param name="inverted" type="bool" value="false"/> <param name="angle_compensate" type="bool" value="true"/> </node> <!-- Connect to Pioneer --> <node pkg = "rosaria" type = "RosAria" name = "RosAria"> <param name="port" value="/dev/ttyUSB1" type="string"/> </node> <!-- Launch p3dx description --> <arg name="model" default="$(find p3dx_description)/urdf/pioneer3dx.xml"/> A.15. Navigation Launch File <launch> <!-- Launch rplidar --> <node pkg="rplidar_ros" type="rplidarNode" name="rplidarNode" output="screen" > <param name="serial_port" type="string" value="/dev/ttyUSB0"/> <param name="serial_baudrate" type="int" value="115200"/><!--A1 /A2 --> <!--param name="serial_baudrate" type="int" value="256000"--><! --A3 --> <param name="frame_id" type="string" value="laser"/> <param name="inverted" type="bool" value="false"/> <param name="angle_compensate" type="bool" value="true"/> </node> <!-- Connect to Pioneer --> <node pkg = "rosaria" type = "RosAria" name = "RosAria"> <param name="port" value="/dev/ttyUSB1" type="string"/> </node> <!-- Launch p3dx description --> A.15. Navigation Launch File A.15. Navigation Launch File <!-- Launch rplidar --> <!-- Launch p3dx description --> 55 <param name="robot_description" textfile="$(arg model)" /> <param name="use_gui" value="$(arg gui)"/> <node name="joint_state_publisher" pkg="joint_state_publisher" type="joint_st ate_publisher" > <node name="robot_state_publisher" pkg="robot_state_publisher" type="state_pu blisher" /> <node name="rviz" pkg="rviz" type="rviz" args="-d $(find urdf_tutorial)/urdf. rviz" /> <!-- transfor configurations --> <node pkg="tf" type="static_transform_publisher" name="link1_broadcaster" arg s="0 0 0.1 0 0 0 odom base_link 100"/> <!-- <node pkg="tf" type="static_transform_publisher" name="link2_broadcaster " args="0 0 0.1 0 0 0 map odom 100"/> --> <node pkg="tf" type="static_transform_publisher" name="link3_broadcaster" arg s="0 0 0.1 0 0 0 base_link laser 100"/> <param name="map_udpate_interval" value="1.0"/> <param name="sigma" value="0.1"/> 56 57 <param name="llsamplerange" value="0.01"/> <param name="llsamplestep" value="0.05"/> <param name="lasamplerange" value="0.05"/> <param name="lasamplestep" value="0.05"/> </node> </launch> <param name="llsamplerange" value="0.01"/> <param name="llsamplestep" value="0.05"/> <param name="lasamplerange" value="0.05"/> <param name="lasamplestep" value="0.05"/> </node> </launch> <param name="llsamplerange" value="0.01"/> <param name="llsamplestep" value="0.05"/> <param name="lasamplerange" value="0.05"/> </node> </node> 58 References [1] H. F. Durrant-Whyte and J. J. Leonard, "Simultaneous map building and localization for an autonomous mobile robot,," IEEE/RSJ International Workshop on Intelligent Robots and Systems '91, vol. 3, pp. 1442-1447, 1991. [1] H. F. Durrant-Whyte and J. J. Leonard, "Simultaneous map building and localization for an autonomous mobile robot,," IEEE/RSJ International Workshop on Intelligent Robots and Systems '91, vol. 3, pp. 1442-1447, 1991. [2] M. Quigley, K. Conley, B. P. Gerkey, J. Faust, T. Foote, J. Leibs, R. Wheeler and A. Y. Ng, "ROS: an open-source Robot Operating System," ICRA Workshop on Open Source Software, 2009. [4] M. Filipenko and I. Afanasyev, "Comparison of Various SLAM Systems for Mobile Robot in an Indoor Environment," in 9th IEEE International Conference on Intelligent Systems, Madeira, Portugal, 2018. [5] A. Diosi, G. Taylor and L. 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Tardos, "Orb-slam:aversatile and accurate monocular slam system,," IEEE Trans. on Robotics, vol. 31, no. 5, p. 1147–1163, 2015. [14] T. Pire, T. Fischer, G. Castro, P. DeCristo ́foris, J. Civera and J. JacoboBerlles, "S-PTAM: Stereo Parallel Tracking and Mapping,," Robotics and Autonomous Systems, vol. 93, p. 27– 42, 2017. [15] B. Gerkey, "ROS WiKi," [Online]. Available: http://wiki.ros.org/slam_karto. [Accessed 15 12 2010]. 60 [16] B. Steux and O. E. Hamzaoui, "tinySLAM: A SLAM algorithm in less than 200 lines C- language program,," 11th International Conference on Control Automation Robotics & Vision, pp. 1975-1979, 2010. [17] L. Carlone, R. Aragues, J. Castellanos and B. Bona, "A linear approximation for graph- based simultaneous localization and mapping," In Proc. of the Int. Conf. Robotics: Science and Systems, 2011. [18] W. Hess, D. Kohler, H. Rapp and D. Andor, "Real-time loop closure in 2d lidar slam," Robotics and Automation (ICRA), p. 1271–1278, 2016. [19] S. Kohlbrecher, O. Stryk, J. Meyer and U. Klingauf, "A flexible and scalable SLAM system with full 3D motion estimation," IEEE International Symposium on Safety, Security, and Rescue Robotics, pp. 155-160, 2011. 0] A. Filatov, A. Filatov and K. Krinkin, "2D SLAM Quality Evaluation Methods," Conference of Open Innovations Association (FRUCT), no. 21st, pp. 120 - 126, 2017. [21] J. M. Santos, D. Portugal and R. P. Rocha, "An evaluation of 2D SLAM techniques available in Robot Operating System,," IEEE International Symposium on Safety, Security, and Rescue Robotics (SSRR), pp. 1-6, 2013. [22] J. Esenkanova, H. Ilhan and S. References Yavuz, "Pre-Mapping System with Single Laser Sensor Based on Gmapping Algorithm," International Journal of Electrical Energy, pp. 97-101, 2013. [23] P. Wang, Z. Chen, Q. Zhang and J. Sun, "A loop closure improvement method of gmapping for low cost and resolution laser scanner," IFAC (International Federation of Automatic Control), 2016. 61 [25] S. Slamtec.Co., "Slamtec," 13 03 2013. [Online]. Available: http://www.slamtec.com/en/lidar/a1. [Accessed 04 07 2016]. [26] E. Marder-Eppstein, E. Berger, T. Foote, B. Gerkey and K. Konolige, "The office marathon: Robust navigation in an indoor office environment," IEEE international conference on robotics and automation, pp. 300-307, 2010. [27] T. Zhang, Z. J. Chong, B. Qin, J. G. M. Fu, S. Pendleton and M. H. Ang Jr., "Sensor fusion for localization, mapping and navigation in an indoor environment," IEEE International Conference Humanoid, Nanotechnology, Information Technology Communication and Control, Environment and Management (HNICEM), no. 7th, 2014. [28] D. V. Lu, D. Hershberger and W. D. Smart, "Layered costmaps for context-sensitive navigation,," IEEE/RSJ International Conference on Intelligent Robots and Systems, pp. 709-715, 2014. [29] S. Thrun, "An online mapping algorithm for teams of mobile robots," Int. J. Robot, vol. 20, no. 5, p. 335–36, 2001. [30] K. Konolige, G. Grisetti, R. Kümmerle, W. Burgard, B. Limketkai and B. Vincent, "Efficient Sparse Pose Adjustment for 2D mapping,," IEEE/RSJ International Conference on Intelligent Robots and Systems, pp. 22-29, 2010. [31] G. Dissanayake, H. Durrant-Whyte and T. Bailey, "A computation- ally efficient solution to the simultaneous localisation and map building (SLAM) problem,," Proc. IEEE Int. Conf. Robot. Autom, p. 1009–1014, 2000. 62 63 63
https://openalex.org/W4382724550
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English
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Maytenus octogona Superoxide Scavenging and Anti-Inflammatory Caspase-1 Inhibition Study Using Cyclic Voltammetry and Computational Docking Techniques
International journal of molecular sciences
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Citation: Caruso, F.; Rossi, M.; Eberhardt, E.; Berinato, M.; Sakib, R.; Surco-Laos, F.; Chavez, H. Maytenus octogona Superoxide Scavenging and Anti-Inflammatory Caspase-1 Inhibition Study Using Cyclic Voltammetry and Computational Docking Techniques. Int. J. Mol. Sci. 2023, 24, 10750. https://doi.org/ 10.3390/ijms241310750 Keywords: Maytenus; caspase-1; inflammation; antioxidants; tingenone; pristimerin; hydroxytingenone; docking; DFT; hydrodynamic voltammetry Academic Editor: Anna Cie´sli´nska o 1,*, Miriam Rossi 1 , Eric Eberhardt 1, Molly Berinato 1, Raiyan Sakib 1, Felipe Surco-Laos avez 2 1 Department of Chemistry, Vassar College, Poughkeepsie, NY 12604, USA 2 Facultad de Farmacia y Bioquímica, Universidad Nacional San Luis Gonzaga, Ica 11004, Peru * Correspondence: caruso@vassar.edu Abstract: The relationship between oxidative stress and inflammation is well known, and exoge- nous antioxidants, primarily phytochemical natural products, may assist the body’s endogenous defense systems in preventing diseases due to excessive inflammation. In this study, we evaluated the antioxidant properties of ethnomedicines from Peru that exhibit anti-inflammatory activity by measuring the superoxide scavenging activity of ethanol extracts of Maytenus octogona aerial parts using hydrodynamic voltammetry at a rotating ring-disk electrode (RRDE). The chemical composi- tions of these extracts are known and the interactions of three methide-quinone compounds found in Maytenus octogona with caspase-1 were analyzed using computational docking studies. Caspase-1 is a critical enzyme triggered during the activation of the inflammasome and its actions are associated with excessive release of cytokines. The most important amino acid involved in active site caspase-1 inhibition is Arg341 and, through docking calculations, we see that this amino acid is stabilized by in- teractions with the three potential methide-quinone Maytenus octogona inhibitors, hydroxytingenone, tingenone, and pristimerin. These findings were also confirmed after more rigorous molecular dy- namics calculations. It is worth noting that, in these three compounds, the methide-quinone carbonyl oxygen is the preferred hydrogen bond acceptor site, although tingenone’s other carbonyl group also shows a similar binding energy preference. The results of these calculations and cyclovoltammetry studies support the effectiveness and use of anti-inflammatory ethnopharmacological ethanol extract of Maytenus octogona (L’Héritier) DC. International Journal of Molecular Sciences International Journal of Molecular Sciences International Journal of Molecular Sciences International Journal of Molecular Sciences Citation: Caruso, F.; Rossi, M.; Eberhardt, E.; Berinato, M.; Sakib, R.; Surco-Laos, F.; Chavez, H. Maytenus octogona Superoxide Scavenging and Anti-Inflammatory Caspase-1 Inhibition Study Using Cyclic Voltammetry and Computational Docking Techniques. Int. J. Mol. Sci. 2023, 24, 10750. https://doi.org/ 10.3390/ijms241310750 1. Introduction A second signal, from various origins, involves releasing reactive oxygen species (ROS) that stimulate inflammasome assembly, leading to the activation of caspase-1 and the subsequent processing of pro-IL-1β into IL-1β and pyroptosis [3]. In some cases, with excessive amounts of cytokines being produced, diseases such as atherosclerosis, cancer, and COVID-19 infection can result. Of late, several known anti-inflammatory medicinal compounds are being reevaluated to counteract the body’s inflammatory re- sponse to COVID-19 virus infection. Antioxidants that suppress ROS production and caspase-1 activation may help diminish the inflammasome response and are promising for the development of a novel therapy. Details of caspase-1 role in inflammation have been described [6], including a recent review [10]. Recently, to analyze the inhibition of caspase-1 by anti-inflammatory drugs, our group used computational methods and measured the antioxidant activity towards the damaging superoxide radical using the RRDE cyclovoltammetry method that was developed in our laboratory [11]. Previously, we associated the anti-COVID-19 biological activity of celastrol, a natural product abundant in flowering plants of the genus Maytenus and the family Celastraceae, with its inhibition of the COVID-19 main protease and its scavenging of superoxide [12]. p The roots, bark, and leaves of Maytenus plants, spread in tropical and sub-tropical regions of the world, are a rich source of widely used triterpenoids in ethnopharmacol- ogy and traditional medicines as anti-tumor, anti-asthmatic, analgesic, anti-inflammatory, antimicrobial, and antiulcer agents [13,14]. These plants are common in Peru, a country that has a rich flora that provides many useful bioactive compounds [15]. Indigenous populations use these plants for their anti-inflammatory properties. In particular, the high sub Andean region of the Amazonian river basin (Peru, Ecuador, Colombia) is home to a Maytenus species named chuchuasha (or chuchuaso), whose alcoholic root bark extracts are used in traditional medicine to reduce inflammation. Because a relationship between oxidative stress and inflammation is known, exogenous antioxidants may provide a poten- tial protective effect by assisting the body’s defense systems in preventing diseases due to excessive inflammation. Phenoldienones such as tingenone and 2-hydroxytingenone are present in the plant, and the biological activities of these compounds are in agreement with those observed when using the plant extracts in traditional health practices [16]. Following our interest in investigating the medicinal properties of the Maytenus genus [17–20], in this study, we analyzed the antioxidant properties of ethanol extracts from the leaves and stems of Maytenus octogona plants. 1. Introduction Received: 13 June 2023 Revised: 24 June 2023 Accepted: 26 June 2023 Published: 28 June 2023 Received: 13 June 2023 Revised: 24 June 2023 Accepted: 26 June 2023 Published: 28 June 2023 Caspases are a highly conserved family of cysteine protease enzymes that may induce apoptosis and inflammation [1]. Caspase-1 plays a crucial role in the inflammatory response by cleaving proteins after triggering the release of proinflammatory cytokines such as interleukin-1 beta (IL-1β) and interleukin-18 (IL-18). During a viral attack, the immune system reacts strongly to this invasion, sometimes overproducing cytokines—a “cytokine storm”. Events associated with the over-activation of the immune response have been connected to poor outcomes in patients with COVID-19 [2,3]. For instance, high levels of proinflammatory cytokine IL-1β were detected in the lung parenchyma of COVID-19 patients [4]. Moreover, increased levels of IL-18 are observed with increased mortality in sepsis-induced acute respiratory distress syndrome (ARDS) [5]. Inhibition of caspase-1 and the inflammasome pathway may provide an opportunity to suppress the heightened immune response and offer an alternative anti-COVID-19 therapy [6]. Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). p py Activation of the inflammasome is a crucial function mediated by the innate immune system [3], Figure S1. Initiation is necessary in cases of cellular or molecular damage or, on https://www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2023, 24, 10750. https://doi.org/10.3390/ijms241310750 Int. J. Mol. Sci. 2023, 24, 10750 2 of 17 infection, when interactions with foreign pathogens occur. Since inflammation is associated with many human diseases, anomalous activation can result in uncontrolled responses responsible for many pathogenic states besides the recent COVID-19 pandemic described earlier. The initial step of inflammasome activation involves the binding of exogenous ligands, such as pathogen-associated molecular patterns (PAMPs) or damage/danger- associated molecular patterns (DAMPs), to a pattern recognition receptor (PRR). Several families of PRRs exist, including the nucleotide-binding domain and leucine-rich repeat- containing proteins (NLRs, also known as NOD-like receptors). PRR binding stimulates a cascade that produces pro-IL-1β and pro-IL-18 in an NFKβ-dependent manner [7], with the relevant NLR oligomerizing becoming a caspase-1-activating scaffold. Active caspase-1 am- plifies the inflammasome signal by cleaving the proinflammatory IL-1 family of cytokines into their bioactive forms, IL-1β and IL-18, and causes pyroptosis, a type of inflammatory cell death [8,9]. 2.1. Caspase 1 Docking 2 1 1 Hydroxytingenone 2.1.1. Hydroxytingenone 2.1.1. Hydroxytingenone Using Materials Studio Dmol3 quantum chemistry program, the molecular structure of hydroxytingenone was obtained through modifying the related crystal structure of celastrol [12]. Molecular geometry optimization of the structure did not include the sol- vent effect. This was suggested by the absence of water molecules in the active site and the resulting hydroxytingenone coordinates were input for the docking study, which was performed using the Discovery Studio molecular mechanics program on caspase-1. From the Protein Data Bank (PDB) [21], we retrieved the PDB 6PZP caspase-1 in complex with a small molecule inhibitor, VX-765 [22], where caspase-1 consisted of two protein subu- nits. After Discovery Studio application of the CHARMm forcefield [23], H atoms were assigned, VX-765 was selected to create a sphere of radius 10 Å and was then removed. H h d i i i l d k d d 10 b i d Using Materials Studio Dmol3 quantum chemistry program, the molecular structure of hydroxytingenone was obtained through modifying the related crystal structure of celastrol [12]. Molecular geometry optimization of the structure did not include the solvent effect. This was suggested by the absence of water molecules in the active site and the resulting hydroxytingenone coordinates were input for the docking study, which was performed using the Discovery Studio molecular mechanics program on caspase-1. From the Protein Data Bank (PDB) [21], we retrieved the PDB 6PZP caspase-1 in complex with a small molecule inhibitor, VX-765 [22], where caspase-1 consisted of two protein subunits. After Discovery Studio application of the CHARMm forcefield [23], H atoms were assigned, VX-765 was selected to create a sphere of radius 10 Å and was then removed. Hence, hydroxytingenone was put in its place, docked, and 10 poses were obtained. Hence, hydroxytingenone was put in its place, docked, and 10 poses were obtained. The relevant moieties of hydroxytingenone able to interact with the active site of caspase-1 are the two carbonyl groups, located at both ends of the structure, as discussed previously [11]. The carbonyl at the methide-quinone end is found in pose 4. A two-di- mensional display of the amino acid interactions of docked hydroxytingenone at the ac- tive site is shown in Figure 2. 1. Introduction We also focused on three components related to celastrol from these plants—tingenone, hydroxytingenone, and pristimerin—and studied their interactions with caspase-1 by performing docking studies to analyze their potential inhibitory effects. Figure 1 shows the studied molecules. The scavenging of superoxide by Maytenus octogona ethanol extracts was also described in this study. The samples used in this study were collected by biologist Alfonso Orellana García in the area of Molletambo, district of Yauca del Rosario, Region and Department of Ica, at georeferenc- ing points (GPS): latitude (S): 14◦11′1.73′′, longitude (W): 75◦22′47.28′′, Voucher AO-113 (UNICA). Int. J. Mol. Sci. 2023, 24, 10750 3 of 17 er AO- Tingenone C28H36O3 Hydroxytingenone C28H36O4 Pristimerin C30H40O4 Celastrol C29H38O4 Figure 1. Two-dimensional canonical structural display of compounds analyzed in this study. Syn- onyms: hydroxytingenone = beta-hydroxytingenone; maytenin = tingenone. Figure 1. Two-dimensional canonical structural display of compounds analyzed in this study. Syn- onyms: hydroxytingenone = beta-hydroxytingenone; maytenin = tingenone. Tingenone C28H36O3 Pristimerin C30H40O4 Hydroxytingenone C28H36O4 Tingenone C28H36O3 Hydroxytingenone C28H36O4 Celastrol C29H38O4 Celastrol C29H38O4 Pristimerin C30H40O4 Figure 1. Two-dimensional canonical structural display of compounds analyzed in this study. Syn- onyms: hydroxytingenone = beta-hydroxytingenone; maytenin = tingenone. Figure 1. Two-dimensional canonical structural display of compounds analyzed in this study. Syn- onyms: hydroxytingenone = beta-hydroxytingenone; maytenin = tingenone. 2.1. Caspase 1 Docking 2 1 1 Hydroxytingenone 2.1.1. Hydroxytingenone The final arrangement, ncluding calculating binding energy (−13.7 kcal/mol), is shown in Figure 4. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone car- bonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl that shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone carbonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl that shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone car- bonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl that shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone car- bonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl that shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone carbonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl that shows no interactions. igure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone car- onyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl hat shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone car- bonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl that shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone carbonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl that shows no interactions. Figure 2. Pose 4 of hydroxytingenone docking, two-dimensional display. The methide-quinone car- bonyl is engaged in hydrogen bond with Arg341 and His237, in contrast with the other carbonyl that shows no interactions. Figure 3. More detailed features of pose 4, hydroxytingenone, docking. The donor guanidino group of Arg341 (turquoise colored C atoms) has a double H-bond interaction with O(methide-quinone) carbonyl, 2.636 Å and 2.979 Å. The O(hydroxyl) associated with the methide-quinone inhibitor has a double H-bond interaction, one with H(Cys285), 1.837 Å, and one with H(His237), 2.772 Å (lower left of figure). Figure 3. More detailed features of pose 4, hydroxytingenone, docking. The donor guanidino group of Arg341 (turquoise colored C atoms) has a double H-bond interaction with O(methide-quinone) carbonyl, 2.636 Å and 2.979 Å. 2.1. Caspase 1 Docking 2 1 1 Hydroxytingenone 2.1.1. Hydroxytingenone Discovery Studio provides the Cdocker interaction energy, which is the non-bonded interaction energy (composed of the van der Waals term and the electrostatic term) between the protein and the potential inhibitor ligand related to the force field CHARMm; this value is −22.4 kcal/mol for hydroxytingenone pose 4. A more y y g p p p The relevant moieties of hydroxytingenone able to interact with the active site of caspase-1 are the two carbonyl groups, located at both ends of the structure, as discussed previously [11]. The carbonyl at the methide-quinone end is found in pose 4. A two- dimensional display of the amino acid interactions of docked hydroxytingenone at the active site is shown in Figure 2. Discovery Studio provides the Cdocker interaction energy, which is the non-bonded interaction energy (composed of the van der Waals term and the electrostatic term) between the protein and the potential inhibitor ligand related to the force field CHARMm; this value is −22.4 kcal/mol for hydroxytingenone pose 4. A more specific display of pose 4 is shown in Figure 3, where besides the H-bonds relevant to the methide-quinone moiety (Arg341 and His237), a Cys285 interaction (upon a slight variation in the cysteine C-C-S-H torsion angle) is seen to establish a very short H-bond distance between H(Cys285) and the hydroxytingenone hydroxyl group, 1.837 Å. However, the Cys285 interaction is not confirmed after a standard dynamic cascade protocol of Discovery Int. J. Mol. Sci. 2023, 24, 10750 4 of 17 varia nd dis- dis- Studio, while Arg341 and His237 are indeed confirmed. The final arrangement, including calculating binding energy (−13.7 kcal/mol), is shown in Figure 4. the Cys285 interaction is not confirmed after a standard dynamic cascade protocol of Dis covery Studio, while Arg341 and His237 are indeed confirmed. The final arrangement, including calculating binding energy (−13.7 kcal/mol), is shown in Figure 4. covery Studio, while Arg341 and His237 are indeed confirmed. The final arrangement, including calculating binding energy (−13.7 kcal/mol), is shown in Figure 4. Studio, while Arg341 and His237 are indeed confirmed. The final arrangement, including calculating binding energy (−13.7 kcal/mol), is shown in Figure 4. the Cys285 interaction is not confirmed after a standard dynamic cascade protocol of Dis covery Studio, while Arg341 and His237 are indeed confirmed. The final arrangement, including calculating binding energy (−13.7 kcal/mol), is shown in Figure 4. covery Studio, while Arg341 and His237 are indeed confirmed. 2.1. Caspase 1 Docking 2 1 1 Hydroxytingenone 2.1.1. Hydroxytingenone The O(hydroxyl) associated with the methide-quinone inhibitor has a double H-bond interaction, one with H(Cys285), 1.837 Å, and one with H(His237), 2.772 Å (lower left of figure). Figure 3. More detailed features of pose 4, hydroxytingenone, docking. The donor guanidino group of Arg341 (turquoise colored C atoms) has a double H-bond interaction with O(methide-quinone) carbonyl, 2.636 Å and 2.979 Å. The O(hydroxyl) associated with the methide-quinone inhibitor has a double H-bond interaction, one with H(Cys285), 1.837 Å, and one with H(His237), 2.772 Å (lower left of figure). 5 of 17 (lower Int. J. Mol. Sci. 2023, 24, 10750 Figure 4. After molecular dynamics pose 4, hydroxytingenone has calculated binding energy of −13.7 kcal/mol. The H-bond interaction between the donor guanidino group of Arg341 and O(methide-quinone) carbonyl is confirmed and strengthened, 2.109 Å, whereas an H-bond of 1.663 Å by acceptor O(Ser339) replaces the former interactions by Cys285 and His237. A comparison with interactions shown by the inhibitor VX-765 at the crystal structure active site [22], shows involve- ment of both amino acids, Arg341 and O(Ser339), also forming hydrogen bonds; the latter interacts with a guanidino HN moiety. Indeed, the role of Arg341 appears very important as it has a double hydrogen bond interaction with two different O(carbonyl) moieties of VX-765. Figure 4. After molecular dynamics pose 4, hydroxytingenone has calculated binding energy of −13.7 kcal/mol. The H-bond interaction between the donor guanidino group of Arg341 and O(methide-quinone) carbonyl is confirmed and strengthened, 2.109 Å, whereas an H-bond of 1.663 Å by acceptor O(Ser339) replaces the former interactions by Cys285 and His237. A comparison with interactions shown by the inhibitor VX-765 at the crystal structure active site [22], shows involvement of both amino acids, Arg341 and O(Ser339), also forming hydrogen bonds; the latter interacts with a guanidino HN moiety. Indeed, the role of Arg341 appears very important as it has a double hydrogen bond interaction with two different O(carbonyl) moieties of VX-765. Another cluster that includes poses 5, 6, 7, 9 shows important interactions at the op- posite end of hydroxytingenone, with Cys285 forming a H-bond to the O(carbonyl). Pose 5 was not confirmed by standard dynamics cascade as the ligand was thoroughly dis- placed from the active site. A smaller cluster was formed by poses 1 and 2, where Cys285 and His237 show H-bonds to the carbonyl opposite the methide-quinone moiety. 2.1. Caspase 1 Docking 2 1 1 Hydroxytingenone 2.1.1. Hydroxytingenone After applying dynamics to pose 1, the binding energy is −7.2 kcal/mol, which is markedly more positive than that of pose 4 (−13.7 kcal/mol). Additionally, pose 3 shows an interaction between the same carbonyl involved in pose 1, having H-bonds with Cys285 and Arg341. After dynamics, the binding energy is −8.9 kcal/mol, slightly better than that of pose 1 but still much less favored than that of pose 4. We conclude that hydroxytingenone molecular mechanics favor a pose 4 arrangement, shown in Figure 4. Another cluster that includes poses 5, 6, 7, 9 shows important interactions at the opposite end of hydroxytingenone, with Cys285 forming a H-bond to the O(carbonyl). Pose 5 was not confirmed by standard dynamics cascade as the ligand was thoroughly displaced from the active site. A smaller cluster was formed by poses 1 and 2, where Cys285 and His237 show H-bonds to the carbonyl opposite the methide-quinone moiety. After applying dynamics to pose 1, the binding energy is −7.2 kcal/mol, which is markedly more positive than that of pose 4 (−13.7 kcal/mol). Additionally, pose 3 shows an interaction between the same carbonyl involved in pose 1, having H-bonds with Cys285 and Arg341. After dynamics, the binding energy is −8.9 kcal/mol, slightly better than that of pose 1 but still much less favored than that of pose 4. We conclude that hydroxytingenone molecular mechanics favor a pose 4 arrangement, shown in Figure 4. 2.1.2. Tingenone 2.1.2. Tingenone g Our next docked compound was tingenone. Its atomic coordinates were derived from hydroxytingenone and minimized with Dmol3. Poses 1 and 5 are representatives of well-distinguished clusters in the docking as the first includes poses 2–4, 6, and 8, whereas pose 5 cluster includes poses 7 and 9. Pose 1 has Cdocker interaction energy −27.9 kcal/mol and shows interactions with the non-methide-quinone carbonyl, involving Arg341 and His237, see Figures 5 and S2. After the standard dynamics cascade, pose 1 is confirmed Our next docked compound was tingenone. Its atomic coordinates were derived from hydroxytingenone and minimized with Dmol3. Poses 1 and 5 are representatives of well-distinguished clusters in the docking as the first includes poses 2–4, 6, and 8, whereas pose 5 cluster includes poses 7 and 9. Pose 1 has Cdocker interaction energy −27.9 kcal/mol and shows interactions with the non-methide-quinone carbonyl, involving Arg341 and His237, see Figures 5 and S2. After the standard dynamics cascade, pose 1 is confirmed and the final arrangement obtained after binding energy calculations, −11.8 kcal/mol, is shown in Figure 6; this does not include His237. Interestingly, a cation-π interaction from another arginine, Arg383, is present at the other end of the molecule involving the methide-quinone moiety (2.752 Å) and so this pose appears tightly bound at the active site. Int. J. Mol. Sci. 2023, 24, 10750 6 of 17 ng the active the ctive Figure 5. Pose 1. The tingenone Docking 2D, Arg341 forms a hydrogen bond to the non-methide- quinone carbonyl, which also has H-bond interaction with H(His237). The methide-quinone moiety appears free of interactions. Figure 5. Pose 1. The tingenone Docking 2D, Arg341 forms a hydrogen bond to the non-methide- quinone carbonyl, which also has H-bond interaction with H(His237). The methide-quinone moiety appears free of interactions. Figure 5. Pose 1. The tingenone Docking 2D, Arg341 forms a hydrogen bond to the non-methide- quinone carbonyl, which also has H-bond interaction with H(His237). The methide-quinone moiety appears free of interactions. Figure 5. Pose 1. The tingenone Docking 2D, Arg341 forms a hydrogen bond to the non-methide- quinone carbonyl, which also has H-bond interaction with H(His237). The methide-quinone moiety appears free of interactions. Figure 5. Pose 1. The tingenone Docking 2D, Arg341 forms a hydrogen bond to the non-methide quinone carbonyl, which also has H-bond interaction with H(His237). The methide-quinone moiety appears free of interactions. igure 5. Pose 1. 2.1.2. Tingenone 2.1.2. Tingenone The tingenone Docking 2D, Arg341 forms a hydrogen bond to the non-methide- uinone carbonyl, which also has H-bond interaction with H(His237). The methide-quinone moiety ppears free of interactions. Figure 6. Pose 1. The tingenone dynamics of pose 1 has a calculated binding energy of −11.8 kcal/mol. The guanidino group of Arg383 (turquoise colored) establishes a cation-π interaction with the methide-quinone ring, 2.752 Å, whereas the originally docked Arg341 (violet colored) has a dou- ble non-chelating H-bond from the guanidino group to the opposite carbonyl, 3.262 Å and 3.088 Å. igure 6. Pose 1. The tingenone dynamics of pose 1 has a calculated binding energy of −11.8 cal/mol. The guanidino group of Arg383 (turquoise colored) establishes a cation-π interaction with he methide-quinone ring, 2.752 Å, whereas the originally docked Arg341 (violet colored) has a dou- le non-chelating H-bond from the guanidino group to the opposite carbonyl, 3.262 Å and 3.088 Å. Figure 6. Pose 1. The tingenone dynamics of pose 1 has a calculated binding energy of −11.8 kcal/mol. The guanidino group of Arg383 (turquoise colored) establishes a cation-π interaction with the methide-quinone ring, 2.752 Å, whereas the originally docked Arg341 (violet colored) has a double non-chelating H-bond from the guanidino group to the opposite carbonyl, 3.262 Å and 3.088 Å. Interestingly, the cation-π interaction reminds us of the interaction that the same amino acid, Arg383, establishes with an aromatic ring of original inhibitor VX-765 in the crystal structure. The only H-bond shown by pose 5 docking (Cdocker interaction ener- gy = −25.1 kcal/mol) is with Arg341, which also involves the non-methide-quinone moiety (Figures 7 and S3), which is confirmed by dynamics and has a calculated binding energy of Int. J. Mol. Sci. 2023, 24, 10750 7 of 17 = −25 1 25 1 −13.0 kcal/mol, Figure 8. Thus, both carbonyls of tingenone show a similar preference due to the equal binding energy of poses 1 and 5. 7 and S3), which is confirmed by dynamics and has a calculated binding energy of −13.0 kcal/mol, Figure 8. Thus, both carbonyls of tingenone show a similar preference due to the equal binding energy of poses 1 and 5. 7 and S3), which is confirmed by dynamics and has a calculated binding energy of −13.0 kcal/mol, Figure 8. Thus, both carbonyls of tingenone show a similar preference due to the qual binding energy of poses 1 and 5. −13.0 kcal/mol, Figure 8. 2.1.3. Pristimerin d d The last docked compound was pristimerin. Pose 4 belongs to the most populated cluster that includes poses 7 and 10. Its Cdocker interaction energy is −26.8 kcal/mol. There is a methide-quinone moiety involved in this cluster, interacting with Arg341 and π-sulfur Cys285 Figure 9 and Figure S4. Dynamics confirms the arrangement and, after calculating binding energy, −9.4 kcal/mol, Figure 10 shows three successive amino acid residues involved, Ser339-Trp340-Arg341, forming H-bonds of 1.524 Å, 2.297 Å and 2.370 Å, respectively. ed compound was pristimerin. Pose 4 belongs to the most populated es poses 7 and 10. Its Cdocker interaction energy is −26.8 kcal/mol. There ne moiety involved in this cluster, interacting with Arg341 and π-sulfur and S4. Dynamics confirms the arrangement and, after calculating bind- al/mol, Figure 10 shows three successive amino acid residues involved, g341, forming H-bonds of 1.524 Å, 2.297 Å and 2.370 Å, respectively. Pristimerin docking results, two-dimensional display. Cys285 shows π-sulfur in- methide-quinone ring and Arg341 has a H-bond to the methide-quinone O(car- Figure 9. Pose 4. Pristimerin docking results, two-dimensional display. Cys285 shows π-sulfur inter- action with the methide-quinone ring and Arg341 has a H-bond to the methide-quinone O(carbonyl). stimerin docking results, two-dimensional display. Cys285 shows π-sulfur in- ethide-quinone ring and Arg341 has a H-bond to the methide-quinone O(car- Figure 9. Pose 4. Pristimerin docking results, two-dimensional display. Cys285 shows π-sulfur inter- action with the methide-quinone ring and Arg341 has a H-bond to the methide-quinone O(carbonyl). (non methide-quinone) located at the other end of pristimerin (pose 1) eractions with Cys285 and Arg341, which is not confirmed by applying merin moves out of the active site. When analyzing the cluster made by H-bond interaction with Asp288 is seen. Upon dynamics of pose 2, this H b d ith C 285 h bi di i 9 3 k l/ l i il The carbonyl (non methide-quinone) located at the other end of pristimerin (pose 1) shows H-bond interactions with Cys285 and Arg341, which is not confirmed by applying dynamics as pristimerin moves out of the active site. When analyzing the cluster made by poses 2 and 3, an H-bond interaction with Asp288 is seen. Upon dynamics of pose 2, this evolves towards an H-bond with Cys285, whose binding energy is −9.3 kcal/mol, similar to that arising from pose 4. No other poses involve this carbonyl opposite the methide-quinone. 2.1.2. Tingenone 2.1.2. Tingenone Thus, both carbonyls of tingenone show a similar preference due to the equal binding energy of poses 1 and 5. 7 and S3), which is confirmed by dynamics and has a calculated binding energy of −13.0 kcal/mol, Figure 8. Thus, both carbonyls of tingenone show a similar preference due to the equal binding energy of poses 1 and 5. and S3), which is confirmed by dynamics and has a calculated binding energy of −13.0 cal/mol, Figure 8. Thus, both carbonyls of tingenone show a similar preference due to the qual binding energy of poses 1 and 5. Figure 7. Pose 5. Tingenone docking 2D interactions. Arg341 establishes an H-bond to the non- methide-quinone moiety. Figure 7. Pose 5. Tingenone docking 2D interactions. Arg341 establishes an H-bond to the non- methide-quinone moiety. Figure 7. Pose 5. Tingenone docking 2D interactions. Arg341 establishes an H-bond to the non- methide-quinone moiety. Figure 7. Pose 5. Tingenone docking 2D interactions. Arg341 establishes an H-bond to the non- methide-quinone moiety. Figure 7. Pose 5. Tingenone docking 2D interactions. Arg341 establishes an H-bond to the non- methide-quinone moiety. gure 7. Pose 5. Tingenone docking 2D interactions. Arg341 establishes an H-bond to the non- ethide-quinone moiety. Figure 8. Pose 5. Tingenone dynamics has a calculated binding energy of −13.0 kcal/mol. It shows a very short H-bond distance of 1.971 Å, from guanidino H(Arg341) to the O(carbonyl) opposed to the methide-quinone carbonyl. Figure 8. Pose 5. Tingenone dynamics has a calculated binding energy of −13.0 kcal/mol. It shows a very short H-bond distance of 1.971 Å, from guanidino H(Arg341) to the O(carbonyl) opposed to the methide-quinone carbonyl. Figure 8. Pose 5. Tingenone dynamics has a calculated binding energy of −13.0 kcal/mol. It shows a very short H-bond distance of 1.971 Å, from guanidino H(Arg341) to the O(carbonyl) opposed to the methide-quinone carbonyl. Int. J. Mol. Sci. 2023, 24, 10750 very short H-bon the methide-quin 8 of 17 o 2.1.3. Pristimerin d d O(methide- quinone-carbonyl) establishes an H-bond to brown colored H(Arg341), 2.370 Å, and to turquoise colored H(Trp340), 2.297 Å, whereas O(Ser339) is 1.524 Å from pristimerin H(hydroxy). Interest- ingly, the above mentioned O(Ser339) interaction seen in hydroxytingenone, and found in VX-765 crystal structure through an HN moiety, is identical to that seen in pristimerin, supporting a poten- tial role of this ligand and hydroxytingenone at the active site. In addition, the interaction between Trp340, indicated as π-alkyl in docking (Figure 9), and directed to the ring adjacent to the methide- quinone, transforms to hydrogen bonding with O(carbonyl) after dynamics, 2.297 Å. Figure 10. Pristimerin pose 4 dynamics after calculating the binding energy, −9.4 kcal. O(methide- quinone-carbonyl) establishes an H-bond to brown colored H(Arg341), 2.370 Å, and to turquoise colored H(Trp340), 2.297 Å, whereas O(Ser339) is 1.524 Å from pristimerin H(hydroxy). Interestingly, the above mentioned O(Ser339) interaction seen in hydroxytingenone, and found in VX-765 crystal structure through an HN moiety, is identical to that seen in pristimerin, supporting a potential role of this ligand and hydroxytingenone at the active site. In addition, the interaction between Trp340, indicated as π-alkyl in docking (Figure 9), and directed to the ring adjacent to the methide-quinone, transforms to hydrogen bonding with O(carbonyl) after dynamics, 2.297 Å. Poses 5 and 8 show π-π interactions with His342 and the dynamics of pose 5 displays no H-bonds; the binding energy of this conformation is −5.8 kcal/mol. Additionally, pose 6 was analyzed and showed only van der Waals interactions. Upon dynamics, Gly238 shows an H-bond and a binding energy of −5.8 kcal/mol. Therefore, pristimerin pose 4, involving the methide-quinone carbonyl, and pose 2, interacting with the opposite car- bonyl, are equally preferred: −9.4 and −9.3 kcal/mol, respectively. A summary of amino acid interactions is displayed in Table 1. From this docking study on these three natural products, we see marked differences to our earlier published findings on dexamethasone and other anti-inflammatory drugs [11] that showed important interactions with Cys285. In the present study, Cys285 shows no interaction with tingenone at docking, whereas hydroxytingenone and pristimerin do show such an interaction, although these are not confirmed after more rigorous molecular dynamics calculations. Here, Arg341 is the more involved amino acid at the caspase-1 active site as it is stabilized by the three potential inhibitors, hydroxytingenone, tingenone, and pristimerin. This interaction is also present after dynamics. 2.1.3. Pristimerin d d n H-bond with Cys285, whose binding energy is −9.3 kcal/mol, similar m pose 4. No other poses involve this carbonyl opposite the methide- q Poses 5 and 8 show π-π interactions with His342 and the dynamics of pose 5 displays no H-bonds; the binding energy of this conformation is −5.8 kcal/mol. Additionally, pose 6 was analyzed and showed only van der Waals interactions. Upon dynamics, Gly238 shows an H-bond and a binding energy of −5.8 kcal/mol. Therefore, pristimerin pose 4, involving the methide-quinone carbonyl, and pose 2, interacting with the opposite carbonyl, are equally preferred: −9.4 and −9.3 kcal/mol, respectively. A summary of amino acid interactions is displayed in Table 1. Int. J. Mol. Sci. 2023, 24, 10750 Int. J. Mol. Sci. 2023, 24, x FOR PE 9 of 17 9 of 17 9 of 17 9 of 17 PEER REVIEW 9 of 17 Figure 10. Pristimerin pose 4 dynamics after calculating the binding energy, −9.4 kcal. O(methide- quinone-carbonyl) establishes an H-bond to brown colored H(Arg341), 2.370 Å, and to turquoise colored H(Trp340), 2.297 Å, whereas O(Ser339) is 1.524 Å from pristimerin H(hydroxy). Interest- ingly, the above mentioned O(Ser339) interaction seen in hydroxytingenone, and found in VX-765 crystal structure through an HN moiety, is identical to that seen in pristimerin, supporting a poten- tial role of this ligand and hydroxytingenone at the active site. In addition, the interaction between Trp340, indicated as π-alkyl in docking (Figure 9), and directed to the ring adjacent to the methide- quinone, transforms to hydrogen bonding with O(carbonyl) after dynamics, 2.297 Å. Figure 10. Pristimerin pose 4 dynamics after calculating the binding energy, −9.4 kcal. O(methide- quinone-carbonyl) establishes an H-bond to brown colored H(Arg341), 2.370 Å, and to turquoise colored H(Trp340), 2.297 Å, whereas O(Ser339) is 1.524 Å from pristimerin H(hydroxy). Interestingly, the above mentioned O(Ser339) interaction seen in hydroxytingenone, and found in VX-765 crystal structure through an HN moiety, is identical to that seen in pristimerin, supporting a potential role of this ligand and hydroxytingenone at the active site. In addition, the interaction between Trp340, indicated as π-alkyl in docking (Figure 9), and directed to the ring adjacent to the methide-quinone, transforms to hydrogen bonding with O(carbonyl) after dynamics, 2.297 Å. Figure 10. Pristimerin pose 4 dynamics after calculating the binding energy, −9.4 kcal. 2.1.3. Pristimerin d d In the three natural products, we see the methide-quinone carbonyl group to be the preferred acceptor involved in hydroxytingenone, tingenone, and pristimerin hydrogen bonding interactions, agreeing with our previous findings [11]; however, the other carbonyl in tingenone shows a similar preference. Moreover, the interactions of our three celastrol derivatives docked at the active site of caspase-1 involve amino acids also engaged by the inhibitor VX-765 in the crystal structure, suggesting a closely related mechanism of inhibition. This includes hydrogen bonds for all three analyzed ligands with Arg341; cation-π interaction with Arg383, established with an aromatic ring of tingenone, and hydrogen bond interaction with O(Ser339) for hydroxytingenone and pristimerin. Int. J. Mol. Sci. 2023, 24, 10750 10 of 17 10 of 17 Table 1. Amino acid H-bond and other interactions (*) with three components of Maytena octogona at the active site of Caspase-1 upon docking. “P” is for pose; “none” indicates only van der Waals interactions; “OUT” indicates that after dynamics the potential inhibitory molecule becomes displaced outside the active site. Numbers (kcal/mol) within each box represent binding energy after dynamics. at the active site of Caspase-1 upon docking. “P” is for pose; “none” indicates only van der Waals interactions; “OUT” indicates that after dynamics the potential inhibitory molecule becomes displaced outside the active site. Numbers (kcal/mol) within each box represent binding energy after dynamics. P1 P2 P3 P4 P5 P6 P7 P8 P9 P10 H- Tingenone Cys285 His237 −7.2 Cys285 His237 −7.2 Arg341 Cys285 −8.9 Arg341 His237 −13.7 Trp340 π OUT Trp340 π OUT Trp340 OUT Arg341 His237 Trp340 π OUT Trp340 Cys285 (unfavored) Tingenone Arg341 His237 −11.8 His237 −11.8 His237 Cys285 −11.8 His237 −11.8 Arg341 * −13.0 His237 −11.8 Arg341 His342 (π-π) * −13.0 His237 Cys285 −11.8 Arg341 His342 (π-π) * −13.0 His237 Cys285 Pristimerin Arg341 Cys285 OUT Asp288 −9.3 Asp288 −9.3 Arg341 Cys285 (π-S) * −9.4 His342 (π-π) * −5.8 none −5.8 Arg341 Cys285 (π-S) * −9.4 His342 (π-π) * −5.8 none Arg341 Cys285 (π-S) * −9.4 2.2. RRDE 2023, 24, 10750 p y p g p p p Maytenus octogona extracts, in contrast with cold-extracted extra virgin olive oil [25]. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific color, for instance the 70 μL aliquot red line can be observed in the upper part, oxidation curve, detected at the ring electrode, which is consistent with the red line detected at the disk electrode for reduction during the same experiment and located at the bottom of the figure. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757, whose slope is associated with the superoxide scavenging capability of the stem extract. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific color, for instance the 70 µL aliquot red line can be observed in the upper part, oxidation curve, detected at the ring electrode, which is consistent with the red line detected at the disk electrode for reduction during the same experiment and located at the bottom of the figure. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific color, for instance the 70 μL aliquot red line can be observed in the upper part, oxidation curve, detected at the ring electrode, which is consistent with the red line detected at the disk electrode for reduction during the same experiment and located at the bottom of the figure. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757, whose slope is associated with the superoxide scavenging capability of the stem extract. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757, whose slope is associated with the superoxide scavenging capability of the stem extract. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific color, for instance the 70 μL aliquot red line can be observed in the upper part, oxidation curve, detected at the ring electrode, which is consistent with the red line detected at the disk electrode for reduction during the same experiment and located at the bottom of the figure. Figure 11. MORUnica (stem extract) RRDE voltammograms. 2.2. RRDE The release of ROS, a signal for inflammasome activation, may come from a variety of pathways, including K+ efflux, lysosomal rupture or mitochondrial dysfunction [6]. Thus, analyzing the antioxidant capability of the plant extracts may provide an explanation for their medicinal use. In our laboratory, we developed an electrochemical method for the direct and quan- titative analysis of scavenging superoxide [24]. Figure 11 shows a collage of the voltam- mograms associated with such an experiment for sample MORUnica (stem extract). The bottom part of the figure shows the amount of superoxide generated after reduction of bubbled O2 in the electrochemical cell (reaction (1), see Section 3.3); this is detected at the disk electrode. The top part of the figure shows superoxide detected at the ring electrode. The first experiment is a blank indicated as a 0 µL line; the last one shows the minimum amount of detected superoxide, for aliquot 510 µL. Each added aliquot decreases the current intensity detected at the ring electrode, and this is due to superoxide consumed by the an- tioxidant components of the extracts. For each voltammogram, the ratio ring current/disk current is defined as the efficiency. The physical interpretation is also associated with the time the generated superoxide (at the disk) takes to reach the ring and be oxidized. g p g In Figure 12, the efficiency of all added aliquots is included, i.e., the collection ef- ficiency is shown at the y axis, while the x axis shows the volume of added aliquot; ultimately, the slope of the line is associated with the antioxidant capability of scaveng- ing. Figures 13 and 14 show equivalent graphs for MOHUnica (leaf extract). Table 2 includes slopes of other natural products studied using the same method. This shows both Maytenus octogona extracts having weaker antioxidant activity, compared with olive oil. This is probably due to the depletion of antioxidants during ethanolic sample preparations of Maytenus octogona extracts, in contrast with cold-extracted extra virgin olive oil [25]. Table 2. Comparison of slopes of the plant products studied in this work with other natural products analyzed using the RRDE method. Table 2. Comparison of slopes of the plant products studied in this work with other natural products analyzed using the RRDE method. Olive Oil [25] Black Seed Oil [26] Propolis [27] MORUnica MOHUnica −0.0838 −0.078 −0.0864 −0.008 −0.023 11 of 17 oil. This tions of Int. J. Mol. Sci. 2.2. RRDE Each run is associated with a specific color, for instance the 70 µL aliquot red line can be observed in the upper part, oxidation curve, detected at the ring electrode, which is consistent with the red line detected at the disk electrode for reduction during the same experiment and located at the bottom of the figure. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific color, for instance the 70 μL aliquot red line can be observed in the upper part, oxidation curve, detected at the ring electrode, which is consistent with the red line detected at the disk electrode for reduction during the same experiment and located at the bottom of the figure. Fi 11 MORU i ( t t t) RRDE lt E h i i t d ith ifi Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific color, for instance the 70 μL aliquot red line can be observed in the upper part, oxidation curve, detected at the ring electrode, which is consistent with the red line detected at the disk electrode for reduction during the same experiment and located at the bottom of the figure. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific color, for instance the 70 µL aliquot red line can be observed in the upper part, oxidation curve, detected at the ring electrode, which is consistent with the red line detected at the disk electrode for reduction during the same experiment and located at the bottom of the figure. (stem extract) RRDE voltammograms. Each run is associated with a specific 70 μL aliquot red line can be observed in the upper part, oxidation curve, ectrode, which is consistent with the red line detected at the disk electrode for same experiment and located at the bottom of the figure. Figure 11. MORUnica (stem extract) RRDE voltammograms. Each run is associated with a specific color, for instance the 70 μL aliquot red line can be observed in the upper part, oxidation curve, detected at the ring electrode, which is consistent with the red line detected at the disk electrode for reduction during the same experiment and located at the bottom of the figure. Figure 11. MORUnica (stem extract) RRDE voltammograms. 2.2. RRDE Each run is associated with a specific color, for instance the 70 µL aliquot red line can be observed in the upper part, oxidation curve, detected at the ring electrode, which is consistent with the red line detected at the disk electrode for reduction during the same experiment and located at the bottom of the figure. a (stem extract) RRDE voltammograms. Each run is associated with a specific e 70 μL aliquot red line can be observed in the upper part, oxidation curve, ectrode, which is consistent with the red line detected at the disk electrode for same experiment and located at the bottom of the figure. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757 whose slope is associated with the superoxide scavenging capability of the stem extract. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757, whose slope is associated with the superoxide scavenging capability of the stem extract. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757, whose slope is associated with the superoxide scavenging capability of the stem extract. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757, whose slope is associated with the superoxide scavenging capability of the stem extract. a collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757, ated with the superoxide scavenging capability of the stem extract. Figure 12. MORUnica collection efficiency shows a linear behavior, y = −0.008x + 12.807, R2 = 0.9757, whose slope is associated with the superoxide scavenging capability of the stem extract. 12 of 17 12 of 17 Int. J. Mol. Sci. 2023, 24, 10750 Int. J. Mol. Sci. 2023, 24, x FOR P 23, 24, x FOR PEER REVIEW Figure 13. MOHUnica (leaf extract) RRDE voltammograms. Figure 14. MOHUnica collection efficiency of the ethanol leaf extract, y = −0.0232x +10.585, R2 = 0.994. Compared with the stem extract (Figure 12), the steeper slope in this figure indicates a stronger capability of scavenging superoxide. Table 2. Comparison of slopes of the plant products studied in this work with other natural prod- ucts analyzed using the RRDE method. Figure 13. MOHUnica (leaf extract) RRDE voltammograms. Figure 13. MOHUnica (leaf extract) RRDE voltammograms. Figure 14. p ucts analyzed u using the RRDE 3.1. Reagents Olive Oil [25] Black Seed Oil [26] Propolis [27] MORUnica MOHUnica −0.0838 −0.078 −0.0864 −0.008 −0.023 ] Black Seed Oil [26] Propolis [27] MORUnica MOHUnica −0.078 −0.0864 −0.008 −0.023 For electrochemical studies, tetrabutylammonium bromide (TBAB; TCI Chemicals, Portland, OR, USA) and 99.9% anhydrous dimethyl sulfoxide (DMSO; Sigma-Aldrich, Inc., St. Louis, MO, USA). 2.2. RRDE MOHUnica collection efficiency of the ethanol leaf extract, y = −0.0232x +10.585, R2 = 0.994. Compared with the stem extract (Figure 12), the steeper slope in this figure indicates a stronger capability of scavenging superoxide. Table 2. Comparison of slopes of the plant products studied in this work with other natural prod- ucts analyzed using the RRDE method. Figure 14. MOHUnica collection efficiency of the ethanol leaf extract, y = −0.0232x + 10.585, R2 = 0.994. Compared with the stem extract (Figure 12), the steeper slope in this figure indicates a stronger capability of scavenging superoxide. 3. Materials and Methods 3.1. Reagents For electrochemical studies tetrabutylammonium bromide (TBAB; TCI Chemicals Figure 13. MOHUnica (leaf extract) RRDE voltammograms. Figure 13. MOHUnica (leaf extract) RRDE voltammograms. HUnica (leaf extract) RRDE voltammograms. Figure 14. MOHUnica collection efficiency of the ethanol leaf extract, y = −0.0232x +10.585, R2 = 0.994. Compared with the stem extract (Figure 12), the steeper slope in this figure indicates a stronger capability of scavenging superoxide. HUnica collection efficiency of the ethanol leaf extract, y = −0.0232x +10.585, R2 = 0.994. h the stem extract (Figure 12), the steeper slope in this figure indicates a stronger avenging superoxide. Figure 14. MOHUnica collection efficiency of the ethanol leaf extract, y = −0.0232x + 10.585, R2 = 0.994. Compared with the stem extract (Figure 12), the steeper slope in this figure indicates a stronger capability of scavenging superoxide. 3.1.2. MOR UNICA (Stem Extract) One kilogram of dried and ground stems of Maytenus octagona was extracted from ethanol 96% in a Soxhlet apparatus until exhaustion. Evaporation of the solvent at reduced pressure provided 275 g of a reddish-brown extract. 3.1.1. MOH UNICA (Leaf Extract) Two methods were used to obtain these samples: Two methods were used to obtain these samples: Int. J. Mol. Sci. 2023, 24, 10750 13 of 17 13 of 17 Method 1. Two kilograms of dry and ground Maytenus octogona leaves were macerated for 20 h in hot (96◦) ethanol and were filtered. After this time, additional ethanol was added and the mixture was refluxed for 4 h. The solution was filtered hot. Method 2. One kilogram of dried and ground leaves of Maytenus octagona were extracted from ethanol 96% in a Soxhlet apparatus until exhaustion. Evaporation of the solvent at reduced pressure provided 260 g of a dark green extract. p p g g Both the filtrates were combined and concentrated in a Buchi rotary evaporator at 40 ◦C and 400 g of a dark green dry extract was obtained. 3.2. Electrochemistry A Pine Research WaveDriver 20 bipotentiostat with the Modulated Speed Electrode Rotator was used to perform the hydrodynamic voltammetry at a rotating ring-disk elec- trode (RRDE). The working electrode is the AFE6R2 gold disk and gold ring rotator tip (Pine Research, Durham, NC, USA) combined with a coiled platinum wire counter elec- trode and a reference electrode consisting of an AgCl coated silver wire immersed in 0.1 M tetrabutyl ammonium bromide (TBAB) in dry DMSO in a fritted glass tube. The electrodes were placed in a five-neck electrochemical cell together with means for either bubbling or blanketing the solution with gas. Voltammograms were collected using Aftermath software release 1.6.10523 provided by Pine Research. Careful cleaning of the electrodes was performed by polishing with 0.05 µm alumina-particle suspension (Allied High Tech Products, Inc., Rancho Dominguez, CA, USA) on a moistened polishing microcloth to eliminate potential film formation [28]. 3.3. Hydrodynamic Voltammetry (RRDE) MOH Unica (0.924 g) and MOR Unica (0.103 g) were dissolved in 8.7 mL and 9.0 mL, respectively, of anhydrous DMSO (99.9% purity). These were the stock solution of analyzed samples. For the experiment, a solution of 0.1 M TBAB electrolyte in anhydrous DMSO (99.9% purity) was bubbled for 5 min with a dry O2/N2 (35%/65%) gas mixture to establish the dissolved oxygen level in the electrochemical cell of 50 mL. The Au/Au disc electrode was then rotated at 1000 rpm, and potential sweep was applied to the disk from 0.2 V to −1.2 V and then back to 0.2 V while the ring was held constant at 0.0 V; the disk voltage sweep rate was set to 25 mV/s. The molecular oxygen reduction peak (reaction 1) was observed around −0.6 V at the disk electrode; the oxidation current (reaction 2) occurred at the ring electrode. An initial blank, in the absence of an antioxidant, was run on this solution and the ratio of the ring/disk current was calculated as the “efficiency”. Next, an antioxidant aliquot was added, the solution bubbled with the gas mixture for 5 min, the voltammogram was rerecorded, and was efficiently obtained. In this way, the rate at which increasing concentrations of antioxidant scavenge the generated superoxide radicals during the electrochemical reaction was determined as each additional antioxidant aliquot was added. Results from each run were collected on Aftermath software Release 1.6.10523 and represented as voltammograms showing current vs. potential graphs that were later analyzed using Microsoft Excel. The used aliquots were indicated in related RRDE graphs. Ultimately, the slope of the overall decrease in efficiency with the addition of antioxidant serves as a quantitative measure of the antioxidant activity of each sample. Any decrease in the collection efficiency was expected to be due to the amount of superoxide removed by the antioxidant. This method has been developed in our lab [24]. MOH Unica (0.924 g) and MOR Unica (0.103 g) were dissolved in 8.7 mL and 9.0 mL, respectively, of anhydrous DMSO (99.9% purity). These were the stock solution of analyzed samples. For the experiment, a solution of 0.1 M TBAB electrolyte in anhydrous DMSO (99.9% purity) was bubbled for 5 min with a dry O2/N2 (35%/65%) gas mixture to establish the dissolved oxygen level in the electrochemical cell of 50 mL. 3.4. Computational Study Calculations were performed using programs from Biovia (Dassault Systèmes, San Diego, CA, USA). Density functional theory (DFT) program Dmol3 was applied to calculate energy, geometry, and frequencies implemented in Materials Studio 7.0 [29]. We employed the double numerical polarized (DNP) basis set that included all the occupied atomic orbitals plus a second set of valence atomic orbitals and polarized d-valence orbitals [30]; the correlation generalized gradient approximation (GGA) was applied, including Becke exchange [31] plus BLYP correlation. All electrons were treated explicitly and the real space cutoff of 5 Å was imposed for numerical integration of the Hamiltonian matrix elements. The self-consistent field convergence criterion was set to the root mean square change in the electronic density to be less than 10−6 electron/Å3. Calculations did not include solvent effects. The convergence criteria applied during geometry optimization were 2.72 × 10−4 eV for energy and 0.054 eV/Å for force. Docking studies were performed with the CDOCKER package in Discovery Studio 2020 version [23]. Standard dynamics cascade protocol in Discovery Studio allows optimization of atomic coordinates and was also applied to the selected poses. 3.3. Hydrodynamic Voltammetry (RRDE) The Au/Au disc electrode was then rotated at 1000 rpm, and potential sweep was applied to the disk from 0.2 V to −1.2 V and then back to 0.2 V while the ring was held constant at 0.0 V; the disk voltage sweep rate was set to 25 mV/s. The molecular oxygen reduction peak (reaction 1) was b d d 0 6 V t th di k l t d th id ti t ( ti 2) d In an RRDE voltammetry experiment, the generation of the superoxide radicals occurs at the disk electrode while the oxidation of the residual superoxide radicals (that have not been scavenged by the antioxidant) occurs at the ring electrode. Int. J. Mol. Sci. 2023, 24, 10750 14 of 17 14 of 17 Reaction (1): Reduction of molecular oxygen at the disk electrode: O2 + e−→O2•− (1) (1) O2 + e−→O2•− Reverse Reaction (2): Oxidation of superoxide radicals at the ring electrode: Reverse Reaction (2): Oxidation of superoxide radicals at the ring electrode: O2•−→O2 + e− (2) (2) O2•−→O2 + e− 4. Conclusions Since inflammation is associated with many human maladies including metabolic and cardiovascular diseases, cancer, and COVID-19, as well as many neurodegenerative conditions, inhibitors of the anomalous activation of the inflammasome are important to identify [32]. Selective, potent small molecule caspase-1 inhibitors such as VX-765 (Bel- nacasan) exist but their strong side effects limit their clinical use [33]. Recent in vivo and in vitro studies on a small molecule caspase-1 inhibitor, NSC697923, showed its effective- ness in an animal model of gouty arthritis. When docking studies were performed that included NSC697923 in the binding pocket A of caspase-1, H-bonds with Arg341 were seen and, consistent with VX-765, the caspase-1 inhibitor was present in the caspase-1 crystal structure used in our studies [34]. In this investigation, aerial parts of Maytenus octogona (ethanol extracts), employed in Peruvian ethnopharmacology as anti-inflammatory agents, were analyzed using a cyclo- voltammetry method able to directly determine the scavenging of the superoxide radical. Leaf extracts were more active than those from stems. A comparison with other natural products analyzed by our group using the same protocol (olive oil [25], propolis [26] and black seed oil [27]) indicates slightly weaker scavenging for these extracts. Recently, a study on the potential anti-inflammatory activity of some phenolic and methide-quinone nor-triterpenes isolated from Maytenus retusa that were evaluated for the inhibition of the NLRP3 inflammasome in macrophages appeared [35]. One of the most potent compounds evaluated was a semisynthetic methide-quinone Br derivative related to the three methide-quinones described in this work. This compound showed markedly reduced caspase-1 activity, IL-1β secretion (IC50 = 0.19 µM), and pyroptosis (IC50 = 0.13 µM). Since caspase-1 inhibition is important in preventing excessive cytokine production that can lead to inflammation, these findings can be associated with our results. In this investigation, three natural methide-quinones derivatives contained in Maytenus octogona extracts were analyzed using molecular mechanics docking calcula- tions. Results of these studies show the possible inhibition of caspase-1 by each of these compounds, thus supporting the anti-inflammatory medicinal use by indigenous popu- lations in the related Peruvian area. Our work shows that Arg341 is the most important Int. J. Mol. Sci. 2023, 24, 10750 15 of 17 15 of 17 amino acid involved in inhibiting the active site of caspase-1. This amino acid is stabi- lized through strong intermolecular interactions for each of the three potential inhibitors, hydroxytingenone, tingenone, and pristimerin. 4. Conclusions The calculated binding energies of these three compounds are −13.7 kcal/mol for hydroxytingenone, −11.8 and 13.0 kcal/mol for tingenone, and −9.3 and −9.4 kcal/mol for pristimerin, which indicate that all three natural products are good inhibitors. Each of these methide-quinones is closely related to the methide-quinone Br derivative mentioned above [35]. That these interactions remain after the more rigorous molecular dynamics calculations underscores their significance. The methide-quinone carbonyl group in hydroxytingenone and pristimerin is preferred as a hydrogen bond acceptor over the other possible carbonyl acceptor located in these ligands, agreeing with results shown in a previous study [11]. This is confirmed by statistics on the 10 poses of pristimerin, showing only poses 1–3 having H-bond interactions with the O(carbonyl) located at the other end of the molecule, whereas for poses 4, 5, 7, 8, 10 the methide-quinone carbonyl is engaged, also in H-bonds. Tingenone shows both carbonyls having a similar preference due to closely related binding energy derived from poses 1 and 5. Our work supports the anti-inflammatory medicinal use of Maytenus octogona by native populations in Peru and provides impetus for studying the chemical mechanisms of additional established traditional remedies. Once again, we have shown that natural products can provide the chemical scaffold that targets important receptor sites such as caspase-1 in the inflammasome pathway for the development of a novel therapy against human diseases. Supplementary Materials: The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ijms241310750/s1. Author Contributions: Conceptualization, F.C.; methodology, H.C.; formal analysis, E.E.; investi- gation, F.C. and H.C.; data curation, M.B., R.S. and F.S.-L.; writing original draft preparation, F.C. and M.R.; writing-review and edit, F.C., M.R. and E.E.; visualization, M.R. All authors have read and agreed to the published version of the manuscript. Funding: This research received no external funding. 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https://openalex.org/W2162456360
https://figshare.com/articles/journal_contribution/A_multiple-baseline_stereo/6591083/1/files/12079595.pdf
English
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A multiple-baseline stereo
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NOTICE WARNING CONCERNING COPYRIGHT RESTRICTIONS: The copyright law of the United States (title 17, U.S. Code) governs the making of photocopies or other reproductions of copyrighted material. Any copying of this document without permission of its author may be prohibited by law. NOTICE WARNING CONCERNING COPYRIGHT RESTRICTIONS: The copyright law of the United States (title 17, U.S. Code) governs the making of photocopies or other reproductions of copyrighted material. Any copying of this document without permission of its author may be prohibited by law. A Multiple-Baseline Stereo This research was supported in part by the Defense Advanced Research Projects Agency (DOD), and monitored by the Avionics Laboratory, Air Force Wright Aeronautical Laboratories, Aeronautical Systems Division (AFSC), Wright-Patterson AFB, Ohio 45433-6543 under Contract F33615-87-C-1499, ARPA Order No. 4976, Amendment 20. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Defense Advanced Research Projects Agency or of the U.S. Government. Keywords: vision, image understanding, stereo Abstract This paper presents a stereo matching method which uses multiple stereo pairs with various baselines to obtain precise depth estimates without suffering from ambiguity. In stereo processing, a short baseline means that the estimated depth will be less precise due to narrow triangulation. For more precise depth estimation, a longer baseline is desired. With a longer baseline, however, a larger disparity range must be searched to find a match. As a result, matching is more difficult and there is a greater possibility of a false match. So there is a trade-off between precision and accuracy in matching. The stereo matching method presented in this paper uses multiple stereo pairs with different baselines generated by a lateral displacement of a camera. Matching is performed simply by computing the sum of squared-difference (SSD) values. The SSD functions for individual stereo pairs are represented with respect to the inverse depth (rather than the disparity, as is usually done), and then are simply added to produce the sum of SSDs. This resulting function is called the SSSD-in-inverse-depth. We show that the SSSD-in-inverse-depth function exhibits a unique and clear minimum at the correct matching position even when the underlying intensity patterns of the scene include ambiguities or repetitive patterns. An advantage of this method is that we can eliminate false matches and increase precision without any search or sequential filtering. This paper first defines a stereo algorithm based on the SSSD-in-inverse-depth and presents a mathematical analysis to show how the algorithm can remove ambiguity and increase pre- cision. Then, a few experimental results with real stereo images are presented to demonstrate the effectiveness of the algorithm. 1 Introduction Stereo is a useful technique for obtaining 3-D information from 2-D images in computer vision. In stereo matching, we measure the disparity d, which is the distance between the corresponding points of left and right images. The disparity d is related to the depth z by d = B F - (1) z d = B F - z d = B F - z (1) where B and F are baseline and focal length, respectively. where B and F are baseline and focal length, respectively. where B and F are baseline and focal length, respectively. This equation indicates that for the same depth the disparity is proportional to the baseline, or that the baseline length B acts as a magnification factor in measuring d in order to obtain z. That is, the estimated depth is more precise if we set the two cameras farther apart from each other, which means a longer baseline. A longer baseline, however, poses its own problem. Because a longer disparity range must be searched, matching is more difficult and thus there is a greater possibility of a false match. So there is a trade-off between precision and accuracy (correctness) in matching. p y ( ) g One of the most common methods to deal with the problem is a coarse-to-fine control strategy [MP79][Gri85]. Matching is done at a low resolution to reduce false matches and then the result is used to limit the search range of matching at a high resolution, where more precise disparity measurements are calculated. Using a coarse resolution, however, does not always remove false matches. This is especially true when there is inherent ambiguity in matching, such as a repeated pattern over a large part of the scene (eg., a scene of a picket fence). Another approach to remove false matches and to increase precision is to use multiple images, especially a sequence of densely sampled images along a camera path [BBM87, Yam88, MSK89]. A short baseline between a pair of consecutive images makes the matching or tracking of features easy, while the structure imposed by the camera motion allows integration of the possibly noisy individual measurements into a precise estimate. The integration has been performed either by exploiting constraints on the EPI [BBM87, Yam88] or by a sequential Kalman filtering technique [MSK89, Hee89]. 2 Mathematical Analysis The essence of stereo matching is, given a point in one image, to find the most similar point in another image. The sum of squared differences (SSD) of the intensity values (or values of preprocessed images, such as bandpass filtered images) over a window is the simplest and most effective criterion for matching. In this section, we define the sum of SSD with respect to the inverse depth (SSSD-in-inverse-depth) for multiple-baseline stereo, and mathematically show its advantage in removing ambiguity and increasing precision. For this analysis, we use 1-D stereo intensity signals, but the extension to two dimensional images is straightforward. 1 Introduction y q g q A stereo matching method presented in this paper belongs to the second approach: use of multiple images with different baselines obtained by a lateral displacement of a camera. Matching, however, is performed in a simple way. The sum of square-difference (SSD) values are computed for each pair of stereo images. The SSD values are represented with respect to the inverse depth \ (rather than the disparity d, as is usually done). Those SSD functions from all the stereo pairs are simply added together to produce the sum of SSDs, which we call SSSD-in-inverse-depth. We show that the SSSD-in-inverse-depth function exhibits a unique and clear minimum at the correct matching position even when the underlying intensity patterns of the scene include ambiguities or repetitive patterns. An advantage of this technique is that we can eliminate false matches and increase precision without any search or sequential filtering. p y q g In the next section we present the method mathematically and show how ambiguity can be removed and precision increased by the method. Section 3 provides a few experimental results with real stereo images to demonstrate the effectiveness of the algorithm. PO PI P2 Pn Bl B2 Bn Figure 1: Camera positions for stereo Pn 2.1 SSD Function Suppose that we have camera positions PO,PI,...,PH and a resulting set of stereo pairs with baselines ... ,BH as shown in figure 1. Let FO(X) and/,(x) be the image pair at the camera positions PO and PI, respectively. Imagine a scene point Z whose depth is z. Its disparity dr® for the image pair taken from PQ and P, is (2) (2) The image intensity functions FO(X) and/,-(x) near the matching positions for Z can be expressed as The image intensity functions FO(X) and/,-(x) near the matching positions for Z can be expressed as FO(X) = F(X) + NO(X) /.(*) = F(X-DM) + RN(X), (3) FO(X) = F(X) + NO(X) /.(*) = F(X-DM) + RN(X), (3) (3) assuming constant distance near Z and independent Gaussian white noise such that NO(X)MX)~N(0,<Tl). (4) uming constant distance near Z and independent Gaussian white noise such that NO(X)MX)~N(0,<Tl). (4) NO(X)MX)~N(0,<Tl). ( (4) The SSD value over a window W at a pixel position X for the candidate disparity is defined as The SSD value over a window W at a pixel position X for the candidate disparity is defined as e«<(o0c,4o) = Y,VO(X+J)-FI(X + D®+ J)) 2 (5) (5) 2 where the Zj&r means summation over the window. The d® that gives a minimum of ed(!)(xy d®) is determined as the estimate of the disparity at x. Since the SSD measurement e^d®) is a random variable, we will compute its expected value in order to analyze its behavior: where the Zj&r means summation over the window. The d® that gives a minimum of ed(!)(xy d®) is determined as the estimate of the disparity at x. Since the SSD measurement e^d®) is a random variable, we will compute its expected value in order to analyze its behavior: £[e« 0(x,d( 0)] = E = E X)(f(* +f> -fix + d(0 - dK0 +j) + no(x +J) - m(x + + j)f £(A*+y) -fix+d® - dm + E + E J2 2<f(* +J) -fix + d® - dr® +j)(no(x +j) - m(x + d*> + J)) X)(«o(* +j) - rnQc + d® +j)) 2 - HVix+D-fix + ^-drv+flf + W^, (6) where Nw is the number of the points within the window. For the rest of the paper, £[] denotes the expected value of a random variable. In deriving the above equation, we have assumed that is constant over the window. where a £ 0 is a constant. Then, from equation (6) where a £ 0 is a constant. Then, from equation (6) Ele^ix, dr®)] = Efa©(x, d^ + a)] = 2NW<%. (8) (8) This means that ambiguity is expected in matching in terms of positions of minimum SSD values. Moreover, the false match at dr® + a appears in exactly the same way for all i"; it is separated from the correct match by a for all the stereo pairs. Using multiple baselines does not help to disambiguate. 2.1 SSD Function Equation (6) says that naturally the SSD function e^ix, d®) is expected to take a minimum when d® = d^, i.e., at the right disparity. Let us examine how the SSD function ed®(x,d®) behaves when there is ambiguity in the underlying intensity function. Suppose that the intensity signal f(x) has the same pattern around pixel positions x and x + a, f(x+J)=f(x + a+f), JEW (7 n from equation (6) f(x+J)=f(x + a+f), JEW (7) hen, from equation (6) f(x+J)=f(x + a+f), JEW (7) here a £ 0 is a constant. Then, from equation (6) (7) From equation and (2), From equation and (2), q ( ), 4® = BIFCR (10) 4o = BIFC, (11) 4® = BIFCR (10) 4o = BIFC, (11) 4® = BIFCR 4o = BIFC, (10) (11) (10) (11) where (r and C are the real and the candidate inverse depth, respectively. Substituting these into equation (5), we have the SSD with respect to the inverse depth, where (r and C are the real and the candidate inverse depth, respectively. Substituting these into equation (5), we have the SSD with respect to the inverse depth, ««»(*, 0 s £(f(*+y) -ffc+BIFC +;)) 2, (12) (12) at position x for a candidate inverse depth (. Its expected value is EBAFLCQ] - E(^Cx+i)-f(x+BIF(( - Q + ; ) ) 2 + 2 A ^ . (13) at position x for a candidate inverse depth (. Its expected value is EBAFLCQ] - E(^Cx+i)-f(x+BIF(( - Q + ; ) ) 2 + 2 A ^ . (13) (13) Finally, we define a new evaluation function £(Q2..«)(x, 0» * e s u m °f SSD functions with respect to the inverse depth (SSSD-in-inverse-depth) for multiple stereo pairs. It is obtained by adding the SSD functions *«i)(x, Q for individual stereo pairs: t«12..«)(z, 0 = E *C©(*i 0- (I 4) (I 4) Its expected value is £[*«i2..*)(*,C)] £[*«i2..*)(*,C)] - 01 = (i5) (i5) In the next three subsections, we will analyze the characteristics of these evaluation functions to see how ambiguity is removed and precision is improved. In the next three subsections, we will analyze the characteristics of these evaluation functions to see how ambiguity is removed and precision is improved. 2.2 SSD with respect to Inverse Depth Now, let us introduce the inverse depth C such that c-i. z (9) 3 c-i. z (9) (9) 3 We can prove that E[eai2)(xo, Q] > 4Nwa 2 n = £[eC(i2)(JCb, 0)1 for C ? (18) (18) (refer to appendix A) In words, e«i2)(*o, 0 is expected to have the smallest value at the correct G- That is, the ambiguity is likely to be eliminated by use of the new evaluation function with two different baselines. (refer to appendix A) In words, e«i2)(*o, 0 is expected to have the smallest value at the correct G- That is, the ambiguity is likely to be eliminated by use of the new evaluation function with two different baselines. We can illustrate this using synthesized data. Suppose the point whose depth we want to determine is at x = 0 and the underlying function / (x) is given by / W J < I ) + 2 (19) ' [ 1 if x < - 4 or 4 < x. (19) Figure 2 (a) shows a plot of / (JC). Assuming that d^\) = 5, a\ = 0.2, and the window size is 5, the expected values of the SSD function ed(\)(xo, d(l)) are as shown in figure 2 (b). We see that there is an ambiguity: the minima occur at the correct match d{\) = 5 and at the false match d(\) = 13. Which match will be selected will depend on the noise, search range, and search strategy. Now suppose we have a longer baseline B2 such that §^ = 1.5. From equations (6) and (10), we obtain E[e<i(i)] as shown in figure 2 (c). Again we encounter an ambiguity, and the separation of the tw minima is the same. Now let us evaluate the SSD values with respect to the inverse depth ( rather than the disparity d by using equations (12) through (15). The expected values of the SSD measurements and £0<(2)] with baselines B\ and B2 are shown in figures 2 (d) and (e), respectively (the plot is normalized such that B\F =1). Note that the minima at the correct inverse depth (C = 5) does not move, while the minima for the false match changes its position as the baseline changes. When the two functions are added to produce the SSSD-in-inverse-depth, its expected values £[£<(i2)] are as shown in figure 2 (f). We can see that the ambiguity has been reduced because the SSSD-in-inverse-depth has a smaller value at the correct match position than at the false match. 2.3 Elimination of Ambiguity (1) As before, suppose the underlying intensity pattern/(x) has the same pattern around x and x + a (equation (7)). Then, according to equation (13), we have As before, suppose the underlying intensity pattern/(x) has the same pattern around x and x + a (equation (7)). Then, according to equation (13), we have We still have an ambiguity; a minimum is expected at a false inverse depth Q = C- + sg?- However, an important point to be observed here is that this minimum for the false inverse depth Q changes 4 us position as the baseline 5, changes, while the minimum for the correct inverse depth £ does not This is the property that the new evaluation function, the SSSD-in-inverse-depth (14), exploits to eliminate the ambiguity. For example, suppose we use two baselines flt and B2 (5, d B2) From equation (15) £[e«i2)C*o, C)] = T>(f( xo +J)-fOco+BiF(C-0)+j)) 2 + E^ +y")-/(^+fi2F(C-C,)+;')) 2 + 4iVw<ra 2 (17) (17) 2.4 Elimination of Ambiguity (2) An extreme case of ambiguity occurs when the underlying function/ (x) is a periodic function, like a scene of a picket fence. We can show that this ambiguity can also be eliminated. 5 (a) (b) (c) (d) (e) (f) •zeta zeta zeta ure 2: Expected values of evaluation functions: (a) Underlying function; (b)E[ed(\)]; (c)£f £[««i)]; («) ^I«<(2)]; (0 £[«c(i2)l 6 (a) •zeta (f) zeta Figure 2: Expected values of evaluation functions: (a) Underlying function; (b)E[ed(\)]; (c)£fap)]; (d) £[««i)]; («) ^I«<(2)]; (0 £[«c(i2)l 6 Let/ (x) be a periodic function with period T. Then, each e<(i)(Jt, Q is expected to be a periodic function of C with the period ^ (for the proof, refer to appendix B). This means that there will be multiple minima of £<(o(x, 0 (i.e., ambiguity in matching) at intervals of jj? in (. When we use two baselines and add their SSD values, the resulting e^nfa, 0 will be still a periodic function of C, but its period T\z is increased to Tn=LCM f T T \ \BXF'B2F)' (20) (20) where LCMQ denotes Least Common Multiple. That is, the period of the expected value of the new evaluation function can be made longer than that of the individual stereo pairs. Furthermore, it can be controlled by choosing the baselines B\ and Zfe appropriately so that the expected value of the evaluation function has only one minimum within the search range. This means that using multiple-baseline stereo pairs simultaneously can eliminate ambiguity, although each individual baseline stereo may suffer from ambiguity. We illustrate this by using real stereo images. Figure 3(a) shows an image of a sample scene. At the top of the scene there is a grid board whose intensity function is nearly periodic. We took ten images of this scene by shifting the camera vertically as in figure 4. The actual distance between consecutive camera positions is 0.05 inches. Let this distance be B. Figure 3 shows the first and the last images of the sequence. We selected a point X within the repetitive grid board area. The SSD values £<(,•)(*, Q over 5-by-5-pixel windows are plotted for various baseline stereo pairs in figure 5. The horizontal axis of all the plots is the inverse depth, normalized such that SBF = 1. Figure 5 illustrates the trade-off between precision and ambiguity in terms of baselines. 2.4 Elimination of Ambiguity (2) That is, for a shorter baseline, there are fewer minima (i.e. less ambiguity), but the SSD curve is flatter (i.e. less precise localization). On the other hand, for a longer baseline, there are more minima (i.e. more ambiguity), but the curve near the minimum is sharper; that is. the estimated depth is more precise if we can find the correct one. Now, let us take two stereo image pairs: one with B = 5B and the other with B = 86. In figure 6, the dashed curve and the dotted curve show the SSD for B * 5B and B » 86, respectively. Let us suppose the search range goes from 0 to 20 in the horizontal axis, which in this case corresponds to 12 to 0 0 inches in depth. Though the SSD values take a minimum at the correct answer near C = 5, there are also other minima for both cases. The solid curve shows the evaluation function for the multiple-baseline stereo, which is the sum of the dashed curve and the dotted curve. The solid curve shows only one clear minimum; that is, the ambiguity is resolved. 7 (a) (b) Figure 3: 'Town" data set: (a) ImageO; (b) Image9 (b) (a) (b) (a) Figure 3: 'Town" data set: (a) ImageO; (b) Image9 imageO imagel image2 image3 image4 imageS image6 image7 image8 image9 Baseline b 2b 3b 4b 5b 6b 7b 8b 9b Figure 4: "Town" data set image sequence 8 8 (a) (b) (c) (d) (e) (f) (g) 9 7000 R g> 60001 °> 5000 R 4000 (h) 5 10 ^15 20 Figure 5: SSD values vs. inverse depth: (a) B = b; (b) B = lb; (c) B = 36; (d) 5 = 4b; (e) 5 = 5 (t)B- 6b; (g) 5 = lb; (h) 5 = Sb. The horizontal axis is normalized such that SbF = 1. Figure 5: SSD values vs. inverse depth: (a) B = b; (b) B = lb; (c) B = 36; (d) 5 = 4b; (e) 5 = 5b; (t)B- 6b; (g) 5 = lb; (h) 5 = Sb. The horizontal axis is normalized such that SbF = 1. 9 Inverse depth Figure 6: Combining two stereo pairs with different baselines Figure 6: Combining two stereo pairs with different baselines So far, we have considered using only two stereo pairs. We can easily extend the idea to multiple-baseline stereo which uses more than two stereo pairs. Corresponding to equation (20), the period of £[*«i2 .-*t)(x, 01 becomes Tn^ = LCM ..., (21) \B\F B2F BHFJ (21) where B\ ,52,. •. ,Bn are baselines for each stereo pair. We will demonstrate how the ambiguity can be further reduced by increasing the number of stereo pairs. From the data of figure 4, we first choose image 1 and image9 as a long baseline stereo pair, ie. (1)5 = 8ft. Then, we increase the number of stereo pairs by dividing the baseline between imagel and imagc9, i.e. (2) B » 4b and 8ft, (3) B * 2ft, 4ft, 6ft and 8ft, (4) B = ft, 2ft, 3ft, 4ft, 5ft, 6ft, 7ft and 8ft. Figure 7 demonstrates that the SSSDs-in-inverse-depth shows the minimum at the correct position more clearly as more stereo pairs are used. 2.5 Precision We have shown that ambiguities can be resolved by using the SSSD-in-inverse-depth computed from multiple baseline stereo pairs. The technique also increases precision in estimating the true inverse depth. We can show this by analyzing the statistical characteristics of the evaluation functions near the correct match. 10 on 40000 § 35000 1 ^» mtloi 30000 i 25000 - 20000 - 15000 - 10000 f 5000 * 0 - B=b3,...,8b 15 20 Inverse depth Figure 7: Combining multiple baseline stereo pairs on 40000 § 35000 1 ^» mtloi 30000 i 25000 - 20000 - 15000 - 10000 f 5000 * 0 - B=b3,...,8b 15 20 Inverse depth Figure 7: Combining multiple baseline stereo pairs Figure 7: Combining multiple baseline stereo pairs p Figure 7: Combining multiple baseline stereo pairs By using the Taylor expansion about we obtain By using the Taylor expansion about we obtain y g y p f(x + BiF(( - <,) +j) «/(x+7) + B,F« - 0V'(x+j). (22) Substituting this into equation (12), we can approximate e^ix, Q near by a quadratic form of £: «cwU»0 « E(" 5' F(C-Cr)/ r'U+y-) + no(j:+7")-«1(x + 5JFC+;-)) 2 jew = BfF 2a(x)(C - Q 1 + WW*) - Ao(x))(C - Cr) + c,-(x), where (23) f(x + BiF(( - <,) +j) «/(x+7) + B,F« - 0V'(x+j). (22) nto equation (12), we can approximate e^ix, Q near by a quadratic form of £: f(x + BiF(( - <,) +j) «/(x+7) + B,F« - 0V'(x+j). (22) Substituting this into equation (12), we can approximate e^ix, Q near by a quadratic form of £: «cwU»0 « E(" 5' F(C-Cr)/ r'U+y-) + no(j:+7")-«1(x + 5JFC+;-)) 2 jew = BfF 2a(x)(C - Q 1 + WW*) - Ao(x))(C - Cr) + c,-(x), h (23) f(x + BiF(( - <,) +j) «/(x+7) + B,F« - 0V'(x+j). (22) Substituting this into equation (12), we can approximate e^ix, Q near by a quadratic form of £: (22 (23) where yew - Ttf'(x+j)nk(x+j) jew d(x) = £ ( , i £ t + ; ) - r t o ( ; c + ; ) ) 2 . From equations (28) and (30), we see that From equations (28) and (30), we see that From equations (28) and (30), we see that 1 * 1 i = - (3D Var(l2^)(C) tlVaruiC)' (3D The inverse of the variance represents the precision of the estimate. Therefore, equation (31) means that by using the SSSD-in-inverse-depth with multiple baseline stereo pairs, the estimate becomes more precise. We can confirm this characteristic in figures 6 and 7 by observing that the curve around the correct inverse depth becomes sharper as more baselines are used. The variance of the estimated inverse depth ( r that minimizes this function is The variance of the estimated inverse depth ( r that minimizes this function is ^ • n w ( 3 0 ) ^ • n w ( 3 0 ) we see that 1 * 1 i = - (3D Var(l2^)(C) tlVaruiC)' ( 3 0 ) 2.5 Precision (24) (25) (26) (24) (25) (26) The estimated inverse depth & is the value C that makes equation (23) minimum; bi(x)-b0(x) 0 = 0 - (27) The estimated inverse depth & is the value C that makes equation (23) minimum; The estimated inverse depth & is the value C that makes equation (23) minimum; bi(x)-b0(x) 0 = 0 - BiFa(x) (27) The estimated inverse depth & is the value C that makes equation (23) minimum; bi(x)-b0(x) 0 = 0 - BiFa(x) (27 bi(x)-b0(x) 0 = 0 - BiFa(x) (27) (27) 11 As shown in (13), the expected value of the estimate Cr is the correct value but it varies due to the noise. Following Appendix A in [MSK89], the variance of this estimate is given by As shown in (13), the expected value of the estimate Cr is the correct value but it varies due to the noise. Following Appendix A in [MSK89], the variance of this estimate is given by v " » < « - i p 4 j - ( 2 8 > ( 2 8 > Basically, for the same amount of noise o%9 the variance is smaller (the estimate is more precise) as the baseline Bt is longer, or as the variation of intensity signal, a(x), is larger. g y g g We can follow the same analysis for £<(i2..*)0t, 0 of (14), the new evaluation function with multiple baselines. Near C-> it is «OT2.H.)CT, 0 * f F 2a(pc)(C - Cr) 2 +. 2 (f>iF<Mx) - b0(x))) ( C + £ cfc). (2 «OT2.H.)CT, 0 * f F 2a(pc)(C - Cr) 2 +. 2 (f>iF<Mx) - b0(x))) ( C + £ cfc). (29 (2 3 Experimental Results This section presents experimental results of the multiple-baseline stereo based on SSSD-in-inverse- depth with real 2D images. A complete description of the algorithm is included in Appendix C. depth with real 2D images. A complete description of the algorithm is included in Appendix C. The first result is for the "Town" data set that we showed in figure 3. Figures 8 (a) and (b) are the depth map and its isometric plot with a short baseline, B = 3b. The result with a single long baseline, B = 9fe, is shown in figure 9. Comparing these two results, we observe that the depth map computed by using the long baseline is smoother on flat surfaces, i.e., more precise, but has gross errors in matching at the top of the scene because of the repeated pattern. These results illustrate the trade-off between ambiguity and precision. Figure 10, on the other hand, shows the depth map and its isometric plot obtained by the new algorithm using three different baselines, 3b, 6b, and 9b. For comparison, the corresponding oblique view of the scene is shown in figure 11. We can note 12 (b) (a) (b) Figure 8: Result with a short baseline, B = 3b: (a) Depth map; (b) Isometric plot of the depth map from the upper left corner. The matching is mosdy correct, but very noisy. (a) (a) (b) Figure 8: Result with a short baseline, B = 3b: (a) Depth map; (b) Isometric plot of the depth map from the upper left corner. The matching is mosdy correct, but very noisy. correct depth ^wrong depth ( b ) correct dept ^wron dep (a) ( b ) Figure 9: Result with a long baseline, B = 9b: (a) Depth map; (b) Isometric plot. The matching is less noisy when it is correct. However, there are many gross mistakes, especially in the top of die image where, due to a repetitive pattern, the matching is completely wrong. (a) (a) ( b ) Figure 9: Result with a long baseline, B = 9b: (a) Depth map; (b) Isometric plot. The matching is less noisy when it is correct. However, there are many gross mistakes, especially in the top of die image where, due to a repetitive pattern, the matching is completely wrong. 3 Experimental Results 13 (b) (a) (b) Figure 10: Result with multiple baseline, B = 3b, 6b, and 9b: (a) Depth map; (b) Isometric plot Compared with figures 9(b) and 10(b), we see that the depth map is less noisy and that gross errors have been removed. (a) (b) (a) Figure 10: Result with multiple baseline, B = 3b, 6b, and 9b: (a) Depth map; (b) Isometric plot Compared with figures 9(b) and 10(b), we see that the depth map is less noisy and that gross errors have been removed. Figure 11: Oblique view Figure 11: Oblique view Figure 11: Oblique view 14 14 W (b) Figure 12: "Coal mine" data set, long-baseline pair (b) W (b) that the computed depth map is less ambiguous and more precise than those of the single-baseline stereo. Figure 12 shows another data set used for our experiment Figures 13 and 14 compare the depth maps computed from the short baseline stereo and the long baseline stereo: the longer baseline is five times longer than the short one. For comparison, the actual oblique view roughly corresponding to the isometric plot is shown in figure 15. Though no repetitive patterns are apparent in the images, we can still observe gross errors in the depth map obtained with the long baseline due to false matching. In contrast, the result from the multiple-baseline stereo shown in figure 16 demonstrates both the advantage of unambiguous matching with a short baseline and that of precise matching with a long baseline. Finally, figure 17 shows the depth map obtained by our stereo matching algorithm with a locally adaptive window, which has been presented in [KO90], for which the depth map of figure 16 is used as the initial estimate. The map exhibits both smoothness for flat surfaces and sharpness at depth edges. 4 Conclusions S Z H Z ? ^ ^ " M W u S t C r C O m a t C h i n g m c t h o d w h i c h u s « multiple baseline stereo f^J^u T overcome A e **k-°ff between precision and accuracy (avoidance of false matches) in stereo. The method is rather straightforward: we represent t £ SSD^Sto to mdmdual stereo pars as a faction of the inverse depth, ami add JL funcno's ^ S t ^ 15 (a) (b) Figure 13: Result with a short baseline: (a) Depth map; (b) Isometric plot of the depth map viewed from the lower left corner (a) (b) (b) (a) (a) (b) Figure 13: Result with a short baseline: (a) Depth map; (b) Isometric plot of the depth map viewed from the lower left corner (a) 0» Figure 14: Result with a long baseline: (a) Depth map; (b) Isometric plot (a) 0» (a) ( ) Figure 14: Result with a long baseline: (a) Depth map; (b) Isometric plot 16 Figure 15: Oblique view Figure 15: Oblique view (a) (b) (c) (d) Figure 17: Isometric plots of the depth map computed by an iterative stereo algorithm with a loca adaptive window, in which the depth map of figure 16 from the multiple-baseline stereo was u as the initial map: (a) and (b) Isometric plot and corresponding view from the lower left corn (c) and (d) Isometric plot and corresponding view from the upper right comer. (a) (c) Figure 17: Isometric plots of the depth map compu adaptive window, in which the depth map of figur as the initial map: (a) and (b) Isometric plot and (c) and (d) Isometric plot and corresponding view (b) (a) (a) (b) (c) (d) Figure 17: Isometric plots of the depth map computed by an iterative stereo algorithm with a locally adaptive window, in which the depth map of figure 16 from the multiple-baseline stereo was used as the initial map: (a) and (b) Isometric plot and corresponding view from the lower left corner, (c) and (d) Isometric plot and corresponding view from the upper right comer. 4 Conclusions (b) (b) (a) (c) (d) (d) (d) (c) Figure 17: Isometric plots of the depth map computed by an iterative stereo algorithm with a locally adaptive window, in which the depth map of figure 16 from the multiple-baseline stereo was used as the initial map: (a) and (b) Isometric plot and corresponding view from the lower left corner, (c) and (d) Isometric plot and corresponding view from the upper right comer. Figure 17: Isometric plots of the depth map computed by an iterative stereo algorithm with a locally adaptive window, in which the depth map of figure 16 from the multiple-baseline stereo was used as the initial map: (a) and (b) Isometric plot and corresponding view from the lower left corner, (c) and (d) Isometric plot and corresponding view from the upper right comer. 18 function, the SSSD-in-inverse-depth, exhibits an unambiguous and sharper minimum at the correct matching position. As a result there is no need for search or sequential estimation procedures. function, the SSSD-in-inverse-depth, exhibits an unambiguous and sharper minimum at the correct matching position. As a result there is no need for search or sequential estimation procedures. g p q p The algorithm is easily amenable to parallel hardware implementation. Figure 4 shows a possible scheme with multiple cameras, SSD calculators, adders and time delays. The key idea of the method is to relate SSD values to the inverse depth rather than the disparity. As an afterthought, this idea is natural. Whereas disparity is a function of the baseline, there is only one true (inverse) depth for each pixel position for all of the stereo pairs. Therefore there must be a single minimum for the SSD values when they are summed and plotted with respect to the inverse depth. We have shown the advantage of the proposed method in removing ambiguity and improving precision by analytical and experimental results. Acknowledgment Jim Rehg and Carol Novak have read the manuscript and improved its readability substantially. 19 19 Camera Delay of units Figure 18: A scheme for parallel hardware implementation of the multiple baseline stereo algorithm by SSSD-in-inverse-depth. We place n + 1 multiple cameras along an axis. All cameras are synchronized. Pairs of camera output signals (the 0-th and the i-th) are fed into nd^ax SSD calculators with appropriate time delays, where d^a* is the maximum disparity for the stereo pair with the longest baseline. Each SSD calculator computes the SSD values between a particular image pair for a particular (quantized) inverse depth. The outputs of the SSD calculators for the same inverse depth are connected to an adder to produce the sum of SSD's (SSSD) for that inverse depth. These SSSD values are compared, and the inverse depth that shows the minimum is selected as the estimate Figure 18: A scheme for parallel hardware implementation of the multiple baseline stereo algorithm by SSSD-in-inverse-depth. We place n + 1 multiple cameras along an axis. All cameras are synchronized. Pairs of camera output signals (the 0-th and the i-th) are fed into nd^ax SSD calculators with appropriate time delays, where d^a* is the maximum disparity for the stereo pair with the longest baseline. Each SSD calculator computes the SSD values between a particular image pair for a particular (quantized) inverse depth. The outputs of the SSD calculators for the same inverse depth are connected to an adder to produce the sum of SSD's (SSSD) for that inverse depth. These SSSD values are compared, and the inverse depth that shows the minimum is selected th ti t o n A SSSD-in-inverse-depth for Ambiguous Pattern Proposition: Suppose that there are two and only two repetitions of the same pattern around positions x and x + A where A ^ 0 is a constant. That is, for y 6 W F(X+J)=F(Z+J), ifandonlyif£=xor£=;c + a. (32) ^£2,forVC,C^Cr, F(X+J)=F(Z+J), ifandonlyif£=xor£=;c + a. (32) l ^£ forVC C^Cr F(X+J)=F(Z+J), ifandonlyif£=xor£=;c + a. (32) F(X+J)=F(Z+J), ifandonlyif£=xor£=;c + a. (32) Then,iffl,^£2,forVC,C^Cr, E[eam(x,0] = HVIX+Ji-FIX+BMC-Q+J)) 2 jew > 4AU* = £[<W*,C)]. (33) F(X+J)=F(Z+J), ifandonlyif£=xor£=;c + a. (32) Then,iffl,^£2,forVC,C^Cr, E[eam(x,0] = HVIX+Ji-FIX+BMC-Q+J)) 2 jew > 4AU* = £[<W*,C)]. (33) (32) = HVIX+Ji-FIX+BMC-Q+J)) 2 jew jew > 4AU* = £[<W*,C)]. (33) jew > 4AU* = £[<W*,C)]. (33) (33) Proof: Tentatively suppose that for 3Q, Q ^ £ ( f ( * + y W ( * + * i F ( £ - Q + D F + EV^+FT-FB+WIQ-C)+J)) 2 = 0. (34) yew yew (34) Then, it must be the case that F(X+J) = /(X + fli+y) and F(X+F) = F(X + A2+J), (35) F(X+J) = /(X + fli+y) and F(X+F) = F(X + A2+J), (35) F(X+J) = /(X + fli+y) and F(X+F) = F(X + A2+J), (35) (35) r; € W, where AX = BxFiQ-Q = B2F($-C). AX = BxFiQ-Q = B2F($-C). Since Bx ^ B2 and £ ft Q, A\ F A (36) Since Bx ^ B2 and £ ft Q, So, we have A\ F A2. (36) A\ F A2. (36) So, we have A\ F A2. (36) (36) So, we have FIX +J) = / (£ +y), for £ = X, X + a l f or X + a2. ( 3 7 ) S " (32) (34)* °' h ii i * ( 3 7 ) ^ssfbST" (32)- (34) *- n°' hoii ie •* —<- 21 Then, Then, C + *m = £[«c©C*, 0], for VC. (41 Since this must be true for all C, let C be From equation (13). JEW Then, C + *m = £[«c©C*, 0], for VC. Since this must be true for all C, let C be From equation (13). (4 C + *m = £[«c©C*, 0], for VC. (41 Since this must be true for all C, let C be From equation (13). JEW Since this must be true for all C, let C be From equation (13). JEW Proof: Let/ (x) be a periodic function with a period T. That is, for VJC, be a periodic function with a period T. That is, for VJC, /(jc)=/(x + *r), for* = 0,±l,±2,..., (38) /(jc)=/(x + *r), for* = 0,±l,±2,..., (38) (38) where T > 0 is the period, and there is no smaller value of T with this property. Using equations (13) and (38), where T > 0 is the period, and there is no smaller value of T with this property. Using equations (13) and (38), where T > 0 is the period, and there is no smaller value of T with this property. Using equations (13) and (38), = E<F(X+fi-F(X + BIF(C-Q+M 2 + 2NWOL JEW JEW = £[*«©(*, C)]. (39) JEW = £[*«©(*, C)]. (39) (39) That is, £[e((!-)(x, C)] is a periodic function of C- Next, we show that ^ is its period. For that, tentatively suppose V is the period such that r < w m That is, £[e((!-)(x, C)] is a periodic function of C- Next, we show that ^ is its period. For that, tentatively suppose V is the period such that r < m That is, £[e((!-)(x, C)] is a periodic function of C- Next, we show that ^ is its period. For that, tentatively suppose V is the period such that r < w m That is, £[e((!-)(x, C)] is a periodic function of C- Next, we show that ^ is its period. For that, tentatively suppose V is the period such that That is, £[e((!-)(x, C)] is a periodic function of C- Next, we show that ^ is its period. For that, tentatively suppose V is the period such that r < w m m B Period of E[E^T)(X, Q] Proposition: If/ (x) is a periodic function with a period T, then E[E^(X^ Q] is a periodic function with the period Proof: Let/ (x) be a periodic function with a period T. That is, for VJC, Proof: Let/ (x) be a periodic function with a period T. That is, for VJC, Therefore, F(X)=F(X + KBIFT). (43) F(X)=F(X + KBIFT). (43) (43) F(X)=F(X + KBIFT). This means that/ (JC) has a period fijFT that is shorter than T because of (40). This is a contradiction and thus V cannot be the period of £[*c(o(*i 01- Therefore, E[E^(X, 01 is a periodic function of C with the period J^. This means that/ (JC) has a period fijFT that is shorter than T because of (40). This is a contradiction and thus V cannot be the period of £[*c(o(*i 01- Therefore, E[E^(X, 01 is a periodic function of C with the period J^. 22 C Multiple-Baseline Stereo Algorithm We present a complete description of the stereo algorithm using multiple-baseline stereo pairs. The task is, given n stereo pairs, find the C that minimizes the SSSD-in-inverse-depth function, SSSD{x, 0 = £ X>o(* +J) -fi(x + BiFC +j)) 2. (44) (44) We will perform this task in two steps: one at pixel resolution by minimum detection and the other at sub-pixel resolution by iterative estimation. We will perform this task in two steps: one at pixel resolution by minimum detection and the other at sub-pixel resolution by iterative estimation. Then, BiFC^RiBnFC^Ri^ (46) (46) where d(n) is the disparity for the stereo pair with baseline Bm. Substituting this into equation (44), where d(n) is the disparity for the stereo pair with baseline Bm. Substituting this into equation (44), isparity for the stereo pair with baseline Bm. Substituting this into equation (44), ty for the stereo pair with baseline Bm. Substituting this into equation (44), SSSD(x, din)) = £ o(* +J) -fi(x + Ri<kn) +y)) 2. (47) (47) We compute the SSSD function for a range of disparity values at the pixel resolution, and identify the disparity that gives the minimum. Note that pixel resolution for the image pair with the longest baseline (Bn) requires calculation of SSD values at sub-pixel resolution for other shorter baseline stereo pairs. Minimum of SSSD at Pixel Resolution For convenience, instead of using the inverse depth, we normalize the disparity values of individual stereo pairs with different baselines to the corresponding values for the largest baseline. Suppose B\ < B2 < • • • < Bn. We define the baseline ratio /?, such that Ri = (45) (45) Iterative Estimation at Sub-pixel Resolution Once we obtain disparity at pixel resolution for the longest baseline stereo, we improve the disparity estimate to sub-pixel resolution by an iterative algorithm presented in [MO89][OK90]. For this iterative estimation, we use only the image pair fo(x) andfn(x) with the longest baseline. This is due to a few reasons. First, since the pixel-level estimate was obtained by using the SSSD-in-inverse- depth, the ambiguity has been eliminated and only improvement of precision is intended at this stage. Second, using only the longest-baseline image pair reduces the computational requirement for SSD calculation by a factor of n, and yet does not degrade precision too significantly. 23 In the experiments shown in section 3, we used the following algorithm for sub-pixel estimation: Let db(n) be the initial disparity estimate obtained at pixel resolution. Then, a more precise estimate is computed by calculating the following two quantities: Ad, = ^Jew(fo(x +j) -/«(x + dbfr) +M'n{x + dm +j) ( 4 g ) Zjew<f& + d<Kn)+J)) 2 - 2 _ 2 < % ( 4 9 ) ( 4 g ( 4 9 ) The value Ad{H) is the estimate of the correction of the disparity to further minimize the SSD, and is its variance. We iterate this procedure by replacing do^ by The value Ad{H) is the estimate of the correction of the disparity to further minimize the SSD, and is its variance. We iterate this procedure by replacing do^ by The value Ad{H) is the estimate of the correction of the disparity to further minimize the SSD, and is its variance. We iterate this procedure by replacing do^ by dob) <- do(ii) + ^ ( « ) (50) (50) until the estimate converges or up to a certain maximum number of iterations. until the estimate converges or up to a certain maximum number of iterations. [MSK89] Larry Matthies, Richard Szeliski, and Takeo Kanade. Kalman filter-based algorithms for estimating depth from image sequences. International Journal of Computer Vision, 3:209-236,1989. [OK90] Masatoshi Okutomi and Takeo Kanade. A locally adaptive window for signal matching. In Proc. Third Infl Conference on Computer Vision, December 1990. [Yam88] Masanobu Yamamoto. The image sequence analysis of three-dimensional dynamic scenes. Technical Report 893, Electrotechnical Laboratory - Agency of Industrial Science and Technology, Tsukuba, Ibaraki, Japan, May 1988. [Yam88] Masanobu Yamamoto. The image sequence analysis of three-dimensional dynamic scenes. Technical Report 893, Electrotechnical Laboratory - Agency of Industrial Science and Technology, Tsukuba, Ibaraki, Japan, May 1988. [OK90] Masatoshi Okutomi and Takeo Kanade. A locally adaptive window for signal matching. In Proc. Third Infl Conference on Computer Vision, December 1990. References [BBM87] R. C. Bolles, H. H. Baker, and D. H. Marimont. Epipolar-plane image analysis: An approach to determining structure from motion. International Journal of Computer Vision, l(l):7-55,1987. [BBM87] R. C. Bolles, H. H. Baker, and D. H. Marimont. Epipolar-plane image analysis: An approach to determining structure from motion. International Journal of Computer Vision, l(l):7-55,1987. [Gri85] W. E. L. Grimson. Computational experiments with a feature based stereo algorithm. IEEE Transactions on Pattern Analysis and Machine Intelligence, 7(1): 17-34, January 1985. [Hee89] Joachim Heel. Dynamic motion vision. In Proceedings of the DARPA Image Under- standing Workshop, pages 702-713, Palo Alto, Ca, May 23-26 1989. [KO90] Takeo Kanade and Masatoshi Okutomi. A stereo matching algorithm with an adap- tive window: Theory and experiment Technical Report CMU-CS-90-120, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213,1990. [M089] Larry Matthies and Masatoshi Okutomi. A bayesian foundation for active stereo vision. In SPIE, Sensor Fusion II: Human and Machine Strategies, November 1989. [MP79] D. Marr and T. Poggio. A theory of human stereo vision. In Proc. Roy. Soc. London, pages 301-328,1979. [MSK89] Larry Matthies, Richard Szeliski, and Takeo Kanade. Kalman filter-based algorithms for estimating depth from image sequences. International Journal of Computer Vision, 3:209-236,1989. 24 [Yam88] Masanobu Yamamoto. The image sequence analysis of three-dimensional dynamic scenes. Technical Report 893, Electrotechnical Laboratory - Agency of Industrial Science and Technology, Tsukuba, Ibaraki, Japan, May 1988. 25
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Efektifitas Sertifikasi Nadzir Dalam Sektor Pengelolaan Wakaf Di Indonesia
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1 Alzaina, N. (2019). Urgensi Pemberdayaan Nadzir Dalam Pengelolaan Wakaf Uang Di Indonesia. Istismar: Jurnal Ekonomi Syariah, 1, 37–42. http://ejournal.unwaha.ac.id/index.php/istismar/article/view/303 2 Sulaeman, A., Bayinah, A. N., & Hidayat, R. (2020). Apakah Kepercayaan Muwakif Ditentukan oleh Akuntabilitas Pengelolaan Wakaf Tunai dan Peran Nadzir ? Jurnal Akuntansi Dan Keuangan Islam, 8(1), 71–86. https://doi.org/10.35836/jakis.v8i1.129 3Umami, N. F. dan K. (2021). Efektivitas Nazir Organisasi Di Majelis Wakil Cabang Nahdlatul Ulama Kecamatan Siman Kabupaten Ponorogo. Jurnal Antologi Hukum, 1(1), 16–33. http://etheses.iainponorogo.ac.id/id/eprint/13759 4 Huda, N., Rini, N., Mardoni, Y., Anggraini, D., & Hudori, K. (2018). Manajemen Pengelolaan Wakaf Di Indonesia Timur. EKUITAS (Jurnal Ekonomi dan Keuangan), 20(1), 1–17. https://doi.org/10.24034/j25485024.y2016.v20.i1.35 5 Umami, N. F. dan K. (2021). Efektivitas Nazir Organisasi. Volume 09, Nomor 1, Juni 2022 Volume 09, Nomor 1, Juni 2022 Madinah : Jurnal Studi Islam ISSN : 1978-659X (Printed),: 2620-9497 (Online) https://ejournal.iai-tabah.ac.id/index.php/madinah Ayu Ruqayyah Yunus Universitas Islam Negeri Alauddin Makassar, Indonesia E-mail: Ayu.ruqayyahy@uin-alauddin.ac.id Ayu Ruqayyah Yunus Universitas Islam Negeri Alauddin Makassar, Indonesia E-mail: Ayu.ruqayyahy@uin-alauddin.ac.id Nurfiah Anwar Universitas Islam Negeri Alauddin Makassar, Indonesia E-mail: Nurfiahanwar05@gmail.com Abstrak: Topik utama dalam penelitian ini adalah bagaimana keabsahan sertifikasi nadzir di departemen manajemen wakaf Indonesia dan validitas peran nadzir di departemen manajemen wakaf Indonesia. pada pokok bahasan penelitian ini? Selanjutnya, tujuan dari penelitian ini adalah untuk mengetahui efektifitas sertifikasi nadzir pada departemen pengelolaan wakaf Indonesia dan efektifitas peran nadzir pada departemen pengelolaan wakaf di Indonesia. Metode pencarian yang digunakan adalah pencarian literatur. Referensi dalam artikel ini didasarkan pada ide dan hasil penelitian sebelumnya seperti jurnal, buku, dan artikel. Hasil penelitian ini menunjukkan bahwa Wakaf Nadzir akan mengeluarkan sertifikat untuk berpindah dari Nadzir individu ke Nadzir kelembagaan atau legal, memastikan keamanan manajemen dan keamanan properti, menjaga persatuan dan masa depan umat. Ini juga menunjukkan bahwa itu membantu untuk menghindari potensi konflik. Dengan kemampuan manusia, manusia teknis dan hubungan yang berkualitas, Nazir yang profesional adalah pemimpin umum di lembaga Wakaf yang mampu mencapai tujuan Wakaf. Kata kunci: Wakaf Sertiikasi Abstract: The topic of the problem in this research is how is the validity of nadzir certification in the Indonesian waqf management department and the validity of the nadzir's role in the Indonesian waqf management department on the subject of this research? Furthermore, the purpose of this study is to determine the effectiveness of nadzir certification in the Indonesian waqf management department and the effectiveness of the 111 Muslihati et al Efektifitas sertifikasi nadzir... . Efektifitas sertifikasi nadzir... . Madinah : Jurnal Studi Islam ISSN : 1978-659X (Printed),: 2620-9497 (Online) https://ejournal.iai-tabah.ac.id/index.php/madinah Volume 09, Nomor 1, Juni 2022 Madinah : Jurnal Studi Islam ISSN : 1978-659X (Printed),: 2620-9497 (Online) https://ejournal.iai-tabah.ac.id/index.php/madinah nadzir's role in the waqf management department in Indonesia. The search method used is a literature search. The references in this article are based on the ideas and results of previous research such as journals, books and articles. The results of this study indicate that Wakaf Nadzir will issue certificates to move from individual Nadzir to institutional or legal Nadzir, ensuring management security and property security, safeguarding the unity and future of the ummah. It also shows that it helps to avoid potential conflicts. Volume 09, Nomor 1, Juni 2022 With human skills, technical people and quality relationships, professional Nazir is a general leader in Waqf institutions who are able to achieve Waqf goals. Keywords: Waqf, Certification PENDAHULUAN Wakaf adalah hukum Islam, sistem kehidupan agama dan sosial. Oleh karena itu, pengelolaan harus dilakukan dengan hati-hati karena tidak hanya berfokus pada kepentingan spiritual masyarakat, tetapi juga pada kegiatan untuk mencapai kemanusiaan sebagai entitas sosial1. Tergantung pada kondisi politik, ekonomi dan budaya daerah, ada banyak perbedaan dalam perkembangan wakaf di setiap daerah. Namun, dalam satu dekade terakhir, kesadaran kebangkitan lembaga wakaf baru muncul di negara-negara Islam2 Islam sejak Islam masuk ke Indonesia. Praktik wakaf yang sering dilakukan oleh masyarakat wakaf adalah harta bendanya untuk tempat ibadah. Jumlah masjid dan musholla sangat banyak seiring dengan tradisi tempat ibadah di Wakaf yang tumbuh dan berkembang3. Secara konseptual, Islam mengakui lembaga wakaf sebagai sumber aset jangka panjang yang menguntungkan. Wakaf diatur untuk memainkan peran penting dalam kesejahteraan orang4. Perkembangan penting dalam Wakaf memfasilitasi pembentukan manajemen Wakaf yang terperinci. Tentu saja, ini melibatkan peran yang sangat besar dalam Nadzir. Dengan kata lain, Nadzir adalah pengelola Wakaf yang bertanggung jawab untuk memelihara, mengelola dan mendistribusikan keuntungan Wakaf ke tempat tujuan Wakaf yang diinginkan5. Lokasi nadzir merupakan isu yang sangat penting dan sentral, karena pihak yang menerima Muslihati et al Efektifitas sertifikasi nadzir... . Madinah : Jurnal Studi Islam ISSN : 1978-659X (Printed),: 2620-9497 (Online) https://ejournal.iai-tabah.ac.id/index.php/madinah Volume 09, Nomor 1, Juni 2022 harta wakaf dari wakaf perlu dikelola dan dikembangkan sesuai dengan takdirnya6 harta wakaf dari wakaf perlu dikelola dan dikembangkan sesuai dengan takdirnya6 Kunci pengelolaan wakaf terletak pada keberadaan pengelola wakaf, khususnya Nadzir, dan tim kerja yang solid untuk memaksimalkan peran wakaf. Hal ini karena kemajuan wakaf sangat tergantung pada baik buruknya pengelolaan pengelolaan wakaf. Oleh karena itu, Nadzir perlu dipromosikan semaksimal mungkin untuk mencapai prestasi dan prestasi setinggi-tingginya 7. Nadzir adalah orang yang paling bertanggung jawab atas harta wakaf yang dipercayakan kepadanya, baik dalam hal pemeliharaan harta wakaf maupun hasil dan upaya pengembangannya8. Para ulama juga sepakat bahwa harta wakaf milik Nadzir adalah amanah9. Menurut Imam Abu Honeyfa, Wakaf adalah pemindahan modal dan keuntungan dari barang di tangan pemilik Wakaf, menggunakan arias dan meminjamkan barang untuk tujuan saleh. saya bisa mengatakan. Dalam ketentuan Pasal 215 Ayat 1 Hukum Islam, pengertian wakaf adalah perbuatan hukum seseorang atau sekelompok orang atau badan hukum, memisahkan mereka dari harta benda dan untuk kepentingan umum sesuai dengan ibadah atau ajaran agama10. Wakaf adalah suatu perbuatan yang dilakukan dengan memegang suatu harta dan terus menerus menyumbangkan keuntungannya untuk kepentingan umum baik untuk keperluan ibadah maupun tujuan sosial11. y , ( ) , p p ( ), 7Kasdi, A. (2014). Peran Nadzir Dalam Pengembangan Wakaf. Jurnal Zakat dan Wakaf, 1(2), 213–226 8Tiswarni. (2014). ( Tinjauan Terhadap Strategi Pemberdayaan Wakaf Badan Wakaf Alquran. Ekonomi syariah, 7(2), 313 6 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 6 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 7Kasdi, A. (2014). Peran Nadzir Dalam Pengembangan Wakaf. Jurnal Zakat dan Wakaf, 1(2), 213–226 8Tiswarni. (2014). ( Tinjauan Terhadap Strategi Pemberdayaan Wakaf Badan Wakaf Alquran. Ekonomi syariah, 7(2), 313 9 Damanuri, A. (2013). Efektivitas Dan Efisiensi Pemanfaatan Harta Wakaf Majlis Wakaf Pimpinan Daerah Muhammadiyah Ponorogo. Kodifikasia, 6(1). https://doi.org/10.21154/kodifikasia.v6i1.197 10Alzaina, N. (2019). Urgensi Pemberdayaan Nadzir Dalam Pengelolaan Wakaf Uang Di Indonesia. Istismar: Jurnal Ekonomi Syariah, 1, 37–42. http://ejournal.unwaha.ac.id/index.php/istismar/article/view/303 11 Huda, N., Rini, N., Mardoni, Y., Anggraini, D., & Hudori, K. (2018). Manajemen Pengelolaan Wakaf Di Indonesia Timur. EKUITAS (Jurnal Ekonomi dan Keuangan), 20(1), 1–17. https://doi.org/10.24034/j25485024.y2016.v20.i1.35 12 Masyhar, A., Arifin, R., & Fuad, A. N. (2019). Sertifikasi Alih Nadzir Badan Hukum Wakaf Perorangan Kepada Nadzir Badan Hukum Bagi Masjid / Musholla di Kecamatan Gunungpati Kota Semarang. JPHI: Jurnal Pengabdian Hukum Indonesia (Indonesian Journal of Legal Community Engagement), 2(1), 60–67. https://journal.unnes.ac.id/sju/index.php/JPHI/article/view/34054 13 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf di Provinsi Gorontalo. Jurnal Diskursus Islam, 2(2), 171 14 Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf pada Lembaga Wakaf: Studi Kasus pada Majelis Wakaf dan Kehartabendaan Pimpinan Daerah Muhammadiyah. https://journal.umy.ac.id/index.php/rab/article/view/10785 14 Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf pada Lembaga Wakaf: Studi Kasus pada Majelis Wakaf dan Kehartabendaan Pimpinan Daerah Muhammadiyah. https://journal.umy.ac.id/index.php/rab/article/view/10785 15 Abdullah, A. (2020). Nadzir dalam Perspektif Kelembagaan Wakaf di Indonesia. Jurnal Ilmiah Ekonomi Islam, 6(3), 403. https://doi.org/10.29040/jiei.v6i3.1216 16 Sulaeman, A., Bayinah, A. N., & Hidayat, R. (2020). Apakah Kepercayaan Muwakif Ditentukan oleh Akuntabilitas Pengelolaan Wakaf Tunai dan Peran Nadzir ? Jurnal Akuntansi Dan Keuangan Islam, 8(1), 71–86. https://doi.org/10.35836/jakis.v8i1.129 17 Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi dan Problematikanya. Li Falah: Jurnal Studi Ekonomi dan Bisnis Islam, 3(2), 62. https://doi.org/10.31332/lifalah.v3i2.1197 18 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 19 Sulaeman, A., Bayinah, A. N., & Hidayat, R. (2020). Apakah Kepercayaan Muwakif Ditentukan oleh Akuntabilitas Pengelolaan Wakaf Tunai dan Peran Nadzir ? , ( ), p // g/ /j 16 Sulaeman, A., Bayinah, A. N., & Hidayat, R. (2020). Apakah Kepercayaan Muwakif Ditentukan oleh Akuntabilitas Pengelolaan Wakaf Tunai dan Peran Nadzir ? Jurnal Akuntansi Dan Keuangan Islam, 8(1), 71–86. https://doi.org/10.35836/jakis.v8i1.129 17 B h ddi A Z & I R Q (2018) N i W k f P f i l St d i i d y p //j y / p p/ / / / Abdullah, A. (2020). Nadzir dalam Perspektif Kelembagaan Wakaf di Indonesia. Jurnal Ilmia konomi Islam, 6(3), 403. https://doi.org/10.29040/jiei.v6i3.1216 p // g/ / 18 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 20 Kasdi, A. (2014). Peran Nadzir Dalam Pengembangan Wakaf. Jurnal Zakat dan Wakaf, 1(2), 213– 226 21 Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi dan Problematikanya. Li Falah: Jurnal Studi Ekonomi dan Bisnis Islam, 3(2), 62. https://doi.org/10.31332/lifalah.v3i2.1197 22 Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf pada Lembaga Wakaf: Studi Kasus pada Majelis Wakaf dan Kehartabendaan Pimpinan Daerah Muhammadiyah 4(2), 99–109. https://journal.umy.ac.id/index.php/rab/article/view/10785 23 Damanuri, A. (2013). Efektivitas Dan Efisiensi Pemanfaatan Harta Wakaf Majlis Wakaf Pimpinan Daerah Muhammadiyah Ponorogo. Kodifikasia, PENDAHULUAN Menurut penyelidikan lain, wakaf menurut Syariah, memotong atau memotong sebagian dari hartanya untuk tujuan ibadah dan / atau kesejahteraan umum, secara permanen atau untuk jangka waktu, untuk kepentingannya. Adalah perbuatan hukum oleh wakif untuk meninggalkan 12(Masyhar et al., 2019). p gg ( y ) Harta wakaf pada dasarnya tidak dapat dipertukarkan, dan jika diperlukan pertukaran, syarat-syaratnya disyaratkan sesuai dengan peraturan yang berlaku. Dengan kata lain, kekal berarti harta wakaf tidak boleh dikurangi, dan ada upaya untuk menghilangkan keberadaan harta wakaf tersebut13. 113 Muslihati et al Efektifitas sertifikasi nadzir... . Volume 09, Nomor 1, Juni 2022 Madinah : Jurnal Studi Islam ISSN : 1978-659X (Printed),: 2620-9497 (Online) https://ejournal.iai-tabah.ac.id/index.php/madinah Wakaf memiliki manfaat yang besar bila digunakan dalam berbagai bidang pendidikan, kesejahteraan sosial, kesehatan dan bisnis. Wakaf memiliki peran yang sangat besar dalam meningkatkan taraf hidup masyarakat Indonesia, khususnya dalam bidang sosial-ekonomi14. Nadzir secara etimologis berasal dari kata kerja Arab yang berarti melihat, melihat. Dalam kaitannya dengan fiqh, nadzir berarti orang yang dilimpahkan wewenang dan kewajiban untuk mengurus dan memelihara harta benda wakaf. 15. Nadzir memegang peranan terpenting dalam pengelolaan dan penghimpunan dana wakaf dan merupakan lembaga atau individu yang paling bertanggung jawab atas harta wakaf yang dititipkan kepadanya, baik dalam hal memelihara harta wakaf maupun akibat dan komitmennya terhadap pembangunan16 Wakaf Nadzir, di sisi lain, berarti orang yang mengelola dan mengelola harta dan pendapatan Wakaf dan memenuhi persyaratan yang ditetapkan oleh Wakaf. Istilah lain yang digunakan oleh fuqaha adalah mutawalli. Secara etimologis berarti seseorang yang mengurus dan melakukan sesuatu ketika ditakdirkan untuknya17. Nadzir ini bertanggung jawab atas pemeliharaan, perawatan dan pengembangan Wakaf untuk memastikan bahwa ia bekerja seperti yang diharapkan. Ini dilakukan sesuai dengan tujuan Syariah18. Pengelolaan Wakaf yang baik dan profesional oleh Nadzir akan meningkatkan kepercayaan masyarakat dan terus meningkatkan jumlah muwakif19. Selain itu, Guru Besar Fakultas Syariah UIN Syarif Hidyatullah Jakarta Fathurrahman Djamil mengatakan, Nadzir memiliki persyaratan umum lainnya. Pertama, Nazhir adalah seorang pemimpin umum dalam Wakaf. Oleh karena itu, Nadzir harus memiliki kepribadian yang luhur, kredibilitas, pengalaman, dan penguasaan manajemen dan keuangan. Kedua, selama masa jabatannya, Nadzir dapat bekerja dalam hukum Wakaf sesuai dengan keputusan organisasi sosial dan dewan. Ketiga, nadzir harus berada di bawah pengawasan Kementerian Agama dan Dewan Direksi Wakaf Indonesia dan menyampaikan laporan keuangan dan administrasi setidaknya triwulanan tentang Wakaf dan kegiatannya. Keempat, 114 Muslihati et al Efektifitas sertifikasi nadzir... . METODE Penelitian ini merupakan studi literatur tentang efektivitas sertifikasi Nadzir. Bahan referensi untuk artikel ini diambil dari pemikiran dan hasil penelitian sebelumnya tentang konsep dan gagasan tentang efektivitas sertifikasi Nadzir di departemen manajemen Wakaf di Indonesia. Hasil dari diskusi ini adalah ide-ide baru, kritik terhadap konsep dan ide yang dikembangkan oleh peneliti sebelumnya, dan kesimpulan. Oleh karena itu, penelusuran literatur ini menjadi dasar untuk penelitian selanjutnya. PENDAHULUAN Madinah : Jurnal Studi Islam ISSN : 1978-659X (Printed),: 2620-9497 (Online) https://ejournal.iai-tabah.ac.id/index.php/madinah Volume 09, Nomor 1, Juni 2022 nadzir bertanggung jawab secara pribadi atas segala kerugian atau kewajiban yang timbul akibat pelanggaran Undang-Undang Wakaf20 . nadzir bertanggung jawab secara pribadi atas segala kerugian atau kewajiban yang timbul akibat pelanggaran Undang-Undang Wakaf20 . y g p gg g g Kewajiban nadzir adalah laporan tentang pengelolaan harta wakaf, pengelolaan dan pengembangan harta wakaf sesuai dengan tujuan dan fungsi penetapan, pengawasan dan perlindungan harta wakaf, dan pelaksanaan kewajiban kepada rakyat Indonesia. Dewan Amil Wakaf. Sebagaimana dinyatakan Tholhah Hasan, selain kewajiban dan tanggung jawab di atas, Nazir dilarang melakukan perbuatan yang dapat menimbulkan tuduhan atau kecurigaan, seperti: meminjam Harta Wakaf untuk diri sendiri atau keluarga dekat21. Menurut Kamus Besar Bahasa Indonesia, efek berasal dari kata effect. Ini memiliki beberapa arti, seperti efektif atau efektif, efektif, menghasilkan, atau efektif. Para ahli mendefinisikan efektivitas sebagai kemampuan individu, kelompok, lembaga, atau organisasi untuk memilih dan menentukan tujuan yang tepat dan menggunakan alat yang tepat untuk mencapainya22. Efektivitas adalah salah satu hasil yang harus dicapai organisasi. Untuk memperoleh teori efektivitas, peneliti dapat menggunakan konsep-konsep dari teori manajemen dan organisasi, terutama yang berkaitan dengan teori efektivitas23. 24 Tiswarni. (2014). ( Tinjauan Terhadap Strategi Pemberdayaan Wakaf Badan Wakaf Alquran. Ekonomi syariah, 7(2), 313 25 Kasdi, A. (2014). Peran Nadzir Dalam Pengembangan Wakaf. Jurnal Zakat dan Wakaf, 1(2), 213– 226 26 Umami, N. F. dan K. (2021). Efektivitas Nazir Organisasi Di Majelis Wakil Cabang Nahdlatul Ulama Kecamatan Siman Kabupaten Ponorogo. Jurnal Antologi Hukum, 1(1), 16–33. http://etheses.iainponorogo.ac.id/id/eprint/13759 27 Lestari, W., & Thantawi, R. (2016). Efektivitas Pengelolaan Wakaf Tunai. Syarikah, 2(1), 214–234. 28Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi dan Problematikanya. Li Falah: Jurnal Studi Ekonomi dan Bisnis Islam. 29Ridwan, M. (2012). Nazhir Profesional Kunci Kesuksesan Wakaf Produktif. Muqtasid: Jurnal Ekonomi dan Perbankan Syariah, 3(1), 91. https://doi.org/10.18326/muqtasid.v3i1.91-109 30 Tiswarni. (2014). ( Tinjauan Terhadap Strategi Pemberdayaan Wakaf Badan Wakaf Alquran. Ekonomi syariah, 7(2), 313 31 Ridwan M (2012) Nazhir Profesional Kunci Kesuksesan HASIL DAN PEMBAHASAN Menurut UIN Syarif Hidayatullah Jakarta dari Pusat Bahasa dan Budaya (PBB), menurut survei terhadap 500 responden Nadzir di 11 negara bagian, Nadzir tidak fokus pada manajemen, kebanyakan bekerja paruh waktu. Tidak ada gaji yang dibayarkan (84%). Dan sangat sedikit orang yang bekerja sepenuhnya secara intensif (16%). Selain itu, Wakaf lebih banyak dikelola oleh perorangan (66%), juga dikenal secara tradisional, dibandingkan oleh organisasi profesi (16%) dan badan hukum (18%) (Kasdi, 2014). Profesionalisme Nadzir dalam mengelola 115 Muslihati et al Efektifitas sertifikasi nadzir... . Madinah : Jurnal Studi Islam ISSN : 1978-659X (Printed),: 2620-9497 (Online) https://ejournal.iai-tabah.ac.id/index.php/madinah Volume 09, Nomor 1, Juni 2022 harta wakaf tidak mungkin tercapai jika kesejahteraannya tidak terpenuhi atau diabaikan. Mereka berhak menerima gaji dari hasil harta wakaf yang mereka kelola sesuai dengan tugasnya dan standar gaji secara umum24. harta wakaf tidak mungkin tercapai jika kesejahteraannya tidak terpenuhi atau diabaikan. Mereka berhak menerima gaji dari hasil harta wakaf yang mereka kelola sesuai dengan tugasnya dan standar gaji secara umum24. g g y g j Achmad Djunaidi dan kawan-kawan menjelaskan bahwa parameter nadzir profesional adalah amanah (dapat dipercaya), shiddiq (jujur), fathanah (cerdas), dan tabligh (transparan). Sumber daya Nadzir yang handal adalah yang terdidik, bermoral, berdaya saing, mampu membagi pekerjaan, memenuhi kewajiban dan memperoleh hak yang adil, standar ketenagakerjaan yang jelas dan terarah25 . Nadzir Profesional adalah orang yang mengandalkan keterampilan dan keahlian tinggi untuk melakukan pekerjaan penuh waktu dan bekerja pada tingkat tinggi. Komitmen pribadi ini membawa banyak tanggung jawab untuk pekerjaannya26. Nadzir harus mampu mengembangkan aset wakaf melalui program-program yang kreatif dan inovatif27. Oleh karena itu, Anda membutuhkan seorang Nadzir profesional dengan keterampilan manusia yang terampil, keterampilan manusia, dan hubungan 28. Kompetensi manusia mengacu pada keahlian Nadzir di bidang tertentu yang terkait dengan amanat pengembangan aset Wakaf. Human Technical, di sisi lain, mengacu pada kemampuan untuk mengelola aset Wakaf. Dengan kata lain, pengelolaan berdasarkan keterbukaan (transparency). Relasi adalah kemampuan Nadzir membangun jaringan untuk kepentingan pengelolaan dan pengembangan wakaf. Pengembangan jaringan sangat penting untuk mencapai tujuan produktif wakaf. Tanpa jaringan, prinsip penawaran dan permintaan tidak dapat diimplementasikan secara stabil29. Inovasi dalam pengembangan aset Wakaf juga sangat mengandalkan kreativitas Nadzir. Nazir Profesional adalah seorang Nazir yang memiliki pemahaman yang baik tentang ajaran agama dan kemampuan yang kredibel untuk mengelola harta wakaf yang dipercayakan kepadanya30. Tugas seorang nadzir profesional tidak hanya sebatas mengelola aset wakaf. Ia juga bertugas mendistribusikan hasil atau manfaat Wakaf yang dikelola kepada penerima manfaat. y ( ) 31 Ridwan, M. (2012). Nazhir Profesional Kunci Kesuksesan 32 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118. g g ), 35 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf di Provinsi Gorontalo. Jurnal Diskursus Islam, 2(2) 36 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 37 Ridwan, M. (2012). Nazhir Profesional Kunci Kesuksesan Wakaf Produktif. Muqtasid: Jurnal Ekonomi dan Perbankan Syariah, 3(1), 91. https://doi.org/10.18326/muqtasid.v3i1.91-109 38 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 32 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118. 33 Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi dan Problematikanya. Li Falah: Jurnal Studi Ekonomi dan Bisnis Islam 34 Masyhar, A., Arifin, R., & Fuad, A. N. (2019). Sertifikasi Alih Nadzir Badan Hukum Wakaf Perorangan Kepada Nadzir Badan Hukum Bagi Masjid / Musholla di Kecamatan Gunungpati Kota Semarang. JPHI: Jurnal Pengabdian Hukum Indonesia (Indonesian Journal of Legal Community Engagement), 171 35 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf di Provinsi Gorontalo. Jurnal Diskursus Islam, 2(2) 36 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 37 Ridwan, M. (2012). Nazhir Profesional Kunci Kesuksesan Wakaf Produktif. Muqtasid: Jurnal Ekonomi dan Perbankan Syariah, 3(1), 91. https://doi.org/10.18326/muqtasid.v3i1.91-109 38 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 y J 34 Masyhar, A., Arifin, R., & Fuad, A. N. (2019). Sertifikasi Alih Nadzir Badan Hukum Wakaf Perorangan Kepada Nadzir Badan Hukum Bagi Masjid / Musholla di Kecamatan Gunungpati Kota Semarang. JPHI: Jurnal Pengabdian Hukum Indonesia (Indonesian Journal of Legal Community Engagement), 171 y ( ) p p ( ) 33 Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi Problematikanya. Li Falah: Jurnal Studi Ekonomi dan Bisnis Islam 32 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118. 33 Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi dan Problematikanya. Li Falah: Jurnal Studi Ekonomi dan Bisnis Islam 34 Masyhar, A., Arifin, R., & Fuad, A. N. (2019). Sertifikasi Alih Nadzir Badan Hukum Wakaf Perorangan Kepada Nadzir Badan Hukum Bagi Masjid / Musholla di Kecamatan Gunungpati Kota Semarang. JPHI: Jurnal Pengabdian Hukum Indonesia (Indonesian Journal of Legal Community Engagement), 171 35 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf di Provinsi Gorontalo. Jurnal Diskursus Islam, 2(2) HASIL DAN PEMBAHASAN Nadzir perlu bagi hasil Wakaf kepada Mustahik31. Muslihati et al 116 Muslihati et al Efektifitas sertifikasi nadzir... . Efektifitas sertifikasi nadzir... . Volume 09, Nomor 1, Juni 2022 Madinah : Jurnal Studi Islam ISSN : 1978-659X (Printed),: 2620-9497 (Online) https://ejournal.iai-tabah.ac.id/index.php/madinah Madinah : Jurnal Studi Islam ISSN : 1978-659X (Printed),: 2620-9497 (Online) https://ejournal.iai-tabah.ac.id/index.php/madinah Pengelolaan wakaf yang profesional adalah suatu keharusan, dan optimalisasi Nadzir Wakaf adalah suatu keharusan. Pengelolaan nazhir wakaf yang optimal dapat meminimalisir permasalahan masyarakat terkait keterbatasan ekonomi32. Untuk itu, ada beberapa istilah yang perlu diubah dalam paradigma dalam edisi nadzir ini. Dengan kata lain, Anda perlu berubah dari kontrol konsumen ke kontrol produktif. Dari Nadzir tradisional berdasarkan kepercayaan murni ke Nadzir individu hingga Nadzir yang dilembagakan untuk memfasilitasi akuntabilitas, diadopsi berdasarkan keahlian di bidangnya masing-masing33. Penerbitan akta migrasi nadzir wakaf dari nadzir individu ke nadzir lembaga atau legal menjamin keamanan administrasi, keamanan harta benda, menjaga persatuan umat dan menghindari potensi konflik di kemudian hari 34 . Potensi wakaf dapat memberikan dampak yang signifikan bagi kehidupan masyarakat jika dikelola dan dikelola dengan baik berdasarkan prinsip-prinsip profesionalisme. Untuk meningkatkan potensi wakaf produktif, diperlukan adanya nadzir profesional pusat35 Relokasi Nazhir Wakaf dapat dilihat dari perkembangan kapasitas kelembagaan Nazhir Wakaf. Hal ini membutuhkan pengembangan bakat profesional di Nadzir Wakaf dan tidak terlepas dari prinsip transparansi, akuntabilitas umum, standar operasional dan efisiensi36. Pendidikan wakaf mencakup aspek sosial dan ekonomi, sistem manajemen yang baik, dan sumber daya profesional yang terpercaya, sehingga lembaga Wakaf memanfaatkan dana Wakaf untuk pendidikan, dowa, dan bantuan kemanusiaan. Dan memprioritaskan kegiatan investasi37. Pengelolaan dan pengembangan nazhir merupakan bagian yang sangat penting dari tugas pengelolaan organisasi pengelola wakaf. Seberapa baik SDM dikelola akan menentukan kesuksesan masa depan organisasi ini. Di sisi lain, jika sumber daya manusia tidak dikelola dengan baik, pengelolaan wakaf tidak akan efektif38. Untuk dapat memanfaatkan harta wakaf secara produktif, lembaga membutuhkan keahlian dalam pengelolaannya. Ini selalu mengandung gagasan tentang efektivitas. Efektivitas pengelolaan harta wakaf dinilai penting dalam 117 Muslihati et al Efektifitas sertifikasi nadzir... . Madinah : Jurnal Studi Islam ISSN : 1978-659X (Printed),: 2620-9497 (Online) https://ejournal.iai-tabah.ac.id/index.php/madinah Volume 09, Nomor 1, Juni 2022 mengukur langkah inventif dan menghindari hal-hal yang dapat merugikan masyarakat39. Madinah : Jurnal Studi Islam ISSN : 1978-659X (Printed),: 2620-9497 (Online) https://ejournal.iai-tabah.ac.id/index.php/madinah Volume 09, Nomor 1, Juni 2022 mengukur langkah inventif dan menghindari hal-hal yang dapat merugikan masyarakat39. mengukur langkah inventif dan menghindari hal-hal yang dapat merugikan masyarakat39. HASIL DAN PEMBAHASAN Optimalisasi pengelolaan harta benda wakaf ditujukan untuk memperoleh hasil yang dapat dimanfaatkan sesuai dengan tujuan wakaf, dan ditujukan untuk pengelolaan nilai ekonomis40. Selain itu, pengelolaan wakaf yang profesional membutuhkan ketelitian dan profesionalisme. Efektivitas dan efisiensi pengelolaan aset wakaf penting untuk mengukur kemajuan dan menghindari tabjil yang merugikan ummat. Menurut Kementerian Agama, efek ini adalah pemanfaatan benda wakaf secara optimal untuk kepentingan umum41. Model pengelolaan yang efektif dan efisien harus dilakukan oleh penerima harta wakaf. Keabsolutan Pengelolaan bertujuan untuk mengaktifkan kekayaan wakaf dalam bentuk usaha yang dibutuhkannya, berupa barang dan jasa42 (Ishak, 2014). Menghubungi pengelola Wakaf yang profesional membutuhkan pembinaan agar dapat menjalankan tugasnya secara profesional. Pembinaan dilakukan dengan menggunakan standar manajemen saat ini, pendidikan formal dan informal, pelatihan, atau bimbingan untuk menghasilkan pengelola dan pengembang aset Wakaf43. BIBLIOGRAFI Abdullah, A. (2020). Nadzir dalam Perspektif Kelembagaan Wakaf di Indonesia. Jurnal Ilmiah Ekonomi Islam, 6(3), 403. https://doi.org/10.29040/jiei.v6i3.1216 Alzaina, N. (2019). Urgensi Pemberdayaan Nadzir Dalam Pengelolaan Wakaf ( ) g 41 Damanuri, A. (2013). Efektivitas Dan Efisiensi Pemanfaatan Harta Wakaf Majlis Wakaf Pimpinan Daerah Muhammadiyah Ponorogo. Kodifikasia, 6(1). https://doi.org/10.21154/kodifikasia.v6i1.197 42 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf. 43 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 39 Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf pada Lembaga Wakaf: Studi Kasus pada Majelis Wakaf dan Kehartabendaan Pimpinan Daerah Muhammadiyah 39 Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf pada Lembaga Wakaf: Studi Kasus pada Majelis Wakaf dan Kehartabendaan Pimpinan Daerah Muhammadiyah 40 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf. 41 Damanuri, A. (2013). Efektivitas Dan Efisiensi Pemanfaatan Harta Wakaf Majlis Wakaf Pimpinan Daerah Muhammadiyah Ponorogo. Kodifikasia, 6(1). https://doi.org/10.21154/kodifikasia.v6i1.197 42 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf. 43 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 Daerah Muhammadiyah Ponorogo. Kodifikasia, 6(1). https://doi.org/10.21154/kodifikasia.v6i1.197 42 Ishak, A. (2014). Efektivitas Pengelolaan Wakaf. 43 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1), 1–118 Efektifitas sertifikasi nadzir... . PENUTUP Keberadaan Wakaf dan pemberdayaannya sangat bergantung pada Nazhir. Nadzir berkomitmen untuk melakukan segala kemungkinan untuk melindungi dan mengelola aset wakaf. Nazhir terdiri dari Nadzir perorangan, organisasi, atau badan hukum. Manajemen wakaf meningkatkan kemungkinan penerapan oleh Nadzir organisasi dan badan hukum dibandingkan dengan Nadzir individu berdasarkan manajemen tradisional. Secara umum pengelolaan wakaf dapat diarahkan dan didorong secara optimal jika nadzir adalah ahli yang dipercaya (terpercaya). Kedua hal ini pada akhirnya menentukan apakah Anda dapat mempercayai institusi tersebut. Dengan kemampuan manusia, hubungan teknis dan manusiawi yang mumpuni, Wakaf Nadzir yang profesional adalah pemimpin umum dalam lembaga Wakaf yang mampu mencapai tujuan Wakaf. BIBLIOGRAFI Abdullah, A. (2020). Nadzir dalam Perspektif Kelembagaan Wakaf di Indonesia. Jurnal Ilmiah Ekonomi Islam, 6(3), 403. https://doi.org/10.29040/jiei.v6i3.1216 Alzaina, N. (2019). Urgensi Pemberdayaan Nadzir Dalam Pengelolaan Wakaf 39 Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf pada Lembaga Wakaf: Studi Kasus pada Majelis Wakaf dan Kehartabendaan Pimpinan Daerah Muhammadiyah Muslihati et al Efektifitas sertifikasi nadzir... . Efektifitas sertifikasi nadzir... . Volume 09, Nomor 1, Juni 2022 Madinah : Jurnal Studi Islam ISSN : 1978-659X (Printed),: 2620-9497 (Online) https://ejournal.iai-tabah.ac.id/index.php/madinah Uang Di Indonesia. Istismar: Jurnal Ekonomi Syariah, 1, 37–42. http://ejournal.unwaha.ac.id/index.php/istismar/article/view Uang Di Indonesia. Istismar: Jurnal Ekonomi Syariah, 1, 37–42. http://ejournal.unwaha.ac.id/index.php/istismar/article/view p j p p Baharuddin, A. Z., & Iman, R. Q. (2018). Nazir Wakaf Profesional, Standarisasi dan Problematikanya. Li Falah: Jurnal Studi Ekonomi dan Bisnis Islam, 3(2), 62. https://doi.org/10.31332/lifalah.v3i2. g Damanuri, A. (2013). Efektivitas Dan Efisiensi Pemanfaatan Harta Wakaf Majlis Wakaf Pimpinan Daerah Muhammadiyah Ponorogo. Kodifikasia, 6(1). https://doi.org/10.21154/kodifikasia.v6i1. g Firdaus, F., & Wibowo, S. A. (2020). Analisis Efektivitas Pengelolaan Tanah Wakaf pada Lembaga Wakaf: Studi Kasus pada Majelis Wakaf dan Kehartabendaan Pimpinan Daerah Muhammadiyah …. Reviu Akuntansi dan Bisnis Indonesia, 4(2), 99–109. https://journal.umy.ac.id/index.php/rab/article/view/10785 Hakim, A. R., Anwar, S., & Setiawan, A. I. (2016). Peran Badan Wakaf Indonesia dalam Pengorganisasian Wakaf Produktif. Jurnal Tadbir: Jurnal Manajemen Dakwah, 1(2) Huda, N., Rini, N., Mardoni, Y., Anggraini, D., & Hudori, K. (2018). Manajemen Pengelolaan Wakaf Di Indonesia Timur. EKUITAS (Jurnal Ekonomi dan Keuangan), 20(1), 1–17. https://doi.org/10.24034/j25485024.y2016.v20.i1.35 Ilyas, M. (2009). Metadata, citation and similar papers at core.ac.uk 1. 2(1) Ishak, A. (2014). Efektivitas Pengelolaan Wakaf di Provinsi Gorontalo. Jurnal Diskursus Islam, Kasdi, A. (2014). Peran Nadzir Dalam Pengembangan Wakaf. Jurnal Zakat dan Wakaf, 1(2) Lestari, W., & Thantawi, R. (2016). Efektivitas Pengelolaan Wakaf Tunai. Syarikah, 2(1) Masyhar, A., Arifin, R., & Fuad, A. N. (2019). PENUTUP Sertifikasi Alih Nadzir Badan Hukum Wakaf Perorangan Kepada Nadzir Badan Hukum Bagi Masjid / Musholla di Kecamatan Gunungpati Kota Semarang. JPHI: Jurnal Pengabdian Hukum Indonesia (Indonesian Journal of Legal Community Engagement), 2(1), 60–67. https://journal.unnes.ac.id/sju/index.php/JPHI/article/view/34054 Ridwan, M. (2012). Nazhir Profesional Kunci Kesuksesan Wakaf Produktif. Muqtasid: Jurnal Ekonomi dan Perbankan Syariah, 3(1), 91. https://doi.org/10.18326/muqtasid.v3i1. Sulaeman, A., Bayinah, A. N., & Hidayat, R. (2020). Apakah Kepercayaan Muwakif Ditentukan oleh Akuntabilitas Pengelolaan Wakaf Tunai dan Peran Nadzir ? Jurnal Akuntansi Dan Keuangan Islam, 8(1), 71–86. https://doi.org/10.35836/jakis.v8i1. Tiswarni. (2014). ( Tinjauan Terhadap Strategi Pemberdayaan Wakaf Badan Wakaf Alquran. Ekonomi syariah, 7(2) Umami, N. F. dan K. (2021). Efektivitas Nazir Organisasi Di Majelis Wakil Cabang Nahdlatul Ulama Kecamatan Siman Kabupaten Ponorogo. Jurnal Antologi Hukum, 1(1), 16–33. http://etheses.iainponorogo.ac.id/id/eprint/13759 119 Muslihati et al Efektifitas sertifikasi nadzir... .
https://openalex.org/W2980186287
https://digibug.ugr.es/bitstream/10481/61784/1/Cockell2019_Article_SampleCollectionAndReturnFromM%20IACT.pdf
English
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Sample Collection and Return from Mars: Optimising Sample Collection Based on the Microbial Ecology of Terrestrial Volcanic Environments
Space science reviews
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Space Sci Rev (2019) 215:44 https://doi.org/10.1007/s11214-019-0609-7 Space Sci Rev (2019) 215:44 https://doi.org/10.1007/s11214-019-0609-7 p g j Q y Edited by Mahesh Anand, Sara Russell, Yangting Lin, Meenakshi Wadhwa, Kuljeet Kaur Marhas and Shogo Tachibana Role of Sample Return in Addressing Major Questions in Planetary Sciences Role of Sample Return in Addressing Major Questions in Planetary Sciences Edited by Mahesh Anand, Sara Russell, Yangting Lin, Meenakshi Wadhwa, Kuljeet Kaur Marhas and Shogo Tachibana B C.S. Cockell c.s.cockell@ed.ac.uk 1 Introduction The search for habitable conditions or life on any planetary body must necessarily be guided by what we know about life on Earth. A very large number of ‘analog’ environments on the Earth have been investigated to understand the factors that influence their microbial inhabitants and determine both the biomass and diversity of life they can support. These environments range from deserts to lakes with physico-chemical conditions, such as extreme aridity, acidity or salinity, that correspond to extant or ancient conditions on Mars (e.g., Dickinson and Rosen 2003; Navarro-González et al. 2003; Cabrol et al. 2007; Preston and Dartnell 2014; Hays et al. 2017; Lim et al. 2019). Over the last two decades our view of Mars as a homogeneous ‘red planet’ has given way to a highly nuanced understanding of the great heterogeneity of past and present en- vironments at kilometre scales (Cabrol and Grin 2001; Bibring et al. 2006; Ehlmann et al. 2009, 2011) down to millimetre scales, where individual mineral grains have been investi- gated (Weitz et al. 2006). Some geochemical records indicate paleoenvironmental conditions permissive for life (Grotzinger et al. 2013; Hurowitz et al. 2017). Despite this impressive ex- pansion in our understanding of Mars, the fact remains that Mars is fundamentally a volcanic planet, with a meagre rock cycle (no plate tectonics) and no extensive surface biosphere, both of which vastly increase the range of viable habitats on the Earth. Even in the realm of volcanic lithologies, Mars is limited in its geological diversity compared to the Earth. For example the lack of a highly productive biosphere to generate large abundances of organic carbon (Field et al. 1998) limits the diversity and extent of volcanic soils, called ‘andosols’, that are a substantial habitat for microbial life on Earth. Although the Earth’s basaltic oceanic crust offers a number of lessons about microbial distribution (Edwards et al. 2003; Lysnes et al. 2004; Santelli et al. 2008), the specific chemical composition of Earth’s sea water and its continuous flow through the basaltic crust over million-year time scales makes even deep-ocean basaltic microbial habitats of potentially limited direct applicability to Mars. On Mars, the composition of hydrothermal fluids in the subsurface is poorly con- strained, the former presence and extent of sustained ocean(s) to generate analogous deep ocean habitats is controversial (Head et al. Keywords Mars · Sample collection · Microbial ecology · Basaltic · Fumaroles Keywords Mars · Sample collection · Microbial ecology · Basaltic · Fumaroles Sample Collection and Return from Mars: Optimising Sample Collection Based on the Microbial Ecology of Terrestrial Volcanic Environments Charles S. Cockell1 · Sean McMahon1 · Darlene S.S. Lim2 · John Rummel3 · Adam Stevens1 · Scott S. Hughes4 · Shannon E. Kobs Nawotniak4 · Allyson L. Brady5 · Viggo Marteinsson6,7 · Javier Martin-Torres8,9,1 · Maria-Paz Zorzano10,8 · Jesse Harrison11 Received: 5 November 2018 / Accepted: 10 September 2019 / Published online: 9 October 2019 © The Author(s) 2019 Abstract With no large-scale granitic continental crust, all environments on Mars are fun- damentally derived from basaltic sources or, in the case of environments such as ices, evap- oritic, and sedimentary deposits, influenced by the composition of the volcanic crust. There- fore, the selection of samples on Mars by robots and humans for investigating habitability or testing for the presence of life should be guided by our understanding of the microbial ecology of volcanic terrains on the Earth. In this paper, we discuss the microbial ecology of volcanic rocks and hydrothermal systems on the Earth. We draw on microbiological in- vestigations of volcanic environments accomplished both by microbiology-focused studies and Mars analog studies such as the NASA BASALT project. A synthesis of these data em- phasises a number of common patterns that include: (1) the heterogeneous distribution of B C.S. Cockell c.s.cockell@ed.ac.uk B C.S. Cockell c.s.cockell@ed.ac.uk 1 UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King’s Buildings, Edinburgh, EH9 3FD, UK 2 NASA Ames Research Center, Moffett Field, CA, USA 2 NASA Ames Research Center, Moffett Field, CA, USA 3 SETI Institute, P.O. Box 2445, Friday Harbor, WA 98250, USA 4 Dept. of Geosciences, Idaho State University, 921 S. 8th Ave, Pocatello, ID 83209, USA 5 School of Geography and Earth Sciences, McMaster University, Hamilton, Ontario, Canada 6 MATIS, Research & Innovation, Vínlandsleið 12, 113 Reykjavik, Iceland 7 Faculty of Food Science and Nutrition, University of Iceland, Reykjavik, Iceland 8 Group of Atmospheric Science, Department of Computer Science, Electrical and Space Engineering, Luleå University of Technology, Luleå, Sweden 9 Instituto Andaluz de Ciencias de la Tierra (CSIC-UGR), Armilla, Granada, Spain 10 Centro de Astrobiología (CSIC-INTA), Torrejon de Ardoz, 28850 Madrid, Spain 11 Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland 44 Page 2 of 25 C.S. Cockell et al. Sample Collection and Return from Mars: Optimising Sample Collection Based on the Microbial Ecology of Terrestrial Volcanic Environments 44 Page 2 of 25 biomass and diversity in all studied materials, (2) physical, chemical, and biological factors that can cause heterogeneous microbial biomass and diversity from sub-millimetre scales to kilometre scales, (3) the difficulty of a priori prediction of which organisms will colonise given materials, and (4) the potential for samples that are habitable, but contain no evidence of a biota. From these observations, we suggest an idealised strategy for sample collection. It includes: (1) collection of multiple samples in any given material type (∼9 or more sam- ples), (2) collection of a coherent sample of sufficient size (∼10 cm3) that takes into account observed heterogeneities in microbial distribution in these materials on Earth, and (3) col- lection of multiple sample suites in the same material across large spatial scales. We suggest that a microbial ecology-driven strategy for investigating the habitability and presence of life on Mars is likely to yield the most promising sample set of the greatest use to the largest number of astrobiologists and planetary scientists. Keywords Mars · Sample collection · Microbial ecology · Basaltic · Fumaroles Sample Collection and Return from Mars... Page 3 of 25 44 There are, of course, environments on the Earth and Mars that are often considered to be independent of the geology of the crust and on Earth host life or preserve biosignatures. For example, ice-sheets and glaciers on Earth host life (Carpenter et al. 2000; Liu et al. 2015; Anesio et al. 2017), as do evaporitic salt deposits (Maturrano et al. 2006; Oren 2008; Robinson et al. 2015). These environments are known to exist on Mars (Head et al. 2003; Lasue et al. 2013; Osterloo et al. 2008, 2010). However, the aqueous and particulate geo- chemistry of these environments are influenced by the geological substratum and thus the nutrients and energy supplies in such settings on Mars would still be linked to a vol- canic geological context. Nevertheless, this paper will not discuss the biological poten- tial and sampling of ices and salts. We draw lessons on sample collection by focusing on primary volcanic rocks and derived weathering materials since they constitute the ma- jority of materials and potentially habitable substrates that would likely be sampled by robotic and human explorers. Although we do not review the literature here, we note that the conclusions we will draw on the heterogeneity of microbial biomass and di- versity in primary volcanic samples also apply to ices and salt deposits in which het- erogeneous biomass and diversity distribution has been observed (e.g., Liu et al. 2015; Robinson et al. 2015). The study of the microbial ecology of volcanic terrains relevant to Mars is surprisingly underdeveloped. For example, the microbial ecology of environments with sustained inter- actions between freshwater and volcanic rocks, including crystalline rocks and glasses, is poorly known. Indeed, limited knowledge exists regarding the overall thickness and extent of volcanic soils and other deposits derived by chemical weathering on Mars. However, a sufficient number of studies have been accomplished to extract knowledge that directly bears on what our most optimistic expectations for microbial ecology on Mars could be (as- suming that there is or was life) and thus how one should go about collecting samples. In this paper, we do not attempt an exhaustive review of microbiology studies in volcanic envi- ronments. Instead, we provide examples used to draw out general principles. The selection of studies used in this paper are shown in Table 1. In this paper, we have two objectives. Sample Collection and Return from Mars... First, we provide a review of microbial life in volcanic rocks to inform the reader about the typical distribution of life in a diversity of ma- terials. This review provides insight into the types of samples of interest to a biologist. One might regard this as an introductory primer on microbial life in volcanic materials. Second, using these examples of the microbial ecology of volcanic materials, we draw out common patterns that allow us to suggest microbial ecology-driven sample collection approaches for investigating habitability and testing the hypothesis of life on Mars. The conclusions we draw in this paper are applicable to the search for both extant and extinct life. The distribution of biomarkers such as biomolecules (e.g., hopanes) and isotopic signatures in volcanic paleohabitats will depend on the original distribution of biomass as well as its potential to be preserved in those environments (McMahon et al. 2018). Thus, the search for extinct life must also take into account taphonomic considerations relevant to the microbial habitats discussed here. 1 Introduction 1999) and long-term hydrological activity ap- pears to have been curtailed by the loss of most surface water in the late Noachian and Hesperian (Lasue et al. 2013). Sample Collection and Return from Mars... 2 A Review of Igneous Petrology from an Astrobiological Perspective Igneous petrology is a vast area of research, but from an astrobiological perspective, sev- eral points can be made about volcanism that are essential to the later discussion in this paper. Volcanic rocks (i.e. igneous rocks derived from the extrusion of lava at the Earth’s surface rather than cooling of magma in the subsurface) vary widely in composition. They 44 Page 4 of 25 C.S. Cockell et al. 44 Page 4 of 25 C.S. Cockell et al ble 1 Studies of the microbial ecology of volcanic environments relevant to Mars used in this paper to suggest a sampling strategy e of environment/material Location Comments Reference altic/andesitic crystalline rock Italy Lichen colonisation of lava flows on Mount Vesuvius Adamo and Violante (1991), Adamo et al. (1993) Iceland Studies on bacterial inhabitants of crystalline rocks (lava) Kelly et al. (2011), Cockell et al. (2013) Iceland Bacterial pioneer colonists of crystalline rocks (lava) Kelly et al. (2014) Iceland Inhabitants of lava flows of differing ages Byloos et al. (2018) USA Inhabitants of transects from fumarolic to non-fumarolic sites including unaltered and weathered basalts (Hawai’i) Cockell et al. (2019) yolitic crystalline rock Iceland Bacterial inhabitants of crystalline rocks (lava) Kelly et al. (2011) altic glass Iceland Bacterial inhabitants of weathered basaltic glass Cockell et al. (2009) Iceland Bacterial inhabitants of weathered basaltic glass Kelly et al. (2010) idian (silica-rich glass) Iceland Bacterial inhabitants of obsidian Herrera et al. (2008, 2009) Iceland Bacterial inhabitants of weathered glasses Kelly et al. (2010) canic fumaroles/active geothermal strates/geothermal lakes Italy Endolithic inhabitants of rocks and soils in active geothermal area Gross et al. (1998) USA Endolithic inhabitants of siliceous geothermal deposits Walker et al. (2005) New Zealand Endolithic inhabitants of siliceous deposits in active geothermal springs Gaylarde et al. (2006) Chile Inhabitants of fumaroles and surrounding soils Costello et al. (2009) Antarctica Inhabitants of fumarolic soils Soo et al. (2009) USA Inhabitants of nonsulphur, sulphur and iron geothermal steam vents Benson et al. (2011) USA Inhabitants of fumaroles Wall et al. (2015) Iceland Geothermal spring microbial and isotopic gradients Cousins et al. (2018) Costa Rica Microbial diversity in Laguna Caliente lake Hynek et al. (2018) Chile Inhabitants of fumarolic soils Solon et al. (2018) USA Inhabitants of transects from fumarolic to non-fumarolic sites (Hawai’i) Cockell et al. 2 A Review of Igneous Petrology from an Astrobiological Perspective (2019) Table 1 Studies of the microbial ecology of volcanic environments relevant to Mars used in this paper to suggest a sampling strategy Type of environment/material Location Comments Reference Basaltic/andesitic crystalline rock Italy Lichen colonisation of lava flows on Mount Vesuvius Adamo and Violante (1991), Adamo et al. (1993) Iceland Studies on bacterial inhabitants of crystalline rocks (lava) Kelly et al. (2011), Cockell et al. (2013) Iceland Bacterial pioneer colonists of crystalline rocks (lava) Kelly et al. (2014) Iceland Inhabitants of lava flows of differing ages Byloos et al. (2018) USA Inhabitants of transects from fumarolic to non-fumarolic sites including unaltered and weathered basalts (Hawai’i) Cockell et al. (2019) Rhyolitic crystalline rock Iceland Bacterial inhabitants of crystalline rocks (lava) Kelly et al. (2011) Basaltic glass Iceland Bacterial inhabitants of weathered basaltic glass Cockell et al. (2009) Iceland Bacterial inhabitants of weathered basaltic glass Kelly et al. (2010) Obsidian (silica-rich glass) Iceland Bacterial inhabitants of obsidian Herrera et al. (2008, 2009) Iceland Bacterial inhabitants of weathered glasses Kelly et al. (2010) Volcanic fumaroles/active geothermal substrates/geothermal lakes Italy Endolithic inhabitants of rocks and soils in active geothermal area Gross et al. (1998) USA Endolithic inhabitants of siliceous geothermal deposits Walker et al. (2005) New Zealand Endolithic inhabitants of siliceous deposits in active geothermal springs Gaylarde et al. (2006) Chile Inhabitants of fumaroles and surrounding soils Costello et al. (2009) Antarctica Inhabitants of fumarolic soils Soo et al. (2009) USA Inhabitants of nonsulphur, sulphur and iron geothermal steam vents Benson et al. (2011) USA Inhabitants of fumaroles Wall et al. (2015) Iceland Geothermal spring microbial and isotopic gradients Cousins et al. (2018) Costa Rica Microbial diversity in Laguna Caliente lake Hynek et al. (2018) Chile Inhabitants of fumarolic soils Solon et al. (2018) USA Inhabitants of transects from fumarolic to non-fumarolic sites (Hawai’i) Cockell et al. (2019) nvironments relevant to Mars used in this paper to suggest a sampling strategy Page 5 of 25 44 Sample Collection and Return from Mars... g Table 1 (Continued) Type of environment/material Location Comments Reference Mud volcanoes Romania Microbial diversity of mud volcanoes Dahigaonkar and Chavan (2018) China Microbial diversity of mud volcanoes Huang et al. (2016) Ash/ash soils/tephra Iceland Colonisation of Surtsey Island Schwabe (1970), Schwabe and Behre (1972); Kristinsson (1970, 1974); Brock (1973); Henriksson and Henriksson (1982); Stefansdottir et al. 2 A Review of Igneous Petrology from an Astrobiological Perspective Ultimately, these categories largely reflect the source composition and thermal evolu- tion of the magma, with more mafic (iron- and magnesium-rich) minerals crystallising from the melt at higher temperatures. Mafic and ultramafic rocks (also referred to as ‘basic’) are formed between ∼1000–1500 ◦C and contain elevated concentrations of pyroxenes, olivines and plagioclase (predominantly Mg, Fe and Ca-containing minerals). The precipitation of these dense minerals within a cooling magma chamber drives the composition of the resid- ual magma towards higher silica content; thus high-silica volcanic rocks (also referred to as ‘acidic’ or ‘felsic’ rocks) generally represent lower temperatures (typically about 700 ◦C). They also have a higher content of orthoclase feldspar (a K-containing silicate mineral) and quartz. Although rare felsic lavas have been detected on Mars, the martian crust is dom- inated by the mafic rock, basalt. In this paper, we will not consider samples spanning the entire ultramafic-felsic continuum, but we will provide examples of the microbial ecology of materials, focusing on basaltic rocks. We also provide comparisons to high-silica obsidian where this is useful to illustrate factors that influence colonisation. A second factor of great importance for a biota is the glassiness or crystallinity of the material. Volcanic melt that comes into contact with ice or water is rapidly quenched be- fore crystals can form, resulting in a homogeneous glass, in contrast to other rocks that are formed subaerially and cool slowly, forming crystalline materials. This is significant in the Martian context because widespread glaciers and ground ice in contact with volcanically ac- tive regions (Cousins and Crawford 2011) may imply that past episodes of volcanism have generated substantial quantities of glass and their weathering products (Horgan and Bell 2012). Why is distinguishing crystalline rock and glass important? First, glasses present a mate- rial with a more homogenised composition to a potential biota, whereas in crystalline mate- rials, bioessential elements are generally localised to particular crystals, meaning that fewer bioessential elements can be found in one location at the micron-scale. Second, basaltic glass, in contrast to crystalline rocks, has a distinctive capacity for weathering to palag- onite, a soft alteration product (Thorseth et al. 1991; Stroncik and Schminke 2002) that tends to form within basaltic vesicles and fractures and may be a more bio-accessible source of nutrients than the crystalline matrix. Third, in crystalline high-silica rocks, the silica is primarily bound up in quartz. 2 A Review of Igneous Petrology from an Astrobiological Perspective (2014) Iceland Colonisation of Heimaey Island Englund (1976) USA Cinder cone colonisation (Hawai’i) Carson and Brown (1978) USA Soil microbial communities (Hawai’i) Nüsslein and Tiedje (1998) USA Recent colonisation of ash and their lithotrophic metabolisms (Hawai’i) King (2003) USA Recent colonisation of ash and their lithotrophic metabolisms (Hawai’i) Nanba et al. (2004) USA Inhabitants of 42–300 year old Hawaiian volcanic deposits (Hawai’i) Dunfield and King (2005) USA Inhabitants of numerous soil and ash deposits of different ages (Hawai’i) Gomez-Alvarez et al. (2006) Antarctica Inhabitants of deposits on geothermally active volcano Fermani et al. (2007) Italy Inhabitants of different aged soils Hopkins et al. (2007) USA Inhabitants of different aged soils Ibekwe et al. (2007) Iceland Biomass and microbial community in fresh volcanic tephra Amador et al. (2015), Gentry et al. (2017) le 1 (Continued) e of environment/material Location Comments Reference d volcanoes Romania Microbial diversity of mud volcanoes Dahigaonkar and Chavan (2018) China Microbial diversity of mud volcanoes Huang et al. (2016) /ash soils/tephra Iceland Colonisation of Surtsey Island Schwabe (1970), Schwabe and Behre (1972); Kristinsson (1970, 1974); Brock (1973); Henriksson and Henriksson (1982); Stefansdottir et al. (2014) Iceland Colonisation of Heimaey Island Englund (1976) USA Cinder cone colonisation (Hawai’i) Carson and Brown (1978) USA Soil microbial communities (Hawai’i) Nüsslein and Tiedje (1998) USA Recent colonisation of ash and their lithotrophic metabolisms (Hawai’i) King (2003) USA Recent colonisation of ash and their lithotrophic metabolisms (Hawai’i) Nanba et al. (2004) USA Inhabitants of 42–300 year old Hawaiian volcanic deposits (Hawai’i) Dunfield and King (2005) USA Inhabitants of numerous soil and ash deposits of different ages (Hawai’i) Gomez-Alvarez et al. (2006) Antarctica Inhabitants of deposits on geothermally active volcano Fermani et al. (2007) Italy Inhabitants of different aged soils Hopkins et al. (2007) USA Inhabitants of different aged soils Ibekwe et al. (2007) Iceland Biomass and microbial community in fresh volcanic tephra Amador et al. (2015), Gentry et al. (2017) 44 Page 6 of 25 C.S. Cockell et al. 44 Page 6 of 2 are classified into fifteen different compositional groups depending upon their silica and alkali content (in this context alkali means the concentration of Na and K) following con- vention established by the International Union of Geological Sciences (IUGS) (Le Bas et al. 1992). 2 A Review of Igneous Petrology from an Astrobiological Perspective However, in glass, this silica (which has no biological use) is distributed throughout and may retard the release of more biologically useful elements such as Fe (Wolff-Boenisch et al. 2004). A priori therefore, in parent rocks on Mars we would expect the concentration of silica and the glassiness of the material to be important considerations in their potential as habitable substrates and how microorganisms would be theoretically distributed within them. These factors are explored in later sections. The weathering of these primary rock types (and of volcanic ash deposits) in aque- ous environments leads to the formation of a variety of cation-rich aluminosilicate clays (or palagonite in the case of basaltic glass). The types of clays formed depend on the thermal regime and aqueous chemistry. On Mars, Fe- and Mg-rich smectites, serpen- tine, and chlorite, resulting from the alteration of basaltic precursor minerals, are partic- ularly widespread (e.g., Poulet et al. 2005; Milliken and Bish 2010; Ehlmann et al. 2011; Bristow et al. 2018). Interactions with clay particles, including smectite, can profoundly influence the fate and residence time of organic matter in the environment and inhibit or promote the growth of different microbial groups. However, little is currently known about the correlation of microbial diversity and biomass to different clay types formed in volcanic Sample Collection and Return from Mars... Page 7 of 25 44 environments, particularly in environments where organic input is low. Most analyses of volcanic clays have occurred in the critical zone (soil-rock interface) in regions of the world where the formation of economically important volcanic soils (andosols) is associated with generally high organic/humic substance concentrations (Kimble et al. 2000). Nevertheless, the studies that have been undertaken in volcanic terrains are sufficient to draw the conclu- sions we make here. We recognise that present-day surface conditions on Mars are very different from the Earth. The desiccated surface, high-ultraviolet and ionising radiation and the presence of perchlorates (Cockell et al. 2000; Dartnell et al. 2007; Hecht et al. 2009; Wadsworth and Cockell 2017), among other factors, make the surface inimical to life and may also impact the preservation of ancient biosignatures (particularly organic biomarkers). 2 A Review of Igneous Petrology from an Astrobiological Perspective In this synthesis, we are assuming that martian samples will be collected from environments that experienced sustained contact with water in the past and have either been drilled from the subsurface or were only exposed to martian atmosphere relatively recently, for example by wind erosion (e.g., Farley et al. 2014; Hurowitz et al. 2017). We also note that more extreme conditions found on Mars, particularly in later stages of its hydrological evolution, if they were to theoretically reduce the potential biomass and diversity of life, would merely strengthen the conclusions we draw about low biomass environments and the need for large sample numbers required to test for life or affirm its absence. A further complication is the aeolian transport of material that becomes entrained in rocks. Microorganisms are known to be transported in atmospheric dust on Earth (Gat et al. 2017). As well as providing a microbial inoculum to new habitats, the aerially transported dust can potentially introduce extraneous geological material into samples, confounding ge- ological analysis. On Mars, aeolian dust transport and mixing over the planetary scale is ubiquitous (Lasue et al. 2018). Aerial transport of particulate matter is also widespread in many volcanic environments on the Earth, including those in which microbial ecological analysis described in this paper have been undertaken, such as environments in Iceland (Ar- nalds et al. 2016). This transport does not compromise geological analysis of the origin of samples or the conclusions about the heterogeneous distribution of biomass and diversity within the sample that is linked to the primary sample type. This is likely to be the case for sample selection on Mars, particularly if samples are cleaned of dust or collected from the near-surface or interior of outcrops. 3 Limits of ‘Analogue’ Materials Not all volcanic environments and materials on Earth are useful analogues to Mars. Two examples are andosols and marine-influenced volcanic rocks. We discuss these here to em- phasise caution in drawing lessons about Mars from some volcanic materials on Earth. Volcanic rocks ultimately weather to soils called andosols, which form an important com- ponent of terrestrial volcanic environments (Kimble et al. 2000). Andosols exist in a variety of states such as extreme pH in soils surrounding geothermal pools, hot and cold desert soils, as well as humid andosols (Oskarsson et al. 2004; Parfitt and Kimble 1989; Arnalds 2004; Belobrov and Ovechkin 2005; Hopkins et al. 2007). However, apart from regions free of vegetation and with low precipitation (deserts), most andosols are fertile because of many years of microbial and floral amelioration. They are generally high in Fe and Al. These metals, in addition to high concentrations of humic acids, make andosols highly effective at immobilising phosphate (Lukito et al. 1998). This retention of biologically available phos- phorus combined with the precipitation of phosphorus, impedes microbial and floral growth 44 Page 8 of 25 C.S. Cockell et al. on younger andosols (Kimble et al. 2000). It is not currently known what the initial microbial colonists are for many andosols as it depends on the chemical composition of each individ- ual soil. Richardson (2001) showed that microorganisms were key to the release of organic and inorganic phosphorus. Nevertheless, even young andosols, although relatively hostile, are capable of sustaining highly diverse microbial communities. Nüsslein and Tiedje (1998) investigated a 200 year-old andosol in Hawai’i with high diversity. They showed that the soil biomass was dominated by a distinct microbial diversity of Pseudomonas, Rhizobium- Agrobacterium and Rhodospirillum species. On many andosols, plants strongly influence microbial colonisation. Some of the first floral species to inhabit Mount St. Helens soils following the 1980 eruption were Lupinus spp., which provide support for nitrogen-fixing cyanobacteria (Halvorson et al. 1992). Although these data are interesting, they nevertheless illustrate that many terrestrial andosols are likely poor analogues to past or present Martian volcanic environments because of the extent of microbial and plant colonisation and the relatively rich organic carbon cycle established within them. An extensive body of literature exists on the microbial ecology of the basaltic oceanic crust. 3 Limits of ‘Analogue’ Materials Although superficially this carbon- and energy-poor environment might appear to be a good analogue for the Martian deep subsurface, there is uncertainty as to how much the communities associated with ocean crust, their biomass and diversity, are influenced by ocean chemistry and factors linked with the Earth’s unusual plate tectonic regime. During the rifting that occurs at plate boundaries in the oceans, basaltic glass is produced. The rate of crustal production may be well over a billion tonnes a year (Bach and Edwards 2003). Insofar as basaltic glass contains many major cations that are biologically useful, including Ca, Mg, K, Na and Fe, then it would be expected to be a source of material for microbial growth (Staudigel et al. 1995, 1998; Thorseth et al. 2001; Santelli et al. 2008). The extent to which oceanic basaltic glass is used by a biota in-situ is unclear (Staudi- gel et al. 1998, 2006, Torsvik et al. 1998). There is evidence for the deep-ocean biological alteration of glass. In investigations of 0–30 Myr old basalts from the region of mid-ocean ridge known as the Australian–Antarctic Discordance, Thorseth et al. (2003) recorded the presence of Mn-rich encrustations which they suggested could be linked to biological Mn- yielding reactions. Partially fossilised endolithic microorganisms were associated with rims of altered glasses. Basaltic glass from the Knipovich Ridge, Arctic shows pervasive coloni- sation of fractures, including stalked, coccoid, rod and filamentous forms. Organisms were found to be associated with the alteration products in the fractures and they were often cov- ered in Fe- and Al-rich precipitates (Thorseth et al. 2001). The organisms that might be involved in weathering glass have been the subject of several investigations. Templeton et al. (2005) showed the presence of Mn-oxidising bacteria in basalts from Loihi Seamount, although autotrophic Mn-oxidisers were not recovered. This suggests Mn oxidation is a secondary process occurring in heterotrophic organisms (Tebo et al. 2005) that might be using organic carbon compounds available in seawater. Diverse neutrophilic Fe-oxidising bacteria have been isolated from oceanic environments (Edwards et al. 2003), although it is not clear to what extent they might be accessing iron from basaltic glass or from the surrounding sea water. The Fe oxide minerals found associated with deep- ocean basalts have been shown to be similar to minerals produced by iron-oxidising bacteria in culture (Daughney et al. 2004). 3 Limits of ‘Analogue’ Materials In a study of the microbial community of the basaltic glasses of the Knipovich Ridge, Arctic, Thorseth et al. (2001) identified heterotrophs and some chemolithotrophs including phylotypes closely matching with S-oxidisers. Fe-reducing organisms were cultured from Arctic Ridge seafloor basaltic glasses by Lysnes et al. (2004) and these authors suggested that this is evidence for an Fe-cycle within seafloor basalts. Phylogenetic analysis of seafloor Sample Collection and Return from Mars.. Page 9 of 25 44 basaltic glasses around Hawai’i show high diversity (Santelli et al. 2008; Orcutt et al. 2009) which is hypothesised to be linked to the chemolithotrophic use of basaltic glass alteration products (Santelli et al. 2008). In summary, there appears to be good evidence for microbial use of elements from basaltic glass directly, particularly Fe, that may suggest that these rocks provide an ana- logue for habitable substrates on Mars. However, the extent to which resources in seawater are used, such as organics and other ions, and the extent to which the biomass and diver- sity of these habitats is established by continuous water flow in the oceanic crust together with the high production rate of fresh substrate through plate tectonics is not known. Plate tectonics, if it existed on Mars at all, ceased early (Yin 2012). Although there is contro- versial evidence for a northern ocean (Head et al. 1999), even if it did exist, its chemical composition and the degree to which it might have sustained crustal hydrothermal cycling to generate habitats analogous to the terrestrial oceanic crust is not known. For these reasons, in this paper we focus on volcanic materials in contact with freshwater, primarily land-based crystalline and glassy volcanic rocks, including materials in land-based volcanic hydrothermal systems. However, heterogeneous distribution of biomass and diver- sity is observed in ocean crust materials (Santelli et al. 2008), so although we do not consider these to be necessarily the best analogue materials to examine here, the consideration of their microbiology would not change our conclusions. 4 Microorganisms Are Heterogeneously Distributed—the Need for Appropriate Sample Size Cells were detected after DAPI staining under UV light (subimage C) and after fluorescence in situ hybridisation (FISH) with bacterial Cy3-EUB338I-III primers targeting most of bacteria (subimage D). Observations B, C and D correspond to an identical area on the thin section (data from Herrera et al. 2008, 2009). Image 2 shown cells in basaltic glass. Subimage A shows SYBR Green I (DNA) staining of microorganisms on a fragment of palagonite also shows in bright field (scale bar 20 µm) (subimage B). Subimage C shows a SYBR Green I stained section of a vesicle in weathered basaltic glass, arrow indicates DNA staining at the rock–palagonite interface with staining also apparent on the surface of the palagonite (scale bar 40 µm) (data from Cockell et al. 2009) Fig. 1 Cells are distributed heterogeneously in materials for different reasons. Examples of heterogeneity in microbial distribution in volcanic glasses. Image 1 shows cells in obsidian. In (A), unaltered glass (G) and altered glass (AG) at the edge of a vesicle (V) are shown. Subimage B shows the region located in the square in image A. Cells were detected after DAPI staining under UV light (subimage C) and after fluorescence in situ hybridisation (FISH) with bacterial Cy3-EUB338I-III primers targeting most of bacteria (subimage D). Observations B, C and D correspond to an identical area on the thin section (data from Herrera et al. 2008, 2009). Image 2 shown cells in basaltic glass. Subimage A shows SYBR Green I (DNA) staining of microorganisms on a fragment of palagonite also shows in bright field (scale bar 20 µm) (subimage B). Subimage C shows a SYBR Green I stained section of a vesicle in weathered basaltic glass, arrow indicates DNA staining at the rock–palagonite interface with staining also apparent on the surface of the palagonite (scale bar 40 µm) (data from Cockell et al. 2009) (Fluorescence In-Situ Hybridisation), found that cells were localised to altered regions in the obsidian glass (Fig. 1). The cells were associated with iron oxide crystals. Subsequent cell enumeration found total bulk cell numbers less than 104 cells/gram. Because the cells were so localised within the obsidian, whole rock cell numbers were unrepresentative. Sig- nificantly, entire chunks to cm3 scales, contained no detectable cells. The localised biofilms associated with alteration zones were often only found in exposed rocks or weathered re- gions where water had penetrated into the material. 4 Microorganisms Are Heterogeneously Distributed—the Need for Appropriate Sample Size Observations of microorganisms in contiguous cryptoendoliths biofilms (e.g., Bell 1993; de la Torre et al. 2003) might give the impression that organisms are generally uni- formly distributed in rocks. Although these distinctive endolithic communities can be observed in volcanic geothermal materials (Gaylarde et al. 2006; Gross et al. 1998; Walker et al. 2005) and cooled volcanic rocks (Herrera et al. 2009), organisms within vol- canic materials are frequently highly heterogeneously distributed at millimetre and sub- millimetre scales, with implications for sample collection (Fig. 1). As a case study, it is worth considering the colonisation and distribution of microbes in basaltic glass and its felsic counterpart, obsidian. In both materials, microbes are observed to be distributed heteroge- neously, but apparently caused by different factors. The distribution of microbes in obsidian, although not directly relevant to Mars as this material has not be detected, provides insights into the factors that influence microbial distribution in surface and near-surface volcanic materials more generally. Basaltic glass weathers to palagonite, a relatively soft weathering product, which forms rinds on the glass (Stroncik and Schminke 2001, 2002). Although weathering of obsid- ian occurs, it is much slower than the weathering of basaltic glass (Wolff-Boenisch et al. 2004, 2006). The higher silica concentration in obsidian impedes the degradation of the ma- terial since the Si-O bonds result in a more extensive silica network that is thought to retard leaching of cations, including bioessential cations, from the rock. These different weathering processes are consistent with observations of varying micro- bial abundance. Cockell et al. (2009) observed high cell numbers in basalt glass samples with bulk cell numbers of ∼107 cells/gram. In this material, most of the observed cells were associated with the weathered palagonite surfaces and potentially a population be- neath the palagonite. Very few cells were associated with the unweathered glass surface. In obsidian, which does not so readily form weathered rinds, Herrera et al. (2008), using FISH 44 Page 10 of 25 C.S. Cockell et al. Fig. 1 Cells are distributed heterogeneously in materials for different reasons. Examples of heterogeneity in microbial distribution in volcanic glasses. Image 1 shows cells in obsidian. In (A), unaltered glass (G) and altered glass (AG) at the edge of a vesicle (V) are shown. Subimage B shows the region located in the square in image A. 4 Microorganisms Are Heterogeneously Distributed—the Need for Appropriate Sample Size Similarly heterogeneous distribution of biomass has been observed in other volcanic en- vironments. The NASA project BASALT (Biologic Analog Science Associated with Lava Terrains; Lim et al. 2019) carried out a study of microbial diversity and biomass in basaltic fumaroles, weathered rocks and unweathered rocks in Hawai’i. Consistent with other stud- ies cited here, all materials were found to host a low diversity, and biomass was highly heterogeneous, ranging from 6.25 × 105 to 4.06 × 107 cells/gram dry weight based on DNA concentration (means shown in Fig. 3). Lipid biomarker-based estimates of biomass also demonstrated heterogeneous distribution within BASALT samples (Brady et al. 2017). The heterogeneous distribution of biomass in basaltic terrains has been noted in both fresh lava (Kelly et al. 2014) and in dispersed volcanic tephra of varying ages (Gentry et al. 2017). Factors that are likely to account for the observed heterogeneity in microbial biomass in volcanic materials include physical influences such as variations in the availability of fracture surfaces and pore/vesicle space for growth, differences in permeability and thus Sample Collection and Return from Mars.. Page 11 of 25 44 fluid flow through fractures, albedo and therefore tendency to absorb sunlight and heat; chemical factors such as the proportion of glass, heterogeneity in leaching of elements from the composite minerals or glasses available for redox couples or as nutrients, variations in the chemical weathering reactions mediated by constituent minerals and elements, differences in the kinetic release rates of elements from rocks (Cockell et al. 2011); and biological factors, e.g. priority effects, whereby first colonisers influence subsequent colonists (Lee et al. 2013). Some of these factors are known to be important determinants in the colonisation of soils (Garcia-Pichel et al. 2003; Vos et al. 2013; O’Brien et al. 2016). These observations across a variety of volcanic materials emphasise the need for appro- priate sample size. It is not possible to state an exact size, since the optimal sample size depends on the material. However, the presence of organisms inhabiting millimetre-scale vesicles, crystals and fractures in many volcanic materials shows that samples with integrity at centimetre scales are required. 4 Microorganisms Are Heterogeneously Distributed—the Need for Appropriate Sample Size These observations of cm3 scale samples or segments of samples devoid of life even in materials on Earth, such as obsidian, shows that typical mini- mum sample sizes of volcanic rock collected in the field for microbiological analysis should be of size ∼10 cm3 and this sample size applies to Mars exploration. 5 Every Sample Is a ‘Microbial Island’—the Need for Multiple Samples from the Same Material Type Although particular volcanic materials host distinct types of community, variations occur within those communities at small scales. Thus, multi- ple samples are required to investigate microbial diversity. In image B, cluster analysis of glass microbial communities was based on DGGE (30–70% denaturant) community fingerprints. The Jaccard UPGMA den- drogram was generated from the presence-absence matrix in GelComparII. Values at nodes represent cophe- netic correlations. Pal represents basalt glass samples from Valafell, Obs represents rhyolitic glass/obsidian samples from Dómadalshraun. Samples ending in C are composites for the given site (data from Kelly et al. 2010, 2011). Note that obsidian and basalt glass samples tend to cluster into two separate groups, but within each group, the microbial community of each individual sample is distinctive Fig. 2 Diversity varies across materials, but also between samples of the same material. (A) Microbial di- versity of basaltic glass and obsidian. (B) Each sample is a ‘microbial island.’ DGGE (Denaturing Gradient Gel Electrophoresis) shows that each rock hosts a distinct community. Although particular volcanic materials host distinct types of community, variations occur within those communities at small scales. Thus, multi- ple samples are required to investigate microbial diversity. In image B, cluster analysis of glass microbial communities was based on DGGE (30–70% denaturant) community fingerprints. The Jaccard UPGMA den- drogram was generated from the presence-absence matrix in GelComparII. Values at nodes represent cophe- netic correlations. Pal represents basalt glass samples from Valafell, Obs represents rhyolitic glass/obsidian samples from Dómadalshraun. Samples ending in C are composites for the given site (data from Kelly et al. 2010, 2011). Note that obsidian and basalt glass samples tend to cluster into two separate groups, but within each group, the microbial community of each individual sample is distinctive These published findings suggest that certain factors reliably influence microbial di- versity, but that combinations of local environmental factors, such as specific mineralogy and age, uniquely determine the microbial community in any given environment making the a priori prediction of which organisms will colonise a given type of environment dif- ficult to achieve. These factors are compounded by biogeographical stochasticity caused by the variations in local microbial populations and their dispersal (Whitaker et al. 2003; Fierer and Jackson 2006). With respect to sample collection, a notable observation is that in all these studies indi- vidual samples of the same material exhibit variations in microbial diversity (Fig. 2). 5 Every Sample Is a ‘Microbial Island’—the Need for Multiple Samples from the Same Material Type Like biomass, the microbial diversity of volcanic materials varies enormously as a function of physical, chemical and biological factors that relate to the functional requirements of life in that environment and/or the specific organisms that first successfully colonise the material. Microbial diversity is significant to the search for life on Mars independent of biomass. For example higher-diversity environments could include more organisms with particularly good preservation potential compared with lower-diversity environments simply because such environments contain a larger cross-section of microbial taxa. For an extant biota, microbial diversity provides critical information about the range of functional capabilities that an environment can support and so diversity can be used as a measure of the habitability of any given environment. Studies have been undertaken on the diversity of volcanic rocks to investigate the role of elemental composition in their colonisation. For example, statistically significant differences were observed in the microbial diversity between basaltic and more silica-rich obsidian glass in Iceland and between basaltic and more silica-rich rhyolitic rocks in juxtaposed locations where environmental factors were unlikely to influence the results (Kelly et al. 2010, 2011). It is now well established that gradients in both physical parameters such as temperature (Soo et al. 2009) and chemical parameters such as pH and sulphur content (Benson et al. 2011) cause small-scale variations in microbial diversity in volcanic environments. These spatial variations in microbial diversity are observed in all volcanic environments investi- gated (Table 1) ranging from geothermal fumaroles (Soo et al. 2009; Benson et al. 2011; Wall et al. 2015) to weathered exposed crystalline and glassy volcanic rocks (Herrera et al. 2009; Kelly et al. 2010, 2011), ash and soils (Gomez-Alvarez et al. 2006; Ibekwe et al. 2007), and mud volcanoes (Huang et al. 2016; Dahigaonkar and Chavan 2018). Variations in the microbial ecology caused by temperature and geochemical spatial gradients were exam- ined in detail in a geothermal setting in Iceland, where differences in microbial phylogeny, function and their associated isotope fractionation values were found in single geothermal outflows (Cousins et al. 2018). 44 Page 12 of 25 C.S. Cockell et al. Fig. 2 Diversity varies across materials, but also between samples of the same material. (A) Microbial di- versity of basaltic glass and obsidian. (B) Each sample is a ‘microbial island.’ DGGE (Denaturing Gradient Gel Electrophoresis) shows that each rock hosts a distinct community. 5 Every Sample Is a ‘Microbial Island’—the Need for Multiple Samples from the Same Material Type In that sense, we can regard each rock or sample as a microbial island. As sample size becomes smaller, especially in outcrops where rock heterogeneities are on a smaller scale compared to sample size, one might expect that diversity differences could increase as smaller patches of colonies are targeted. At large scales, biogeographical factors (such as environmental differences) will come into play. Thus, within any given sample size, physical, chemical and biological factors are likely to make it extremely unlikely that two samples will exhibit exactly the same microbial diversity. Sample Collection and Return from Mars.. Page 13 of 25 44 As with biomass, much of the diversity of surface volcanic environments on Earth is ei- ther directly influenced by the oxygenated environment on Earth (e.g., containing aerobic microorganisms) or indirectly (e.g., the presence of electron donors such as organic matter or electron acceptors such as sulfate or oxidised iron). Some of these factors are irrelevant for Mars (such as widespread oxic conditions), while others are relevant; for example, al- though Mars is generally anoxic, it does host very abundant sulfate and iron oxides (Gendrin et al. 2005; McSween et al. 2009; Grindrod et al. 2012). Extrapolating a theoretical pattern of colonisation of Martian volcanic materials is not possible, since Martian volcanic mate- rials are in some sense uniquely Martian. However, the general lessons we suggest about these environments on the Earth (such as heterogeneous microbial biomass and diversity) would be applicable since physical, chemical and biological factors will influence microbial colonisation of rocks at sub-millimetre to kilometre scales, even if the specific concatenation of those factors was uniquely Martian. From the point of view of sample collection, these observations emphasise the need for multiple samples to gain statistically meaningful insights into microbial diversity and its variation. These conclusions also apply to the search for relict biomarkers. Indeed, the vari- ation in microbial diversity even at single sample level suggests the conjectural possibility of a rare organism producing a preservable biomarker that was present in one sample, but not another. In Hawai’ian basalts, lipid biomarkers have been shown to vary between samples, illustrating how heterogeneity in microbial diversity also translates into heterogeneity in preservable biomarkers (Brady et al. 2017). Different molecular biomarkers have also been shown to vary in distribution even within the same samples over centimetre scales (Gentry et al. 2017). 6 More Hydrological Activity Does Not Imply Greater Microbial Biomass or Diversity—Select Samples in a Non-discriminatory Way An implicit assumption in Mars sample selection is the notion that where there is more water or more sustained water, there is likely to be more life. This paradigm has been en- couraged by the maxim, ‘follow the water’ (Hubbard et al. 2002). Although the notion that longer-lived hydrothermal systems or lakes are more likely to sustain long-lived habitable conditions and therefore higher biomass and more diverse microbial communities makes in- tuitive sense, countervailing results can be observed in many volcanic environments (Fig. 3). The results of the NASA BASALT study in Hawai’i showed several significant results with respect to Mars sample collection. The hypothesis that active fumaroles (locations where meteoric or magmatic water circulates through active geothermal regions) would be sites of enhanced microbial diversity (since high water availability and the presence of di- verse elements in solution would be conducive to life) was not supported (Cockell et al. 2019). Of all sample types, active fumaroles had the lowest diversity. One hypothesis to explain the relatively low diversity of bacterial communities within active fumaroles is that their high temperatures might prohibit colonisation by certain taxa. High temperatures in geothermal settings have previously been found to restrict microbial diversity compared to more mesophilic environments. Sharp et al. (2014) found that in geothermal environments, peak diversity occurred at 24 ◦C. Thus, merely picking sites that appeared to have hosted active hydrothermal systems may not a priori guarantee samples with the highest biologi- cal potential. Similarly low diversities are observed in other volcanic Mars-analogue sites where physical and chemical extremes, for example in volcanic lakes, limit life (Hynek et al. 44 Page 14 of 25 C.S. Cockell et al. Fig. 3 Both the abundance and diversity of microorganisms do not necessarily correlate directly with the hydrological cycle. Investigation of different volcanic materials in Hawai’i by the NASA BASALT project. The materials are: Active fumaroles (material exposed to active venting within a fumarole), active intermedi- ate (material from the periphery of one of the active fumaroles), intermediate fumarole (material associated with fumaroles showing low levels of activity and/or transient activity, with temperatures between 30–70 ◦C), relict fumarole (material associated with an inactive fumarole), unaltered (material associated with unweath- ered basalt), syn-emplacement (material associated with basalt altered during its emplacement primarily by magmatically associated water and gas or meteoric water associated with the heated environment around the lava). 6 More Hydrological Activity Does Not Imply Greater Microbial Biomass or Diversity—Select Samples in a Non-discriminatory Way The data in (A) show that microbial abundance is highly variable and not correlated with material type and its exposure to water. Image B shows microbial diversity in the different materials at phylum level. Image C shows the microbial diversity of the materials as three different measures of diversity (Observed, Chao 1 and Shannon diversity). Note that relict fumaroles have higher overall bacterial diversity than active fumaroles, but this trend was not obvious for archaeal communities, with one phylum, Crenarchaeota, only occurring in the active fumaroles (D). Data from Cockell et al. (2019) Fig. 3 Both the abundance and diversity of microorganisms do not necessarily correlate directly with the hydrological cycle. Investigation of different volcanic materials in Hawai’i by the NASA BASALT project. The materials are: Active fumaroles (material exposed to active venting within a fumarole), active intermedi- ate (material from the periphery of one of the active fumaroles), intermediate fumarole (material associated with fumaroles showing low levels of activity and/or transient activity, with temperatures between 30–70 ◦C), relict fumarole (material associated with an inactive fumarole), unaltered (material associated with unweath- ered basalt), syn-emplacement (material associated with basalt altered during its emplacement primarily by magmatically associated water and gas or meteoric water associated with the heated environment around the lava). The data in (A) show that microbial abundance is highly variable and not correlated with material type and its exposure to water. Image B shows microbial diversity in the different materials at phylum level. Image C shows the microbial diversity of the materials as three different measures of diversity (Observed, Chao 1 and Shannon diversity). Note that relict fumaroles have higher overall bacterial diversity than active fumaroles, but this trend was not obvious for archaeal communities, with one phylum, Crenarchaeota, only occurring in the active fumaroles (D). Data from Cockell et al. (2019) 2018). The NASA BASALT study found that as fumaroles transition to a relict state, aver- age alpha diversity increases. This could be explained by the development of less extreme temperature conditions, even though the potential flux of bioavailable nutrients in fumarolic water is reduced. 2018). The NASA BASALT study found that as fumaroles transition to a relict state, aver- age alpha diversity increases. This could be explained by the development of less extreme temperature conditions, even though the potential flux of bioavailable nutrients in fumarolic water is reduced. 6 More Hydrological Activity Does Not Imply Greater Microbial Biomass or Diversity—Select Samples in a Non-discriminatory Way Despite these findings, fumarolic environments can harbour a diversity of extremophiles in extreme deserts where water flow is enhanced compared to persistently dry environments that surround them (Costello et al. 2009; Soo et al. 2009; Wall et al. 2015) and although extreme physical conditions can limit diversity, fumaroles are nevertheless high priority sites for sample collection and for biological material that may yield insights into deep-branching thermophilic lineages. Sample Collection and Return from Mars.. Page 15 of 25 44 The complexity of sample selection is exacerbated by the fact that the most diverse biota may not always be the most likely to produce long-lasting biosignatures. For example, al- though active fumaroles studied by NASA BASALT had the lowest overall bacterial diver- sity, they contained the most diverse populations of archaea (Fig. 3; Cockell et al. 2019). Ether-bound intact polar lipids found in archaea are believed to be more stable than ester- bound bacterial lipids and thus expected to survive longer over geological timescales (e.g. Harvey et al. 1986; Logemann et al. 2011). A preferential survival of archaeal lipids could theoretically mean that the active fumaroles would leave a more detectable signature of past life than other locations. The possibility for a lack of correlation between microbial biomass, diversity and preservation potential emphasises the need for multiple samples from diverse hydrological regimens. From the point of view of Mars sample collection, however, the lesson is clear. Ap- parently intuitive ideas may not be borne out by microbial ecology and therefore sample collection on Mars should be informed by terrestrial ecology. Predicting how biomass and diversity would be influenced by a series of diverse hydro- logical regimes in any given local environment is problematic. Although the paradigm of collecting from more hydrologically active environments is merited, the results from the NASA BASALT project show that ideally a large number of samples from different hydro- logical regimens should be collected to maximise the chance of finding rock materials that could have potentially hosted the highest biomass and diversity. These observations on microbial diversity in volcanic environments on Earth suggest that rather than ‘follow the water’ the overall strategy should be the more cumbrous, but more accurate: ‘follow the water to large-scale environments that have been exposed to long-lived hydrological cycles, but collect across all hydrological gradients within that area’. 7 Short-Lived or Recently Formed Habitats May Contain Low Biomass and Diversity There are very few studies that examine the microbial communities associated with newly formed volcanic materials that can be considered analogous to young materials on Mars or volcanic materials that experienced transient interactions with liquid water. In gen- eral, microbial biomass and diversity increases over time in the first years after coloni- sation of a lava flow, but most studies have focused on lava flows many tens or even hundreds of years old. Over these time periods, it is known that volcanic terrains on Earth make felicitous places for microbial colonisation. It has been known for a long time, particularly from studies before the use of molecular biology, that volcanic mate- rials are colonised early by oxygenic photosynthesisers such as algae and cyanobacteria (Kristinsson 1970, 1974; Schwabe 1970; Schwabe and Behre 1972; Brock 1973; Englund 1976; Henriksson and Henriksson 1982; Adamo and Violante 1991; Adamo et al. 1993; Carson and Brown 1978; Fermani et al. 2007; Stefansdottir et al. 2014). Other studies have also shown lithotrophs as early components of volcanic communities, such as organ- isms that oxidise volcanically-derived CO and H2 (King 2003; Dunfield and King 2005; Nanba et al. 2004). Dunfield and King (2005) showed that the diversity of CO-oxidisers (based on amplification of coxL genes) was low in a recent (42 years old) lava flow in Hawai’i, but lava between 108 and 300 years old had similar diversity. In volcanic environ- ments where CO and sulphur gases (e.g., H2S, SO2) are actively emitted, chemoautotrophic primary production in newly formed volcanic rocks may ultimately generate organic carbon sufficient to sustain heterotrophs. C.S. Cockell et al. 44 Page 16 of 25 Fig. 4 Newly formed materials and those exposed to transient habitability contain highly heterogeneous, low-diversity populations. The newly formed lava flows of the Fimmvörðuháls lava flow, Eyjafjallajökull, Iceland in 2010 were colonised within 3 to 5 months by a low diversity biota. (A) Location of lava flows in Iceland (arrow), (B) Map of lava flows showing sample sites 1, 5 and 9 from which diversity analy- sis was undertaken, (C) Microbial abundance measured as direct cell counts at sample sites (error bars are standard deviation) taken on July 5 and August 31, 2010 showing heterogeneity. (D) Microbial diversity at phylum level shows communities dominated by Proteobacteria (specifically Betaproteobacteria). ‘J’ samples are samples collected in July; ‘A’ samples are samples collected in August. 7 Short-Lived or Recently Formed Habitats May Contain Low Biomass and Diversity ‘Weathered’ samples are samples from the basaltic Hnausahraun lava flow, erupted circa 150–300 A.D. and is given for comparison. ‘Others’ phylum refers to other phyla, each represented by a maximum of two clones in any Fimmvörðuháls library (data from Kelly et al. 2014) Fig. 4 Newly formed materials and those exposed to transient habitability contain highly heterogeneous, low-diversity populations. The newly formed lava flows of the Fimmvörðuháls lava flow, Eyjafjallajökull, Iceland in 2010 were colonised within 3 to 5 months by a low diversity biota. (A) Location of lava flows in Iceland (arrow), (B) Map of lava flows showing sample sites 1, 5 and 9 from which diversity analy- sis was undertaken, (C) Microbial abundance measured as direct cell counts at sample sites (error bars are standard deviation) taken on July 5 and August 31, 2010 showing heterogeneity. (D) Microbial diversity at phylum level shows communities dominated by Proteobacteria (specifically Betaproteobacteria). ‘J’ samples are samples collected in July; ‘A’ samples are samples collected in August. ‘Weathered’ samples are samples from the basaltic Hnausahraun lava flow, erupted circa 150–300 A.D. and is given for comparison. ‘Others’ phylum refers to other phyla, each represented by a maximum of two clones in any Fimmvörðuháls library (data from Kelly et al. 2014) Where studies on the early (less than a year old) colonisation of volcanic terrains have been undertaken, they have shown the extremely low diversity that is often sustained by new volcanic materials, even on Earth, where atmospheric inoculation occurs and microbially- accessible organic carbon is available. A study of the early colonisation of Icelandic lava flows showed that within three months after the eruption of Eyjafjallajökull in 2010, coloni- sation had occurred (Fig. 4) (Kelly et al. 2014). Biomass in some sites was low, but at others exceeded 106 cells/g dry weight (Fig. 4) in samples of ∼50 cm3. Nevertheless, the diver- sity was low and was dominated by Betaproteobacteria, in contrast to older lava flows that typically contain an order of magnitude more biomass and have higher abundance of Aci- dobacteria and Actinobacteria (Kelly et al. 2010, 2011; Byloos et al. 2018). 8 Is It Possible for Samples to Be Habitable, but Devoid of Life? Is there a possibility of collecting samples on Mars that fully satisfy the conditions for hab- itability but are devoid of a biota? If Mars never hosted an origin of life or a transfer of life to that planet then all environments that have energy sources, CHNOPS elements and liquid water and are habitable by terrestrial standards would be devoid of life. However, even if Mars has hosted life, transient habitats such as near-surface water melted by impacts could be devoid of life if that habitat remained disconnected from inhabited regions (Cock- ell 2011). If sample collection is undertaken within a confined area (for example, a single impact crater or outflow channel), the possibility of sampling a once habitable, but never inhabited palaeoenvironment is conceivable. As we cannot quantify this likelihood in the absence of a knowledge of life on Mars, this theoretical possibility would suggest that col- lecting samples from different environments, not merely within the same local environment but across much wider areas, should be a priority to maximise the chances of collecting samples containing life (Cockell and McMahon 2019). It is important to note that if Mars was lifeless, this strategy will also strengthen the conclusion that the planet was lifeless by multiplying the number of sampled habitable environments that can be shown to be devoid of life. An important distinction is whether uncolonised regions in a sample are devoid of life because they lack some fundamental requirement for life making them uninhabitable, or whether they are habitable zones that can support life, but they have not yet been colonised. For example, uncolonised regions of obsidian studied by Herrera et al. (2008) are likely uncolonised because of the lack of freely available iron. In other words, they may be unin- habitable. On Earth, habitable samples devoid of life at the centimetre scale do seem to be rare. As organisms reproduce, fluid flow tends to carry them into new habitable spaces so that at micron-scales, some part of that habitable space is colonised. Although not all habitable space will be colonised, the movement of microbes does lead to the ecological reality that when habitable samples are examined at centimetre scales, they usually contain life. 7 Short-Lived or Recently Formed Habitats May Contain Low Biomass and Diversity Although some of the organisms on the fresh lava may have used organic material atmospherically delivered to the surface of the lava flows, the presence of chemoautotrophic members of the Thiobacil- lus genus suggested that some of the population may have used iron and sulphur from the primary volcanic materials (Kelly et al. 2014). It is a significant point that arguments about the evolutionary likelihood of particular metabolisms on Mars (i.e. whether it is relevant to discuss searching for biomarkers of the relatively biochemically and evolutionarily advanced oxygenic photosynthesis compared to chemolithotrophic metabolisms) are irrelevant to the points made in this paper. All metabolic Sample Collection and Return from Mars.. Page 17 of 25 44 and taxonomic groups of microorganisms examined on early lava flows on Earth have shown a heterogeneous distribution with a low biomass and diversity. These observations empha- sise the points in Sects. 4–6. If volcanic materials have not been exposed to long-lived hydrological regimens and mature microbial communities have not been established, then the heterogeneous distribution of biomass and diversity may be exacerbated by overall low biomass, emphasising the need for multiple samples and suitable sample size. 8 Is It Possible for Samples to Be Habitable, but Devoid of Life? Real examples on Earth of pervasive centimetre-scale habitable samples devoid of life are recently formed lava flows in which hours to days after cooling to below the upper temperature limit for life, microbes are so heterogeneous and sparse that at centimetre scales some rocks remain uncolonised, particularly those beneath the surface of the flow that have not been subject to atmospheric colonisation (Cockell 2014). These ecological considerations lead to relevant observations. In general, where life has accessed an environment, fluid flow ensures that even though space can be habitable but unoccupied, at macroscopic centimetre scales samples generally contain examples of life. In environments where habitable conditions were extremely transient, this assumption may break down and habitable samples devoid of life at centimetre scales may be prevalent. In the specific case of Mars, if the planet was lifeless or the biomass extremely localised to 44 Page 18 of 25 C.S. Cockell et al. certain regions, entire regions or environments may be habitable but devoid of life. Large samples suites are required to test these hypotheses. certain regions, entire regions or environments may be habitable but devoid of life. Large samples suites are required to test these hypotheses. An important question is how many samples are minimally required to determine that a given material is devoid of life in all examples of that material. On the Earth, a high level of biological confidence might be obtained by showing that life was not present in three sets of three triplicates of such a material across one location with this sample set repeated across three geographically separated regions of that material, whether on the surface or subsurface. It may never be possible to demonstrate conclusively that Mars has always been lifeless, since short-lived, localised pockets of life could have left scant or undetectable evidence, or no evidence at all. However, if the sampling regimen described in the previous paragraph was deployed across the geological records of diverse palaeohabitats with good potential to preserve biosignatures (e.g., lake sediments, evaporitic deposits, and hydrothermal sinter deposits) and no evidence of life was found, the balance of evidence would shift in favour of the hypothesis that Mars has never been inhabited. In principle, a Bayesian approach could be developed to model this shift; these statistical issues merit greater attention. 9 A Strategy for Sample Collection on Mars In this section, we summarise six recommendations for sample collection on Mars based on observations of the microbial ecology of volcanic materials on Earth. We provide a brief rationale for each. The strategy does not take into account cost, mass, or space restrictions associated with specific missions such as robotic Mars sample return missions (Sherwood et al. 2003; MEPAG 2008; iMOST 2018), but rather provides an insight into a biologically ideal sample suite, whether it be collected by robot or human explorers. 9.1 Collect Sufficiently Large Samples Heterogeneity in microbial biomass and diversity has been observed in all volcanic materi- als. These effects are likely to be caused by physical, chemical and biological influences that will vary in different samples. ‘Sufficient’ size cannot be easily quantified, but observations on volcanic rocks discussed here suggest that typical sample sizes should be a minimum 10 cm3 to retain millimetre-scale vesicles, fractures and mineral grains and their associ- ated biological targets. Defining ideal samples based on mass is less important than volume. For example, a lower density sample can contain more pore space for potential microbial colonisation than a higher density sample, counterintuitively making a lighter sample of comparable volume potentially more valuable to a biologist than a more massive sample. Less is sometimes more. Less is sometimes more. 9.4 Collect Across Varied Hydrological Regimes ‘Follow the water’ is broadly a correct view with respect to the fundamental requirement that all known life has used liquid water as a solvent. However, microbial ecology shows that lo- cations with a high abundance of liquid water do not always harbour the most biomass and diversity. As we have discussed here, in volcanic hydrothermal regimens, high temperatures can limit life to lower biomass and diversity than drier locations at more mesophilic tem- peratures. It is well known that in some locations liquid water can even be uninhabitable. For example, on the Earth, magnesium chloride brines can have water activities so low as to be uninhabitable (Hallsworth et al. 2007) and such brines may exist on Mars. The lessons from volcanic environments show that sampling should be carried out across hydrological gradients and not merely in locations that appear to have hosted the most vigorous hydro- logical regimes. Transects capture the variation in the interaction between geochemistry and physical conditions that can influence habitability in a way independent of the quantity of liquid water. ‘Follow the water’ is broadly a correct view with respect to the fundamental requirement that all known life has used liquid water as a solvent. However, microbial ecology shows that lo- cations with a high abundance of liquid water do not always harbour the most biomass and diversity. As we have discussed here, in volcanic hydrothermal regimens, high temperatures can limit life to lower biomass and diversity than drier locations at more mesophilic tem- peratures. It is well known that in some locations liquid water can even be uninhabitable. F l h E h i hl id b i h i i i l 9.5 Maintain Sample Integrity Cells are distributed heterogeneously and their locations provide information on the factors that control life (e.g. presence of iron-bearing crystals, alteration rinds, fracture networks). It is therefore essential to maintain sample integrity. Where possible they should be collected with minimal damage caused by drilling, excavation etc. Sample integrity also includes the need to collect aseptically to avoid external biological contamination. 9.3 Collect Samples of the Same Material from Different Locations Following directly from point (2) is the recognition that the heterogeneity in the biomass and diversity of life is related to large-scale biogeographical influences. It is therefore important to collect samples of the same material, but from different locations separated by ∼kilometre distances. This allows for stronger statistical statements about the distribution of life over large scales. If true replication is to be achieved, avoiding the pitfall of pseudo-replication by sampling the same region, then the sample suite discussed in point (2) must be repeated in three completely geographically separated regions of the same material, yielding 27 sam- ples in total of a given sample type. If a habitable environment was transient, this strategy maximises the chances of obtaining life-bearing rocks or being able to conclude with greater confidence that all such materials in all geographical locations are devoid of life. 9.2 Collect Sufficiently Many Samples Heterogeneity in samples, particularly in those where habitability is short-lived, results in high standard deviations in biomass and diversity. Statistically, to derive meaningful state- ments on the distribution of life, multiple samples should be collected. Three samples is a typical statistical minimum. However, microbial ecological analysis yields suggestions on preferred numbers. For example, based on sample strategies used to investigate het- erogeneities in low biomass volcanic rocks (Kelly et al. 2014) sample collection numbers such as nine provide for a more comprehensive analysis, made up of three independent Sample Collection and Return from Mars.. Page 19 of 25 44 sets of three triplicates from the same material at regional scale. Additional samples add to the robustness of the study, but might be limited by field time and cost. If environ- ments are devoid of life, large sample sizes can increase the robustness of the conclu- sion that they were never inhabited. These sample number recommendations do not take into account separate samples used in other studies such as geology, atmospheric history and investigations for future resource use that might be collected in the limited sample sets envisaged for robotic Mars sample return (e.g., Sherwood et al. 2003; MEPAG 2008; iMOST 2018). 10 Conclusions Mars is a planet of volcanically derived materials. The search for life on Mars and the study of the distribution of habitable conditions is therefore greatly advanced by investigating the microbial ecology of similar environments on Earth where biomass and diversity can be directly quantified and related to environmental variables with a statistically high level of confidence. Keeping in mind environmental differences between present-day Earth and Mars, one purpose of this paper has been to provide a review of well-studied volcanic ma- terials and their enclosed biota. We have used volcanic environments on Earth to extract general patterns of microbial growth that are applicable across many types of volcanic ma- terial. Using these patterns, we suggest principles of sample collection that, combined with appropriate taphonomic considerations, will yield maximum information for astrobiologists and planetary scientists. These principles apply to robotic exploration and to the human exploration of the planet. Ultimately, to be able to test hypotheses with high statistical con- fidence, sample sets with sufficient coverage and diversity, exploration across large scales, and multiple replicates are required. Acknowledgements This paper was made possible by support from the Science and Technology Facilities Council (STFC). Grant: ST/R000875/1. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 Inter- national License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 9.6 Minimise Post-Collection Modifications Once collected, samples should receive minimal alteration. 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NARRATIVA, MITO, CIÊNCIA E TECNOLOGIA: O ENSINO DE CIÊNCIAS NA ESCOLA E NO MUSEU
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Volume 02 / Número 1 – Març. 2002 Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências NARRATIVA, MITO, CIÊNCIA E TECNOLOGIA: O ENSINO DE CIÊNCIAS NA ESCOLA E NO MUSEU Maria Cristina Leal1 Guaracira Gouvêa2 Mostramos neste artigo as possibilidades e a necessidade de se trabalhar a alfabetização científica, integrando ensino formal, não-formal e divulgação científica. Entendemos que a perspectiva de alfabetização científica está diretamente vinculada ao ensino com base nas relações Ciência, Tecnologia e Sociedade - CTS. Após uma breve resenha do significado de alfabetização científica e CTS, ressaltamos a importância de se articular narrativa, mito, ciência e tecnologia no ensino de ciências. Nos apoiamos em uma sondagem feita com 108 professores participantes de um curso, 18 participantes de um seminário e 12 observações de turmas em visita a um museu de ciências para retratar, de um lado, as possibilidades que os professores vislumbram de se trabalhar ciências via CTS e, de outro, as incoerências que emergem quando certos conteúdos escolares são explorados na visita de alunos a um museu de ciências. 1 Fac. Educação, UFF 2 Depto Educação, Mast Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 “(...) Conferimos as mais recentes tecnologias que as empresas estão desenvolvendo... Vimos doenças erradicadas, viagens a outros planetas, deficientes tendo uma vida melhor, plantas mais nutritivas e abundantes. Encontramos crianças estudando a centenas de quilômetros dos professores, computadores que vêem e falam, materiais ultra-eficientes, energias limpas e muito baratas” (França et al., 1999:37). Além do espaço reservado para essa discussão na mídia, observa-se a crescente penetração desse debate nos livros didáticos e materiais paradidáticos. um fato a destacar é que, nos parâmetros curriculares nacionais, elaborados pelo mec (parâmetros curriculares nacionais, ciências naturais, 5ª a 8ª séries, brasília, mec, 1998), tanto os do ensino fundamental como os do ensino médio, uma das diretrizes apontadas é a necessidade de se colocar, no currículo, o debate entre ciência, tecnologia e sociedade. Tambem vale destacar “que a ciencia esta cada vez mais incorporada ao cotidiano das pessoas, mas poucos continuam tendo acesso a sua forma de organização e ao seu corpo de conhecimento”. assim, “as ciencias naturais, enquanto patrimonio da humanidade, parte da cultura universal, tem justificado sua inclusão no curriculo escolar; por outro lado, não tem garantido que os alunos passem a identificar este conhecimento como um instrumental possivel de analise e interferencia no universo que os cerca” (pierson e hosoume, 1997: 87). A dimensão pública do impacto da C&T na sociedade nos levou a pensar na necessidade de uma pesquisa que se debruçasse sobre a relação CTS na educação. A partir daí, produzimos o projeto “Ciência, Tecnologia e Sociedade no contexto da alfabetização científica”, o qual foi desenvolvido de 1997 a 1999 com o apoio da Finep, do CNPq e da Faperj. Seu objetivo foi identificar e analisar as narrativas que, em contextos de ensino-aprendizagem formal e não-formal, discutissem a relação CTS, visando à formação do cidadão por meio da escola e do museu. Na sua primeira etapa, a pesquisa esteve centrada, de um lado, no levantamento de informações sobre as visões dos professores (de ciências e de outras disciplinas) a respeito da possibilidade de se trabalhar a educação científica e tecnológica na escola através do estabelecimento da relação CTS. ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 De outro lado, foi realizado um trabalho de observação de visitas de professores à exposição permanente do Museu de Astronomia e Ciências Afins (Mast/MCT), além de seminários para professores, com a finalidade de se dimensionar a relação entre educação formal e não-formal. O objeto da pesquisa - narrativas em CTS no ensino formal e não-formal, visando à alfabetização científica - mostrou a importância de discutirmos a relação entre narrativa, mito, ciência e tecnologia. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 INTRODUÇÃO O espaço dedicado, atualmente na mídia, à divulgação científica, por meio de filmes e programas de TV, artigos de jornais e revistas, pode-nos dar a dimensão da importância que a ciência e a tecnologia têm no processo de transformação do mundo de hoje. Alguns desses veículos apresentam e discutem temas que permitem ao grande público conhecer certa dimensão dos problemas e das transformações a serem enfrentados em face do uso exacerbado da tecnologia. Entre eles, vale mencionar o bug do milênio, o qual faria com que o computador confundiria os dois últimos algarismos do ano 2000 com os do ano 1900, provocando problemas de diversos tipos e prejuízos calculados em US$600 bilhões. Exemplos de problemas potencialmente gerados pelo bug do milênio são os satélites que sincronizam algumas usinas elétricas e o processo de transferências internacionais de fundos. Se o problema não fosse solucionado a tempo, as usinas deixariam de funcionar e a contagem de tempo, para transferência de fundos, se não fosse computada em segundos (como deve ser), seria em anos, o que acarretaria cobrança de juros que poderiam chegar à casa dos trilhões de dólares (Zuckerman, 1999: 3). Um artigo de divulgação científica, publicado na revista Época, pode indicar como a mídia elabora idéias sobre os tipos de transformações que a ciência e a tecnologia (C&T) apontam para o próximo milênio: Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 5 NARRATIVA Uma das formas de se apreenderem processos interativos a respeito de resultados de aprendizagens, que visem à ampliação do capital científico e tecnológico dos aprendizes. Consiste no levantamento de narrativas individuais e coletivas que expressem concepções de Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 6 6 Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências ciências e de seu ensino. Adotamos, para isso, o ponto de vista de Levine (1995), que defende, como meio válido de investigação, o estudo da narrativa coletiva de determinados grupos sociais: “(...) O exame de histórias disciplinares produzidas pelos praticantes dessas disciplinas revela uma variedade de formas de narrativas. Em alguns casos, elas enfatizam o valor do trabalho científico em seu campo, como quando louvam as realizações de grandes cientistas ou glorificam a ciência como atividade humana distintamente progressista. Em outros casos, valorizam certas direções no trabalho científico, como quando reforçam uma determinada abordagem científica ou anunciam uma transformação conceitual no campo. Outras ainda servem para demarcar as fronteiras de um domínio intelectual, como quando celebram o surgimento de uma nova disciplina ou descrevem conexões com sistemas filosóficos antecedentes” (Levine, 1995: 22). A reflexão de Levine sobre as narrativas nos inspirou em dois sentidos. O primeiro foi buscar saber, mesmo que por meio de uma sondagem exploratória (uso de questionário), como os professores (sujeitos partícipes de histórias disciplinares) se posicionavam diante de um momento de transição entre uma perspectiva de ensino tradicional de ciências e a abordagem de ensino via CTS. O segundo indicou a necessidade de se reconstituir um pouco da origem do ensino de ciências na perspectiva de CTS. O valor da narrativa, nas pesquisas em ensino de ciências tende a crescer a partir de argumentos como os de Bruner (1996), para quem a ela constitui instrumento importante de compreensão do significado humano de aquisição de cultura. Para Bruner, a narrativa é um modo de pensamento que funciona por imagens, o qual não segue uma lógica linear, mas que é analógico e pode complementar o pensamento paradigmático (lógico-matemático ou científico). O pensamento narrativo consiste na prática de se contarem histórias a cada um para construir significados, dar sentido às nossas experiências. NARRATIVA Uma diferença marcante entre os modos de pensamento narrativo e paradigmático é que, no primeiro, a capacidade abstrata surge do interesse particular, daquilo que é inesperado, irregular, enquanto que, no segundo, privilegia-se o abstrato isto é, os aspectos conceituais mais universais e gerais. ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Volume 02 / Número 1 – Març. 2002 Como exemplo de mito na primeira acepção, trazemos à cena a narrativa tradicional chinesa: Yi e os dez sóis. Esta relata a existência de dez sóis que, de modo revezado, ordenado, forneciam calor e luz à Terra até que, um dia, resolvem trabalhar juntos e começam a destruir a Terra (desordem). Somente com a intervenção do imperador da China e de um hábil arqueiro, a ordem se restabelece pela eliminação de nove sóis e a manutenção de apenas um. A narrativa traz a marca da cultura e do poder para dar conta de fenômenos naturais que se movimentam de forma ordenada/desordenada. Para ilustrar a segunda acepção, recorremos a um trecho da análise de Barthes (1993) sobre o cérebro de Einstein: “... claramente o funcionamento do processo, Einstein fotografado ao lado de uma lousa coberta de signos matemáticos de uma complexidade visível, quer dizer, como se trabalha a imagem de Einstein sempre se referindo, tentando fazer e dar o significado da sua genialidade; Einstein desenhando, isto é, tendo entrado portanto na lenda, uma vez mais de giz na mão, acabando de escrever sobre uma lousa limpa, como se preparasse a fórmula máxima do mundo. A mitologia respeita assim a natureza das tarefas, a investigação propriamente dita mobiliza engrenagens mecânicas, tendo como sede um órgão material monstruoso, apenas por sua complicação cibernética, a descoberta pelo contrário da essência mágica simples como um corpo primordial.” ( Barthes, 1993: 61) Vemos, assim, a construção da representação do mito da genialidade por meio da capacidade máxima do homem de criar fórmulas capazes de decifrar os grandes segredos da natureza. O mito encontra-se presente no discurso científico, alimentando seus encantos e desencantos, as suas contradições. A vontade de se superar o mito, na sua positividade, faz-se presente na ciência quando esta recorre às perspectivas criacionistas (Big-Bang, Teoria do Caos etc.) para explicar racionalmente as nossas origens, evolução, relações. O mito também se apresenta na ciência quando esta passa a priorizar o poder e a alimentar a crença em sua onipotência. Para Chrétien (1994), a hegemonia da ciência, nas sociedades modernas, coloca-a na condição de assumir as funções cujos titulares ela expulsou, isto é, os mitos. ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Não tivemos aqui a intenção de esgotar, mas, sim, de introduzir uma discussão que entendemos necessária para os estudiosos da ciência e para aqueles engajados na perspectiva de educação em CTS. Consideramos necessário mencioná-la, pois ela orientou a primeira fase de realização da pesquisa. No caso da pesquisa, os modos de pensamento narrativo e paradigmático ganham sentido quando analisados no contexto da alfabetização científica e numa perspectiva de ensino em CTS. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 O MITO O mito é tomado aqui em duas acepções básicas. Na primeira, identificamos o mito como afirmação e nos reportamos às narrativas tradicionais que, por tempo bastante longo, foram transmitidas de geração a geração para dar explicações acerca da origem do homem, do mundo, da vida. Essas narrativas diversificadas e transpassadas pelas vozes das culturas, das religiões, do imaginário, das relações de poder, do gênero etc. apresentam em comum o fato de manipularem a emoção, a crença, os dogmas. Na segunda acepção de mito, encontramos a sua negação, despolitização e esvaziamento. Tal acepção é formulada por Barthes (1993), quando estuda as maneiras como a sociedade burguesa cria seus mitos a partir de características como despolitização, esvaziamento de contextos, simplificação, ingenuidade e harmonia. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 7 CIÊNCIA, TECNOLOGIA E SOCIEDADE NO ENSINO DE CIÊNCIAS O conceito de alfabetização científica pressupõe, em linhas gerais, uma discussão que envolve a comunidade científica, a educacional e os profissionais de comunicação sobre o que o cidadão comum sabe e deveria saber a respeito da relação CTS. Como o que o cidadão Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 8 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 comum sabe, ou deveria saber, a respeito dessa relação abrange, necessariamente, elementos ligados à sua formação e às informações disponíveis, essa discussão está situada no ensino de ciências praticado nas escolas e nos museus, na mídia e na Internet. Essas instâncias, dependendo de sua maior ou menor presença na sociedade, são as principais responsáveis pela formação da opinião pública a respeito de C&T. Ao definir o que é alfabetização científica, Shen (1975, apud Cazelli, 1992) estabelece três dimensões capazes de identificar o conceito a partir de variações em termos de objetivos, conteúdos, formas e público. A primeira é a dimensão prática, que habilita os indivíduos a resolverem problemas que exigem conhecimentos básicos; a segunda é a cívica, isto é, refere- se à consciência sobre os problemas e usos da C&T; a terceira é a cultural, que consiste na obtenção de conhecimentos de C&T aprimorados. Para Miller (1987), a alfabetização científica compreende a capacidade de o público entender os processos de investigação científica, as normas e os métodos da ciência, os temas científicos básicos e a consciência do impacto da C&T sobre a sociedade. Finalmente, para Arons (1983, apud Cazelli, 1992), o indivíduo científica e tecnologicamente alfabetizado é aquele capaz de (1) compreender a distinção entre observação e inferência, isto é, de realizar exames minuciosos de dedução e raciocínio, distinguir entre papel da descoberta acidental e estratégia deliberada de formulação de hipóteses e de entender, através de exemplos específicos, que os conceitos e as teorias científicas são mutáveis e provisórios e precisam, portanto, de permanente aperfeiçoamento; (2) reconhecer que os conceitos científicos são elaborados pela inteligência e imaginação humanas e que, para serem entendidos e aplicados, devem ser operacionalizados; (3) desenvolver conhecimentos básicos que possibilitem uma leitura inteligente e uma aprendizagem permanente, sem necessidade de recursos exclusivos do ensino formal; finalmente, (4) ser capaz de entender que a relação CTS envolve aspectos morais, éticos e sociais. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 CIÊNCIA, TECNOLOGIA E SOCIEDADE NO ENSINO DE CIÊNCIAS Para Barros (1990: 86), “a sociedade moderna exige de todos os seus cidadãos uma compreensão básica da ciência e da tecnologia, devido ao papel que estas possuem para a vida pessoal dos indivíduos. Trata-se, pois, de pensar na alfabetização científica de todos os integrantes da sociedade...” Morin (1996) e Angotti (1991) consideram que a sociedade deva ser alfabetizada científica e tecnologicamente para que tenha algum controle sobre o sistema ciência e tecnologia. A raiz deste debate é, no entanto, mais ampla e se localiza na relação CTS, questão complexa que vem sendo discutida por filósofos, sociólogos e educadores. Os primeiros têm-se dedicado, principalmente, a qualificar os conceitos de C&T, a estabelecer relações de dependência entre eles, a afirmar ou negar a possibilidade de a tecnologia ter autonomia em relação à ciência, a identificar e diferenciar os problemas metodológicos das pesquisas científicas e tecnológicas; a refletir sobre a capacidade da tecnologia de garantir o progresso ou de levar a humanidade à autodestruição. Já os sociólogos, a despeito de tratarem de algumas dessas questões, estão empenhados em discutir a fundo duas teses que, no campo da ciência social, se confrontam e antecedem qualquer outro tipo de debate sobre CTS. Trata-se do problema determinismo da sociedade sobre a tecnologia versus autonomia da tecnologia sobre a ordem social. Finalmente, os educadores centram-se na problemática de discutir se o ensino em CTS representa uma crítica ou um aperfeiçoamento às formas tradicionais de ensino de Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 9 9 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 ciências, se a abordagem científica por meio de CTS deve ser ou não institucionalizada na escola, com que objetivos e como deve ser tratada nos currículos e programas escolares. Da Filosofia da Ciência e da Tecnologia, cabe destacar que a relação CTS tem seus primórdios na sociedade moderna, na qual se situam os conhecimentos produzidos por Galileu e Newton. Fundamentados na Física e na Matemática, a observação e os dados ganham, por meio desses conhecimentos científicos, representações possíveis de serem mensuradas e logicamente aplicadas. Abre-se, a partir daí, a possibilidade de a tecnologia se firmar e se desenvolver, uma vez que ela consiste na “aplicação de vários conhecimentos científicos reunidos com vistas à realização de uma finalidade prática”. CIÊNCIA, TECNOLOGIA E SOCIEDADE NO ENSINO DE CIÊNCIAS (Rodrigues, 1997: 12) Na Sociologia, a discussão sobre a capacidade de a ciência e a tecnologia moldarem a sociedade ou de serem moldadas por ela não é recente e remonta aos primórdios da Revolução Industrial. Entre os deterministas tecnológicos atuais, encontramos Mcluhan (1967) e Robeens e Webster (1989). Segundo esses últimos, o uso do computador deverá transformar o mundo social em todos os níveis. Os críticos do determinismo tecnológico afirmam que os aspectos sociais e os temas políticos contam mais do que a tecnologia em si, pois importa saber principalmente “quem usa, quem controla, para que usa, como se amolda na estrutura de poder, como é expandida e distribuída a tecnologia”. (Finnegan, 1988: 176) Seja ou não a tecnologia o determinante da ordem social o fato concreto é que o debate sobre a relação entre elas se intensificou e ganhou contornos muito nítidos nos meios intelectuais e educacionais. No contexto do ensino, a complexidade dessa relação cresce em um mundo globalizado. Graças ao acentuado e acelerado progresso tecnológico, há uma exigência cada vez maior de cidadãos capazes de competências cognitivas específicas para administrar o cotidiano. Na escola, essas competências precisam ser oferecidas às novas gerações, o que exige reformulação na cultura escolar. Vale salientar que a idéia de cultura escolar pressupõe a transmissão de saberes, competências, formas de expressão, mitos e símbolos socialmente reconhecidos por meio de transposições didáticas, isto é, transmissão mediada da ciência do sábio, da obra do artista, do pensamento do filósofo nas matérias e disciplinas, nos exercícios e textos escolares etc. A transposição didática, por sua vez, impõe o aparecimento de configurações cognitivas específicas - saberes e modos de pensar tipicamente escolares (Forquin, 1993). Assim, coloca-se a questão de como inserir nas práticas educativas escolares o debate CTS. A relação educação e tecnologia é tema polêmico em voga entre educadores. Há correntes mais ajustadas aos interesses empresariais que entendem a escola como espaço de formação geral mínima para produção de trabalhadores flexíveis e propensos a serem rapidamente treinados e reciclados no próprio local de trabalho. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 No Brasil, a partir da década de 90, emergem elaborações sobre o conceito de alfabetização científica e tecnológica, apreendida por nós como o que o público deve saber sobre ciência, tecnologia e sociedade (CTS), com base em conhecimentos adquiridos em contextos diversos (escola, museus, revistas etc.), atitude pública sobre ciência e tecnologia, informações obtidas em meios de divulgação científica e tecnológica. As articulações entre ciência e tecnologia e sociedade por meio de práticas educativas, na escola e fora dela, definirão tipos de alfabetização científica e tecnológica; assim, nas escolas, o ensino de ciências e a divulgação científica nos meios de comunicação são elementos articuladores dessa relação. Esse enfoque do ensino de ciências há muito é discutido em vários países. Um dos estudiosos da questão, o pesquisador inglês Ziman é crítico do ensino tradicional fragmentado em disciplinas, com o propósito de transmitir uma “representação esquemática idônea de um grande repertório de observações e dados experimentais" (Ziman, 1985: 39), o qual, em geral, consegue apenas parodiar o processo real de investigação científica. Para ele o ensino de CTS deveria substituir o ensino tradicional, pois permitiria, de forma interdisciplinar (ciência, tecnologia, psicologia, história, filosofia, sociologia), romper a impressão unilateral do ensino tradicional. No seu entendimento, a principal meta do ensino de CTS deve ser a de “opor-se ao cientificismo e tecnocracia e rechaçar qualquer fórmula estreita que pretenda conhecer todas as perguntas e todos os problemas de nosso tempo”. (Ziman, 1985: 152) Outra estudiosa inglesa do movimento de CTS no ensino é Solomon (1993). Para ela, o ensino de CTS deve visar, sobretudo, ao desenvolvimento de atitudes para se enfocar e solucionar, de modo significativo, os problemas da aplicação da ciência na sociedade, além de se ensinar a compreender o modo como a ciência atua no contexto social. Solomon aponta, como características específicas de CTS na educação, a compreensão das ameaças ambientais para a qualidade de vida de todo o globo, a compreensão de que a ciência tem uma natureza falível, a discussão de opiniões e valores sociais para produção de ações democráticas e a dimensão multicultural de visão de CTS. O movimento de CTS no ensino não ficou restrito ao contexto inglês. CIÊNCIA, TECNOLOGIA E SOCIEDADE NO ENSINO DE CIÊNCIAS As correntes contrárias a essa visão não consideram que a escola deva fornecer o mínimo, mas algo próximo ao mínimo múltiplo comum, ou seja, garantir “(...) uma formação polivalente que capacite para desempenhar uma família de empregos qualificados e, sobretudo, para compreender as bases gerais, técnico-científicas e socioeconômicas de produção em seu conjunto, que reúna a aquisição de habilidades e destrezas genéricas e específicas com o desenvolvimento de capacidades intelectuais e estéticas; que unifique, em definitivo, formação teórica e prática”. (Enguita, 1988: 51) A relação educação e tecnologia é tema polêmico em voga entre educadores. Há correntes mais ajustadas aos interesses empresariais que entendem a escola como espaço de formação geral mínima para produção de trabalhadores flexíveis e propensos a serem rapidamente treinados e reciclados no próprio local de trabalho. As correntes contrárias a essa visão não consideram que a escola deva fornecer o mínimo, mas algo próximo ao mínimo múltiplo comum, ou seja, garantir “(...) uma formação polivalente que capacite para desempenhar uma família de empregos qualificados e, sobretudo, para compreender as bases gerais, técnico-científicas e socioeconômicas de produção em seu conjunto, que reúna a aquisição de habilidades e destrezas genéricas e específicas com o desenvolvimento de capacidades intelectuais e estéticas; que unifique, em definitivo, formação teórica e prática”. (Enguita, 1988: 51) 10 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 10 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Revela-se, na verdade, como a tendência dominante nos anos 90 e tem-se expandido para diversos países, dentro dos quais destacamos os projetos: PLON (holandês), SISCON e SATIS (britânicos), APQUA (Califórnia – EUA), e o Projeto 2001 (EUA), do qual originou-se o livro “Ciência para todos” (Rutherford e Ahlgren, 1995). No Brasil, dentre outros, destacam-se as experiências do Grupo de Reformulação do Ensino de Física – GREF-USP (1991) e Física – Coleção Magistério (1991). Nos EUA, por exemplo, uma das preocupações do movimento de CTS consiste em produzir “uma compreensão de conceitos científicos-chave que unifiquem as ciências com outras disciplinas e que dêem conta das interações entre CTS” (Rye, 1998: 3).Outra intenção da educação em CTS “é de fazer com que os estudantes fiquem mais motivados para aprender ciência e conduzir melhor os experimentos científicos” (Scharmann,1998: 3). Na Austrália o ensino de CTS é entendido de modo interdisciplinar (perspectiva de Ziman) e se preocupa em discutir as origens, a natureza e o impacto social da C&T (Hallingen, 1998: 2). Para Menezes (1988), Zanetic (1989) e Angotti (1991), os conhecimentos científicos, abordados nas escolas Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 11 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 brasileiras, constituem-se em fragmentos de uma ciência, descolados de qualquer outra área de conhecimento. Ao se inserir a discussão CTS no ensino de ciências, considera-se que “o aluno é um ser social, a apropriação do conhecimento científico como elemento importante na capacitação do sujeito para o pleno exercício de sua cidadania. O olhar da ciência enquanto parte importante da cultura, que, por direito, pertence ao aluno e por esta razão deve ser a ele devolvida, decodificada, leva a uma outra organização do conhecimento” (Pierson e Hosoume, 1997: 89). Realizar esse debate “não significa defender uma ciência do como funciona. A sociedade atual não é apenas tecnológica pelos aparatos e instrumentos que incorporou ao nosso dia-a-dia, mas, principalmente, pela forma através da qual passamos a ver e interpretar as coisas à nossa volta, as explicações que procuramos dar aos eventos, às profissões de fé que fazemos a cada momento” (Pierson e Hosoume, 1997: 88). Para Auler (1997), uma forma de se introduzirem temáticas na perspectiva CTS no currículo convencional são as intervenções curriculares e o trabalho sistemático de acompanhamento os quais podem fazer surgir conflitos. ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 “Conflitos, estes, que se estabelecem entre a satisfação de um trabalho diferenciado, reconhecido por professores e alunos, e as práticas rotineiras. Destes conflitos emergem espaços, aberturas, para alterações curriculares mais abrangentes”. (Auler, 1997: 191) No âmbito do ensino, é preciso mencionar as críticas dirigidas à introdução da CTS nos currículos escolares as quais atentam para o perigo de se utilizar o conhecimento sociológico como mais um mecanismo de controle e de reforço à valorização da C&T: “(...) Uma análise do discurso da educação CTS pode conduzir à previsão de profundas alterações na educação científica. É, sem dúvida, uma mudança, mas não é profunda. A educação CTS torna claras e sem ambigüidades as relações de poder entre categorias (discursos, agentes, agências), legitimando a função reprodutora da escola. O elevado estatuto e poder actualmente atribuídos à ciência e à tecnologia na sociedade são agora subtilmente introduzidos na escola. E a vez dada às ciências sociais, nomeadamente à sociologia, dentro e fora da escola, representa apenas, como foi dito, uma modalidade de controle que permite dar mais força à força da ciência e da tecnologia .”(Moraes, 1994: 97) “(...) Uma análise do discurso da educação CTS pode conduzir à previsão de profundas alterações na educação científica. É, sem dúvida, uma mudança, mas não é profunda. A educação CTS torna claras e sem ambigüidades as relações de poder entre categorias (discursos, agentes, agências), legitimando a função reprodutora da escola. O elevado estatuto e poder actualmente atribuídos à ciência e à tecnologia na sociedade são agora subtilmente introduzidos na escola. E a vez dada às ciências sociais, nomeadamente à sociologia, dentro e fora da escola, representa apenas, como foi dito, uma modalidade de controle que permite dar mais força à força da ciência e da tecnologia .”(Moraes, 1994: 97) O uso da inovação CTS para fins de reforço e de legitimação do status quo, sem dúvida, é um dos problemas a serem considerados quando se pensa num ensino em CTS. À medida que caminhamos em direção a uma perspectiva de ensino e de alfabetização científica e tecnológica com base na relação CTS, procede também a busca de integração entre modos de pensamento narrativo e paradigmático que levem em consideração, inclusive, o papel de pensamento mítico, gênese dos modos de pensamento anteriormente mencionados. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 contemporânea. Vale lembrar ainda que a tecnologia pode, em algumas circunstâncias, reforçar a ciência como mito e ser referência importante de organização da vida social. contemporânea. Vale lembrar ainda que a tecnologia pode, em algumas circunstâncias, reforçar a ciência como mito e ser referência importante de organização da vida social. METODOLOGIA Nossa investigação teve caráter exploratório e focalizou fragmentos de narrativas de professores, profissionais do MAST – Museu de Astronomia e Ciências Afins e alunos que participam de processos de alfabetização científica e tecnológica. Nas escolas e nos cursos de atualização e aperfeiçoamento de professores, tivemos a oportunidade de aplicar um questionário (anexo 1) para saber como eles lidam hoje com a relação CTS (mesmo que ainda inseridos em um contexto de ensino tradicional). Foram distribuídos cerca de 500 questionários; em geral, os professores os levavam para casa, com a promessa de devolvê-los preenchidos. Retornaram 108 (21%) deles, os quais foram digitados e tabulados no programa Sphinx. Esse programa, além de produzir tabelas e gráficos, também quantifica termos, conceitos e expressões através da análise de conteúdo. Além do questionário, trabalhamos especificamente com os professores, em dois seminários, propondo-lhes atividades que visaram a levantar as representações desses agentes sobre o tempo. A temática do tempo foi explorada em seminários de atualização realizados em duas situações: num projeto de extensão da Universidade Federal Fluminense e no Museu de Astronomia e Ciências Afins, ambos no Estado do Rio de Janeiro. O museu foi também o local escolhido para acompanharmos visitas de 11 turmas à sua exposição permanente. Durante as visitas, valemo-nos do método da observação direta para levantar dados sobre o comportamento dos visitantes (anexo 2). Os dados e as análises a seguir dão uma idéia do que foi investigado. ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Entendemos que a investigação de práticas educativas, por meio das narrativas, nos ensinos formal e não-formal, pode apontar as possibilidades de articulação entre mito, ciência, tecnologia e sociedade na medida em que o mito, além de ser considerado o ponto de partida dos pensamentos narrativo e paradigmático, encontra-se presente no cotidiano. Além disso, o discurso científico é considerado por alguns estudiosos como um dos mitos da sociedade Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 12 12 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 contemporânea. Vale lembrar ainda que a tecnologia pode, em algumas circunstâncias, reforçar a ciência como mito e ser referência importante de organização da vida social. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 CTS NO ENSINO FORMAL Na pesquisa sobre alfabetização científica e tecnológica que estamos desenvolvendo elaboramos e aplicamos, na sua fase inicial, um questionário para saber em que medida os professores de ciências estão atentos à discussão da relação CTS. As tabelas 2 e 3 (anexo 3) traçam um perfil dos professores pesquisados em termos de disciplina lecionada, série de atuação, tipo de escola e tempo de magistério. Por elas, observamos que o número maior de respondentes é da área de ciência, ecologia e biologia (40%), seguidos de professores que lecionam no ensino de 1ª a 4ª séries - núcleo comum (18%). Os professores atuam, na sua maioria, na rede pública (72%). Quanto ao tempo de magistério, constatamos que, em primeiro lugar, aparecem os que lecionam pelo menos há 6 anos (22%), seguidos dos que têm entre 11 e 17 anos de magistério (11%). A despeito da variação de tempo de magistério, em geral, os professores tendem a seguir um padrão tradicional de ensino de ciências determinado pelas orientações contidas nos currículos oficiais e nos livros didáticos. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 13 13 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. CTS NO ENSINO FORMAL 2002 Quando perguntamos sobre a relação dos conteúdos hoje ensinados com a CTS, obtivemos os resultados que são apresentados na tabela e nos quadros abaixo: Tabela 1 - Relação entre Conteúdos Escolares e CTS: Tabela 1 - Relação entre Conteúdos Escolares e CTS: Respostas 1ª a 4ª séries N = 25 5ª a 8ª séries N = 26 Todos 11 15 Quase todos/ maioria 04 01 Ciências Biológicas 02 00 Questão ambiental 02 07 Não responde 06 03 Quadro 1 - Detalhamento dos conteúdos escolares, conceitos científicos e CTS de 1ª a 4ª séries: Relação Conteúdos Escolares e CTS Conceitos Científicos Identificados Esquema corporal, tempo e relógio Tempo, espaço Trabalho, força, corpo e necessidades alimentares Transformação, conservação Recursos naturais, seres vivos, noções de higiene, planeta Meio ambiente, saúde Desmatamento, alimentação, reciclagem do lixo Transformação, conservação Saúde, higiene, meio ambiente Saúde, conservação Sexo, drogas, violência, meio ambiente Saúde, conservação Quadro 1 - Detalhamento dos conteúdos escolares, conceitos científicos e CTS de 1ª a 4ª séries: Quadro 2 - Detalhamento dos conteúdos escolares, conceitos científicos e CTS de 5ª a 8ª séries: Relação Conteúdos Escolares e CTS Conceitos Científicos Identificados Radiações, poluição ambiental, química dos alimentos, fome, desperdício e reaproveitamento de alimentos Transformação, conservação, preservação, saúde, acumulação Usina nuclear, informatização Transformação, comunicação Formação do Universo, sistema solar, planetas Tempo, espaço Corpo humano, Aids, câncer, aborto, controle de natalidade Saúde, prevenção, demografia Energia atômica, energia elétrica, utilidade das máquinas no cotidiano Transformação, conservação, cotidiano Sistema solar, tratamento e qualidade da água, tecnologia ambiental, ciclos e importância das fl t Tempo, espaço, transformação, meio ambiente, ciclos Quadro 2 - Detalhamento dos conteúdos escolares, conceitos científicos e CTS de 5ª a 8ª séries: Quadro 2 - Detalhamento dos conteúdos escolares, conceitos científicos e CTS de 5ª a 8ª séries: Relação Conteúdos Escolares e CTS Conceitos Científicos Identificados Radiações, poluição ambiental, química dos alimentos, fome, desperdício e reaproveitamento de alimentos Transformação, conservação, preservação, saúde, acumulação Usina nuclear, informatização Transformação, comunicação Formação do Universo, sistema solar, planetas Tempo, espaço Corpo humano, Aids, câncer, aborto, controle de natalidade Saúde, prevenção, demografia Energia atômica, energia elétrica, utilidade das máquinas no cotidiano Transformação, conservação, cotidiano Sistema solar, tratamento e qualidade da água, tecnologia ambiental, ciclos e importância das Tempo, espaço, transformação, meio ambiente, ciclos 14 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 14 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 tecnologia ambiental, ciclos e importância das florestas meio ambiente, ciclos Ecologia e seres vivos Meio ambiente, ciclos Física aplicada, energia Conservação, cotidiano Ecologia, corpo humano, genética Ciclos, transformação, informação Doenças epidemiológicas Saúde, prevenção Matéria, energia, poluição do ar, água, origem da vida, nutrição e saúde Transformação, conservação, ciclos, evolução, saúde Tempo, espaço, terra Tempo, espaço, meio ambiente Biodiversidade Evolução, biodiversidade Drogas, invenções e sexualidade Prevenção, conservação, cotidiano Genética, eletricidade, eletromagnetismo Informação, transformação, conservação Clonagem, drogas, sexualidade Informação, prevenção meio ambiente, ciclos Meio ambiente, ciclos Conservação, cotidiano Ciclos, transformação, informação Saúde, prevenção Transformação, conservação, ciclos, evolução, saúde Tempo, espaço, meio ambiente Evolução, biodiversidade Prevenção, conservação, cotidiano Informação, transformação, conservação Informação, prevenção meio ambiente, ciclos Meio ambiente, ciclos Conservação, cotidiano Ciclos, transformação, informação Saúde, prevenção Transformação, conservação, ciclos, evolução, saúde Tempo, espaço, meio ambiente Evolução, biodiversidade Prevenção, conservação, cotidiano Informação, transformação, conservação Informação, prevenção Clonagem, drogas, sexualidade A tabela 1 mostra como os professores de 1ª a 8ª séries respondem sobre os conteúdos com os quais trabalham e as possibilidades de explorar neles a relação CTS. Para a maioria (44% de 1ª a 4ª e 57% de 5ª a 8ª ), todos os conteúdos podem ser relacionados ao ensino de CTS. Vale lembrar, contudo, que o significado de “todos” de 1ª a 4ª séries contempla todas as disciplinas do núcleo comum, enquanto que o “todos” de 5ª a 8ª séries refere-se aos conteúdos de ciências e geografia, principalmente. Um tema destacado pelos professores, em geral, e também valorizado pelos estudiosos de CTS (Solomon, 1993) é a questão ambiental. Nos quadros 1 e 2, aparece um detalhamento dos conteúdos relacionados pelos professores. No primeiro, séries iniciais, os aspectos vinculados à saúde do ambiente e do corpo são priorizados nos conteúdos. No segundo (5ª a 8ª ), além de conteúdos relacionados ao ambiente e ao corpo humano, são lembrados conteúdos decorrentes do desenvolvimento tecnológico (clonagem, eletricidade, utilidade das máquinas no cotidiano, química dos alimentos, tecnologia ambiental etc.). Observamos, também, que os professores de 5ª a 8ª séries detalham mais os conceitos científicos quando se referem à relação entre conteúdos e ensino de CTS. Ao estabelecermos relação entre essas respostas e o que é proposto pelos estudiosos de CTS e alfabetização científica, podemos considerar que muitos dos conteúdos listados estão próximos aos objetivos e preocupações da educação científica alinhados à CTS. No quadro 3, especificamos as respostas dos professores da área científica do ensino médio à pergunta sobre a relação entre os conteúdos escolares e CTS (pergunta 2.2, anexo 1). Lembramos, no entanto, que, além desses 17 professores (70%), outros 6 de outras áreas responderam ao questionário, perfazendo um total de 24. Do total de respondentes desse grau de ensino, 73% também afirmaram que todos os conteúdos (ou a maioria) podem ser vinculados à CTS. Dos professores da área científica, 50% eram de Biologia; 20%, de Química e somente 5%, de Física. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 15 15 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 O quadro apresenta uma síntese das respostas dos professores. Nelas, podemos constatar que, em geral, o ensino de CTS diz respeito ao vivido, a problemas e soluções que afetam o ambiente e a saúde humana, de modo positivo ou negativo. As respostas indicam como os professores com formação específica de ciências fazem referências ao processo de produção do conhecimento científico, relacionando-o à sociedade e à tecnologia. como os professores com formação específica de ciências fazem referências ao processo produção do conhecimento científico, relacionando-o à sociedade e à tecnologia. Quadro 3 - Relação entre conteúdos escolares e CTS citados pelos professores ensino médio Biologia = 12 Química = 4 Física = 2 Todos os conteúdos. Ciência é uma atividade humana sujeita a influência e impactos sociais; o aspecto tecnológico é parceiro da ciência no processo de conhecimento. Todos conteúdos - Química ( necessidade que o homem tem de resolver seus problemas orgânicos ou não). Física aplicada e energia. Todos os conteúdos. A tecnologia como parte integrante da vida, e tudo que diz respeito à vida diz respeito à sociedade. A maior parte dos conteúdos. Porém, parece estar fora do controle social. Conceitos ligados à energia e sua conservação, evolução da física. Todos os conteúdos quando abordados de uma forma dinâmica, privilegiando aspectos da natureza, aplicação no cotidiano, solução de problemas, participação ativa no meio. Conteúdos estão mais para ciências, relacionados com a tecnologia e a sociedade nos pontos em que se passou pela vivência. Todos os conteúdos. Interferência de substâncias e misturas no meio ambiente. Quase todos. Genética (3º ano), melhoramento genético, plantas, animais; importância da medicina; questão ética. (interfere na cultura, no pensamento, na opinião da sociedade). Ecologia, pesquisas de doenças e genética. Qualquer conteúdo de bi l i ( ã tã id t Quadro 3 - Relação entre conteúdos escolares e CTS citados pelos professores do ensino médio Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 Quadro 3 - Relação entre conteúdos escolares e CTS citados pelos professores do ensino médio Quadro 3 - Relação entre conteúdos escolares e CTS citados pelos professores do ensino médio A vidente Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 vidente Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 16 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 doenças e genética. Qualquer conteúdo de biologia (não tão evidente a princípio). Conteúdos de ecologia, seres vivos e química, mais facilmente relacionados com o cotidiano do aluno e com fatos que ocorrem no, meio, científico e tecnológico. Noções de Química: criação de novas substâncias que irão facilitar a vida do homem. Na Química. Os aspectos histórico e social em relação aos aspectos apresentados. Instrumentos ópticos e eletrônicos sofisticados que possibilitam entender melhor o funcionamento de organismos, com utilização de fundamentos da área de saúde. Em termos de recursos didáticos para o desenvolvimento das aulas, além do livro, adotado assumidamente por 17 deles (15%), os professores referem-se, com mais freqüência, ao uso de artigos de revistas e jornais (dominando as revistas). Das revistas assinaladas, vale destacar: Globo Ciência, Superinteressante, Revista Nova Escola, Veja, Cadernos do 3º Mundo. Há indicação de uso de vídeo (Série Cosmos), realização de experiências simples, elaboração de modelos, pesquisa em bibliotecas, visitas a museus, postos de saúde, Jardim Botânico, planetário, caminhadas em áreas verdes e assentamentos agrícolas. Sobre a relação desses conteúdos com a CTS, vale aqui a reflexão crítica de uma professora de escola pública: “(...)O ensino de ciências tem-se limitado à transmissão de uma série de conceitos para simples memorização, não se articulando com os grandes avanços obtidos pela ciência e que são bombardeados quase que diariamente através da mídia. Apesar da precária Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 17 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 17 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 situação do ensino público, tais recursos didáticos, quando contextualizados numa boa prática pedagógica, podem funcionar para estabelecer o nexo entre esta ciência proposta pelos currículos e o desenvolvimento da ciência e tecnologia que cresce a uma velocidade extraordinária e invade a vida de todos os cidadãos. Quadro 3 - Relação entre conteúdos escolares e CTS citados pelos professores do ensino médio Sendo assim, a utilização de artigos científicos pode ser o ponto de partida para a busca de sua fundamentação, encontrada nos conteúdos abordados em aula, ou, ao contrário, a partir de conteúdos discutidos, caminhar no sentido de sua aplicabilidade, tendo como apoio tais artigos científicos... A experimentação visa que o aluno vivencie o método científico elaborando hipóteses, organizando a atividade, estabelecendo conclusões, diferentemente da idéia de experimentação apresentada como receita de bolo... De posse dos princípios fundamentais da ciência, articulando-os e aplicando-os, os alunos poderão compreender sobre os grandes eventos realizados nesta área,... passando a exercer o seu papel de cidadãos, posicionando-se e decidindo criticamente diante deles.” Da ligação entre a Química e CTS, destacamos o seguinte depoimento: “(...) quando falo das substâncias químicas presentes nos alimentos, levo os alunos a questionarem sobre a fome... levo-os à reflexão também sobre a questão do desperdício de alimentos, e então falo sobre as alternativas para aproveitamento desses alimentos.” Além da aplicação do questionário, fizemos um trabalho voltado para identificação da relação CTS nos ensinos formal (escola) e não-formal (museu), em duas etapas. Na primeira, oferecemos uma palestra seguida de uma dinâmica para cerca de 70 professores da Zona Oeste do Rio de Janeiro, sobre alfabetização científica. Na dinâmica, trabalhamos com o tema "Tempo" de duas maneiras. Primeiro, solicitando aos professores que escrevessem e representassem em desenho o significado da palavra tempo. Algumas das respostas estão aqui reproduzidas: No segundo momento da dinâmica, distribuímos algumas crônicas sobre o tempo (Lightman, 1966). Os professores, divididos em grupo, leram, discutiram e apresentaram considerações sobre as leituras. Dos comentários finais, selecionamos um bastante significativo: “(...) Até Newton, você tem uma idéia de tempo absoluto, de um tempo que pode ser dito, codificado e é sempre o mesmo em qualquer lugar. Com Einstein, você tem uma nova idéia de tempo, nesse sentido, e mais influenciado por outras pessoas, uma idéia de que o tempo é relativo, que a massa e o espaço são relativos e que se influenciam. Isso também vai influenciar como vamos pensar a questão do tempo. Infelizmente, nas escolas, trabalham muito pouco com as idéias da física mais moderna... Existe muito medo da física de Einstein, e esse texto pode dar pistas também para trabalharmos essa questão. Essa questão da velocidade, a velocidade da informação; quem não tem acesso rápido à informação está alienado, não sabe o que está acontecendo. CTS NO ENSINO NÃO-FORMAL A pesquisa, no Museu de Ciência (Mast/MCT), foi realizada em duas fases. Na primeira, foram feitas observações de turmas (11 no total) que visitaram o museu. Na segunda, foi realizado um seminário dando continuação à discussão sobre o conceito de tempo, anteriormente explorado. Foram convidados todos os professores (70) que participaram do 1º seminário, mas somente 18 compareceram. Quadro 3 - Relação entre conteúdos escolares e CTS citados pelos professores do ensino médio Existe o computador que acessa a Internet e tem como se comunicar com o mundo inteiro. “(...) Até Newton, você tem uma idéia de tempo absoluto, de um tempo que pode ser dito, codificado e é sempre o mesmo em qualquer lugar. Com Einstein, você tem uma nova idéia de tempo, nesse sentido, e mais influenciado por outras pessoas, uma idéia de que o tempo é relativo, que a massa e o espaço são relativos e que se influenciam. Isso também vai influenciar como vamos pensar a questão do tempo. Infelizmente, nas escolas, trabalham muito pouco com as idéias da física mais moderna... Existe muito medo da física de Einstein, e esse texto pode dar pistas também para trabalharmos essa questão. Essa questão da velocidade, a velocidade da informação; quem não tem acesso rápido à informação está alienado, não sabe o que está acontecendo. Existe o computador que acessa a Internet e tem como se comunicar com o mundo inteiro. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 18 18 Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Quem não tem acesso a isso está perdendo nesse mundo da mesma forma que aqueles que têm fome, que aqueles que não têm salário digno.” A visita O quadro 4 apresenta uma caracterização geral dos visitantes. Destacamos nele a forma como os professores são inseridos no contexto do Mast: a maioria leva as turmas após passar por um treinamento para compreender a proposta e poder colaborar no dia da visita. O quadro 4 apresenta uma caracterização geral dos visitantes. Destacamos nele a forma como os professores são inseridos no contexto do Mast: a maioria leva as turmas após passar por um treinamento para compreender a proposta e poder colaborar no dia da visita. Quadro 4 - Caracterização dos visitantes escolares ao Mast SÉRIE ESCOLA FORMAÇÃO DO PROFESSOR ENTRADA NO Mast MOTIVO DA VISITA 3ª Série Particular Administração e Pedagogia Treinamento Fixar a matéria (Planetas) Particular Matemática e Pedagogia Treinamento Por estar dando o conteúdo e pela curiosidade das crianças 4ª Série Particular Sem informação Treinamento Matéria dada (astros para a criança ver no concreto) Particular Pedagogia e Letras Conta própria Para visualizar o que é dado em sala 5ª Série Particular Biologia Treinamento Sem informação Particular Supervisora em Artes e Psicologia Sem informação Sem informação Particular História e Geografia Sem informação Sem informação Quadro 4 - Caracterização dos visitantes escolares ao Mast Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 19 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 SÉRIE ESCOLA FORMAÇÃO DO PROFESSOR ENTRADA NO Mast MOTIVO DA VISITA Mistas (3ª e 4ª ) Particular Especialização em Literatura Treinamento Trabalhar conteúdos (começa em espaço e termina em Microcosmo) Particular Psicologia e Pedagogia Treinamento Trabalhar conteúdo (Universo) e para sair do abstrato. Mistas (2ª , 3ª e 4ª ) Particular Pedagogia Treinamento Está dando o conteúdo Pública Municipal Pedagogia Sem informação Sem informação. Das 11 turmas que visitaram o Mast, 10 eram de escolas particulares. Vale ainda destacar que a maioria dos professores, além de não pertencer à área de ciências, costuma levar os alunos para fixar conteúdos com que estão trabalhando em sala de aula. As observações ficaram restritas a uma parte da exposição permanente. ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 O quadro a seguir apresenta uma síntese das reações das turmas quando visitaram a exposição permanente. Lembramos que a coleta dessas observações foi feita por duas bolsistas, que registravam as reações dos visitantes em um formulário próprio (anexo 3), durante o período de duração da visita – uma hora. Foram realizadas 12 observações em um período de quatro meses, somente na parte da exposição permanente que aborda a relação CTS por meio da evolução do conceito de espaço e tempo. Quadro 5 - Reações das turmas em visita à exposição permanente SÉRIE SALA BRANCA (Modelo Geocêntrico). SALAS INTERMEDIÁRIAS (Modelo Heliocêntrico) SALA ESCURA (Visão do céu a partir da Terra) 3ª Série (2 e 4) Nº 2: O monitor estimula as crianças a falar das imagens que podem retratar as estações do ano. Também menciona a inclinação da Terra, além de chamar a atenção para a imagem do mês de fevereiro, no qual está nevando. As crianças dizem que deve ser em outro país e não no Brasil. Nº 4: A professora começou explicando o livro das horas, reforçou a explicação dos STONEHENGE, falando do pôr-do-sol, como também do sistema geocêntrico. A professora pergunta para os alunos por que, no mês de fevereiro, seria inverno no continente europeu. Os alunos rapidamente responderam: “Por causa da vestimenta." Nº 2: As crianças observam atentamente a parte dos descobrimentos. Percebem o quanto é perigoso tentar observar o Sol com luneta, lupa etc. Averiguam que é muito mais fácil usar um astrolábio para medir as estrelas. Ao chegar à parte do sistema solar, falam dos planetas (tudo decorado). Nº 4: As crianças respondem atentamente à rota dos descobrimentos. No diálogo, a professora relembra uma das suas aulas e pede que alguma criança exponha o que já foi visto. Explica também como foi difícil Galileu convencer os outros (mostra o diálogo). No sistema solar, uma das crianças menciona que a Terra está girando muito rápido. O monitor explica que é só uma órbita imaginária. Nº 2: As crianças só fizeram ligações com os signos. Nº 4: Ao entrarem na sala, as crianças procuram logo seus signos. A professora pediu que as crianças observassem a escala dos meses e o melhor período para ver as constelações de cada signo. A visita Nessa exposição, Quatro Cantos de Origem, o Mast se propõe a desenvolver as noções de tempo e espaço a partir das narrativas tradicionais (mito) e das narrativas modernas (científicas).A "musealização do acervo constitui-se como meio eficiente de enriquecimento da aprendizagem científica, uma vez que parte do pressuposto de que o público que o visita já detém informações preliminares sobre o que vai encontrar" (MAST, 1992). O museu pretende ser uma espécie de contexto-síntese do debate mito, ciência e tecnologia ao confrontar os dois primeiros e ao expor provas materiais dos avanços científico e tecnológico (relógios, lunetas, telescópios, mapas celestes etc.). Além de permitir um aprofundamento do deslocamento do modelo geocêntrico e sua substituição pelo modelo heliocêntrico, das noções de tempo circular e linear, de espaço e tempo limitados e infinitos, a integração do que se aprende na escola com o que o museu possibilita ver e aprofundar permite, inclusive, perceber de que modo fragmentos das narrativas primitivas permanecem nos modelos e nas concepções científicas: "(...) O Zodíaco, este conjunto de estrelas distribuídas numa faixa do céu, aparece como um elemento importante para se definir o tempo. Grupo de estrelas do Zodíaco foi associado às figuras que transpunham, de forma simbólica, elementos terrestres para o céu.(...) A ciência moderna teve sua base fundada na observação astronômica. Durante o século XVII, as tabelas astronômicas servem de base para a formulação da física. O céu simbólico serve de meio para refletir sobre o homem e seus ciclos. Homem e Universo integram-se" .(MAST, 1992: 25). Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 20 20 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Partindo daí, o monitor aprofundou suas explicações sobre o motivo que levava as pessoas a pensarem assim. Surge uma nova pergunta por parte de um dos alunos, interessado em saber se um planeta estava dentro do outro. O N d s a N “d p N a d m C A q F p m c tê N m ro N u o errada no sistema geocêntrico. Uma criança afirmou que o Sol girava em torno da Terra (todos os outros a vaiaram). Depois desse acontecimento, o monitor explicou o sistema geocêntrico, conseguindo prender a atenção de todos os alunos. A partir daí, algumas crianças fizeram perguntas referentes ao assunto. Podemos citar como exemplo: "O que significa estas linhas azuis?” (R: Esferas de cristais). Na parte dos planetas, eles falam seus nomes na sua devida seqüência. as constelações, só depois perceberam os signos. 5ª Série (9, 10 e 11) Nº 9: As crianças ouviram as explicações do sistema geocêntrico com muita atenção e ainda afirmaram que o Sol estava no centro. Nº 10: Parece que a professora já havia avisado aos alunos sobre o que encontrariam no museu, visto que ela, havia participado da visita no ano passado. Além disso, as crianças percebem logo a diferença no mês de fevereiro. Nº 11: Esse grupo acertou, de primeira, que a Terra estava no centro. Partindo daí, o monitor aprofundou suas explicações sobre o motivo que levava as pessoas a pensarem assim. Surge uma nova pergunta por parte de um dos alunos, interessado em saber se um planeta Nº 9: As crianças falam dos descobrimentos. Logo em seguida, o monitor vai para a parte do sistema solar. Novamente aparece a “decoreba” da ordem dos planetas. Nº 10: Um aluno perguntou ao monitor se Cabral tinha descoberto o Brasil na mesma época em que Colombo descobriu a América. Outro aluno questionou o fato de Fernão de Magalhães ser o primeiro a dar a volta ao mundo, visto que, se chegou morto, não poderia tê-lo feito. Nº 11: As crianças manipulam a parte das rotas dos descobrimentos. Na parte do sistema solar, uma criança percebe que Nº 9: As crianças ficaram fascinadas com as figuras das constelações e com o fato de encontrarem seu signo. Nº 11: As crianças tiveram dificuldade de encontrar seus signos, talvez por não terem conhecimentos de “latim”. Na parte dos planetas, eles falam seus nomes na sua devida seqüência. ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 4ª Série (7e 8) Nº 7: As crianças observaram que havia alguma coisa Nº 8: Os alunos manuseiam o astrolábio. Nº 8: As crianças ficaram observando uadro 5 - Reações das turmas em visita à exposição permanente ÉRIE SALA BRANCA (Modelo Geocêntrico). SALAS INTERMEDIÁRIAS (Modelo Heliocêntrico) SALA ESCUR (Visão do céu partir da Terr Série e 4) Nº 2: O monitor estimula as crianças a falar das imagens que podem retratar as estações do ano. Também menciona a inclinação da Terra, além de chamar a atenção para a imagem do mês de fevereiro, no qual está nevando. As crianças dizem que deve ser em outro país e não no Brasil. Nº 4: A professora começou Nº 2: As crianças observam atentamente a parte dos descobrimentos. Percebem o quanto é perigoso tentar observar o Sol com luneta, lupa etc. Averiguam que é muito mais fácil usar um astrolábio para medir as estrelas. Ao chegar à parte do sistema solar, falam dos planetas (tudo decorado). Nº 4: As crianças Nº 2: As crianç fizeram ligações os signos. Nº 4: Ao entrare sala, as cria procuram logo signos. A profe pediu que as cria observassem a e dos meses e o m período para ve constelações de Quadro 5 - Reações das turmas em visita à exposição permanente Nº 4: Ao entrarem na sala, as crianças procuram logo seus signos. A professora pediu que as crianças observassem a escala dos meses e o melhor período para ver as constelações de cada signo. Nº 4: Ao entrarem na sala, as crianças procuram logo seus signos. A professora pediu que as crianças observassem a escala dos meses e o melhor período para ver as constelações de cada signo. o Sol girava em erra (todos os devida seqüência. sig Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 21 ENSAIO – Pesquisa em Educação em Ciências ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 errada no sistema geocêntrico. Uma criança afirmou que o Sol girava em torno da Terra (todos os outros a vaiaram). Depois desse acontecimento, o monitor explicou o sistema geocêntrico, conseguindo prender a atenção de todos os alunos. A partir daí, algumas crianças fizeram perguntas referentes ao assunto. Podemos citar como exemplo: "O que significa estas linhas azuis?” (R: Esferas de cristais). ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Na parte dos planetas, eles falam seus nomes na sua devida seqüência. 5ª Série (9, 10 e 11) Nº 9: As crianças ouviram as explicações do sistema geocêntrico com muita atenção e ainda afirmaram que o Sol estava no centro. Nº 10: Parece que a professora já havia avisado aos alunos sobre o que encontrariam no museu, visto que ela, havia participado da visita no ano passado. Além disso, as crianças percebem logo a diferença no mês de fevereiro. Nº 11: Esse grupo acertou, de primeira, que a Terra estava no centro. Partindo daí, o monitor aprofundou suas explicações sobre o motivo que levava as pessoas a pensarem assim. Surge uma nova pergunta por parte de um dos alunos, interessado em saber se um planeta estava dentro do outro. O monitor esclareceu que as esferas é que estavam uma Nº 9: As crianças falam do descobrimentos. Logo em seguida, o monitor vai para a parte do sistema solar Novamente aparece a “decoreba” da ordem dos planetas. Nº 10: Um aluno pergunto ao monitor se Cabral tinha descoberto o Brasil na mesma época em que Colombo descobriu a América. Outro aluno questionou o fato de Fernão de Magalhães ser o primeiro a dar a volta ao mundo, visto que, se chegou morto, não poderia tê-lo feito. Nº 11: As criança manipulam a parte das rotas dos descobrimentos Na parte do sistema solar uma criança percebe que os planetas mais próximos do Sol giram mais rápido. errada no sistema geocêntrico. Uma criança afirmou que o Sol girava em torno da Terra (todos os outros a vaiaram). Depois desse acontecimento, o monitor explicou o sistema geocêntrico, conseguindo prender a atenção de todos os alunos. A partir daí, algumas crianças fizeram perguntas referentes ao assunto. Podemos citar como exemplo: "O que significa estas linhas azuis?” (R: Esferas de cristais). N fa d 5ª Série (9, 10 e 11) Nº 9: As crianças ouviram as explicações do sistema geocêntrico com muita atenção e ainda afirmaram que o Sol estava no centro. Nº 10: Parece que a professora já havia avisado aos alunos sobre o que encontrariam no museu, visto que ela, havia participado da visita no ano passado. Além disso, as crianças percebem logo a diferença no mês de fevereiro. Nº 11: Esse grupo acertou, de primeira, que a Terra estava no centro. ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 No calendário, o monitor menciona as estações do ano. Nº 11: No sistema geocêntrico, uma criança perguntou (em meio à explicação do monitor) se Júpiter e Plutão não eram vistos por serem planetas gasosos. Uma outra pergunta que um aluno fez foi sobre o cinturão de asteróides. O monitor disse que naquela Nº 5: As crianças falam sobre os descobrimentos, observam o astrolábio e, na parte dos planetas, não sabem a ordem, mas ficam muito interessadas pela luneta astronômica. Nº 11: As crianças observam o quadro das rotas, manipulam o astrolábio, ficam encantadas olhando para o sistema solar e percebem que os planetas mais próximos do Sol giram mais rápido que os mais afastados. Nº 5: As cria atrapalharam procura dos mas ao enco tiveram curi em observa constelações. Nº 11: As procuraram log signo. monitor esclareceu que as esferas é que estavam uma dentro da outra. do Sol gir Mistas – 3ª e 4ª séries (3 e 6) Nº 3: O monitor incentiva as crianças a perguntarem. Elas respondem o que é calendário; percebem as diferenças entre os meses no Brasil e na Europa. Na parte em que é exposta a distância entre a Terra e o Sol, a professora pede explicação ao monitor. Ela faz ligação da geometria com a astronomia, mencionando que já havia dado a matéria de triângulos e ângulos. Nº 6: A estavam interessa sim, em todos o liberdade atenção astrolábio sistema s não sabi Arriscava pareciam planetas. Mistas – 2ª ,3ª e 4ª séries (5 e11) Nº 5: Na explicação sobre o sistema geocêntrico, as crianças afirmaram que o Sol é que estava no centro, mas, após a explicação do monitor, passaram a responder com precisão às suas perguntas: Uma criança indagou: “Por que tem uma estrela em cada bolinha ? O que são elas?” Resposta: As bolinhas são os planetas que, vistos da Terra, parecem estrelas. No calendário, o monitor menciona as estações do ano. Nº 11: No sistema geocêntrico, uma criança perguntou (em meio à explicação do monitor) se Júpiter e Plutão não eram vistos por serem planetas gasosos. Uma outra pergunta que um aluno fez foi sobre o cinturão de asteróides. ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Na parte dos planetas, eles falam seus nomes na sua devida seqüência. Nº 9: As crianças ficaram fascinadas com as figuras das constelações e com o fato de encontrarem seu signo. Nº 9: As crianças falam dos descobrimentos. Logo em seguida, o monitor vai para a parte do sistema solar. Novamente aparece a “decoreba” da ordem dos planetas. Nº 11: As crianças tiveram dificuldade de encontrar seus signos, talvez por não terem conhecimentos de “latim”. Nº 10: Um aluno perguntou ao monitor se Cabral tinha descoberto o Brasil na mesma época em que Colombo descobriu a América. Outro aluno questionou o fato de Fernão de Magalhães ser o primeiro a dar a volta ao mundo, visto que, se chegou morto, não poderia tê-lo feito. ra. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 22 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 monitor esclareceu que as esferas é que estavam uma dentro da outra. do Sol giram mais rápido. Mistas – 3ª e 4ª séries (3 e 6) Nº 3: O monitor incentiva as crianças a perguntarem. Elas respondem o que é calendário; percebem as diferenças entre os meses no Brasil e na Europa. Na parte em que é exposta a distância entre a Terra e o Sol, a professora pede explicação ao monitor. Ela faz ligação da geometria com a astronomia, mencionando que já havia dado a matéria de triângulos e ângulos. Nº 6: As crianças não estavam muito interessadas em ouvir e, sim, em ver e explorar todos os cantos com liberdade. Só deram mais atenção à explicação do astrolábio. Na hora do sistema solar, as crianças não sabiam a seqüência. Arriscavam os nomes; pareciam não conhecer os planetas. Nº 3: As dizem que es espaço flutua somente preocupam em os seus signos Nº 6: As ficaram entusiasmadas pareciam esta coisas do mundo. procuraram signos, sem atenção à expl Mistas – 2ª ,3ª e 4ª séries (5 e11) Nº 5: Na explicação sobre o sistema geocêntrico, as crianças afirmaram que o Sol é que estava no centro, mas, após a explicação do monitor, passaram a responder com precisão às suas perguntas: Uma criança indagou: “Por que tem uma estrela em cada bolinha ? O que são elas?” Resposta: As bolinhas são os planetas que, vistos da Terra, parecem estrelas. ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 O monitor disse q e naq ela Nº 5: A sobre os observam na parte sabem a muito in luneta as Nº 11: observam rotas, astrolábio encantad sistema s que os próximos mais ráp afastados Nº 5: As crianças falam sobre os descobrimentos, observam o astrolábio e, na parte dos planetas, não sabem a ordem, mas ficam muito interessadas pela luneta astronômica. Nº 11: As crianças observam o quadro das rotas, manipulam o astrolábio, ficam Nº 11: As crianças procuraram logo o seu signo. Nº 11: As crianças observam o quadro das rotas, manipulam o astrolábio, ficam Nº 11: As crianças procuraram logo o seu signo. encantadas olhando para o sistema solar e percebem que os planetas mais próximos do Sol giram mais rápido que os mais afastados. conheciam. No as, as crianças Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 23 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 cinturão de asteróides. O monitor disse que naquela época não o conheciam. No livro das horas, as crianças dizem que é outro país, devido ao mês de fevereiro. Logo a seguir, o monitor explica os hemisférios e fala sobre as estações. cinturão de asteróides. O monitor disse que naquela época não o conheciam. No livro das horas, as crianças dizem que é outro país, devido ao mês de fevereiro. Logo a seguir, o monitor explica os hemisférios e fala sobre as estações. Por esse quadro, é possível dizer que a visita ao museu expõe professores e alunos a um conflito que resulta do fato de o museu e a escola trabalharem os mesmos temas de modo bastante diferenciado, pois, enquanto os professores trabalham os conteúdos de modo descontextualizado, a exposição contextualiza e ressalta a história da ciência. Pelo fato de o museu ter uma exposição que busca articular CTS, ele se encontra mais próximo de um projeto de alfabetização científica do que a escola. O quadro 6 confirma essa observação, especialmente quando registra que, em geral, os alunos não sabem que o modelo geocêntrico antecedeu o modelo heliocêntrico. Por meio dele também é possível constatar dois outros aspectos significativos. ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 O primeiro deles é a preocupação da exposição em passar certas noções de tempo e de espaço com as quais os alunos não estão ainda familiarizados. O segundo refere-se à identificação dos alunos com a perspectiva mítica (astrologia), quando visitam a sala escura. Desse modo revela-se, para alunos e professores, a possibilidade, através do ensino não-formal, de se trabalhar mais próximo da articulação CTS pela via da narrativa, do mito, da ciência . Vale destacar que a questão tecnológica, mesmo estando presente na exposição permanente, não é suficientemente percebida e trabalhada pelos professores e monitores. Quadro 6 - Reações em face dos modelos geocêntrico e heliocêntrico Série Sala Branca Sala Intermediária Sala Escura 4ª Série As explicações centram- se no sistema geocêntrico. A visita às salas é corrida. Destacam-se o manuseio do astrolábio e a ordem correta da nomeação dos planetas. Observação dos signos e das constelações. 5ª Série As explicações centram- se no sistema geocêntrico, mas os alunos incorrem no erro explicativo sobre o modelo (vêem o Sol no centro). Novamente explicação relacionando os descobrimentos (História) com as novas possibilidades de visão e conhecimento do Universo (Ciências). Destaque para a observação de uma criança sobre movimentos mais rápidos dos planetas As crianças observam, “fascinadas”, as constelações e os signos. Revelam dificuldade com o latim e, por isso, demoram a identificar seu signo Quadro 6 - Reações em face dos modelos geocêntrico e heliocêntrico Quadro 6 - Reações em face dos modelos geocêntrico e heliocêntrico Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 24 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 mais rápidos dos planetas mais próximos do Sol. identificar seu signo respectivo. Séries Mistas Tanto discutem os modelos (alunos incorrem no erro de afirmar que o Sol está no centro do modelo geocêntrico) quanto as estações do ano e a impossibilidade de se ver a época certa dos planetas. Um aluno (nº 12) busca explicação própria para o fato de os planetas (como Plutão) não serem vistos (eram gasosos). Trabalha-se a relação História (descobrimento) e Ciências (visão do céu). As crianças observam o astrolábio, nomeiam os planetas e notam que os planetas mais próximos do Sol giram mais rápido (simulação do modelo heliocêntrico); As crianças buscam, principalmente, seu signo. ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Por ser o tempo uma dimensão relevante para a ciência e por ela estar destacada na exposição permanente, consideramos oportuno convidar alguns professores, que haviam discutido o tema em um dos cursos de extensão, para visitar o museu e rediscutir a temática por meio de um seminário. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 O seminário Os professores (18) que compareceram ao Museu de Astronomia assistiram num primeiro momento, a uma palestra que abordou a história da construção do calendário e as diferentes concepções de tempo ao longo da história da humanidade e de diferentes civilizações. A idéia era caracterizar a categoria tempo como uma construção humana e abordar questões abertas que ainda precisam ser resolvidas. Num segundo momento, visitaram a Casa da Hora, instituição vinculada ao Observatório Nacional e responsável pela determinação da hora local brasileira. Nessa instituição, um técnico responsável mostrou-lhes aparatos de medir o tempo com diferentes precisões. Num terceiro momento, os professores percorreram, orientados por um técnico, os espaços que constituem a exposição permanente do Museu de Astronomia, podendo, então, observar como as relações espaço-tempo eram estabelecidas na Idade Média, durante o Renascimento e na Idade Moderna. A sala dedicada aos instrumentos de medida de tempo foi particularmente explorada. Num quarto momento, os professores foram convidados a escrever e apresentar em desenho, o significado da palavra tempo. Algumas das respostas estão aqui apresentadas. Os quatro desenhos e as frases escolhidas para dar significado ao conceito de tempo entre professores (1ª a 8ª séries), comparados com os desenhos da primeira fase do trabalho, reproduzem as mesmas concepções sobre o tempo. Observa-se que o tempo da escola, Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 25 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Volume 02 / Número 1 – Març. 2002 também, está presente, e o tempo mecânico simbolizado pelo relógio permanece com dimensões existenciais. Em relação ao conceito de tempo ensinado, este está associado às equações do movimento e à linha do tempo. Percebe-se, então, que os professores oscilam suas representações entre as apoiadas em pensamento paradigmático e pensamento narrativo e, quando se expressam por meio de pensamento paradigmático, utilizam-se de conteúdos escolares. Como a visita se dá num tempo curto, fica difícil obter informações sobre possíveis mudanças no conceito de tempo dos professores. Seria necessário, portanto, realizar um trabalho mais longo e contínuo junto a esses professores para perceber possíveis mudanças. Entretanto, fica claro como o pensar sobre a categoria tempo, expressa aqui por meio de desenhos, explicita as relações entre mito, ciência e tecnologia. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 CONCLUSÕES A discussão teórica com que iniciamos este artigo, envolvendo o movimento de CTS no ensino de ciências e os modos de pensamento narrativo e paradigmático, foi significativa para procedermos a uma avaliação do estado da educação científica na escola e no museu. Ela iluminou a construção dos instrumentos e a análise dos dados coletados, mostrando, por exemplo, que não há sintonia entre o ensino formal (predominantemente apoiado no pensamento paradigmático e distante do narrativo) e o ensino não-formal (mais propenso a uma articulação entre os dois modos de pensamento). Percebemos que, no caso do ensino não-formal apresentado pelo Mast, há uma tendência a incorporar mito e ciência na narrativa, possibilitando, assim, um aprendizado mais próximo das concepções do cotidiano. Por outro lado, há dificuldade por parte dos idealizadores em articular os elementos da tecnologia via narrativas apoiadas nos objetos. Essa dificuldade está contida na fala dos estudantes e dos professores, que discutem mais os modelos apresentados. O uso das narrativas, no ensino de ciências, apresenta condições para explorar a relação CTS, na medida em que pode propiciar reflexões acerca dos aspectos éticos e epistemológicos da ciência e da tecnologia, além de dar a dimensão da presença da ciência e da tecnologia na sociedade. A análise dos dados levantados nas escolas indica que, embora os professores ainda estejam atrelados ao ensino tradicional de ciências (em grande parte por determinação dos currículos, programas oficiais e livros didáticos), há por parte deles um esforço no sentido de trabalhar esses conhecimentos de modo menos fragmentado e, na medida do possível, mais próximo das realidades social e tecnológica. Atestam essas predisposições o uso de recursos como jornais, revistas, vídeos; o desenvolvimento de atividades como visitas a museus, postos de saúde, assentamentos agrícolas e o empenho em promover debates e reflexões que articulem ciência e tecnologia à nossa realidade. No desenvolvimento da relação CTS, sob a ótica do conceito de tempo, nos contextos formal e não-formal de educação, seja nos cursos e seminários, seja nas visitas, tivemos a oportunidade de constatar como aparatos tecnológicos (relógios) reforçam determinados conceitos científicos, mas, por outro lado, como relações estabelecidas entre o tradicional e o moderno, o conhecimento abstrato e a reflexão existencial possibilitam uma perspectiva Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 26 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. CONCLUSÕES 2002 interdisciplinar do debate, em que as relações mito, ciência e tecnologia podem ser abordadas. A esse respeito, vale lembrar que as representações produzidas pelos professores sobre o conceito de tempo estão fundamentadas nos conceitos social e tecnológico, expressos nos desenhos do relógio mecânico, e que tende a encobrir a história desse conceito, tornando-o natural, o que é, na verdade, uma construção social do tempo. Neste trabalho, fizemos um esforço no sentido de estabelecer um paralelo entre a educação científica formal e a não-formal disponível em escolas e no Museu de Ciências do Estado do Rio de Janeiro, para identificar a sua proximidade com uma das tendências do ensino de ciências: ensino de CTS. No museu, a pedagogia implementada articula as ações envolvendo espaço, objeto e tempo, pois nos museus as narrativas construídas em torno dos objetos que se dispõem em determinados espaços são apreendidas em tempo próprio pelos visitantes e de forma autônoma. As narrativas presentes no museu não estão necessariamente atreladas ao currículo escolar, permitindo ao seu elaborador escolhas diversificadas, tanto em relação aos conteúdos científicos como aos recursos comunicacionais. Assim, constatamos que, apesar de ainda estarmos muito atrelados a um ensino fragmentado de ciências, a oferta educacional de um museu de ciências com uma proposta histórica e contextualizada da ciência pode contemplar uma educação em CTS. Embora no ensino formal, verifiquemos que os currículos, programas e livros didáticos, em sua maioria, ainda estão presos a uma visão científica fragmentada, observamos que os professores tendem a trabalhar, na sala de aula, alguns conteúdos que se aproximam da perspectiva de CTS. Há, no entanto, necessidade de se aprofundarem as reformas de ensino de ciências, visando à ampliação da oportunidade de se trabalhar melhor a relação CTS e levando em conta, sobretudo, a essencial articulação entre os ensinos formal, não-formal e os meios de divulgação científica. O aprofundamento do estudo das narrativas abordando a relação mito, ciência e tecnologia poderia constituir um caminho interessante de integração entre o ensino formal, o não-formal e a divulgação científica. Essa perspectiva, além de nortear cursos de atualização de professores, poderia orientar as ações das instituições envolvidas com a educação científica, objetivando a ampliação da alfabetização científica. As autoras agradecem à bolsista Fátima Pereira Duque (Pibic/CNPq/UFF) pela montagem dos Quadros 4, 5 e 6. Anexo 1 - Questionário de sondagem para professores: Universidade Federal Fluminense Centro de Estudos Sociais Aplicados Faculdade de Educação Pesquisa CTS no contexto da alfabetização científica. Prezado(a) professor(a), Agradecimentos As autoras agradecem à bolsista Fátima Pereira Duque (Pibic/CNPq/UFF) pela montagem dos Quadros 4, 5 e 6. 27 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 Volume 02 / Número 1 – Març. 2002 Volume 02 / Número 1 – Març. 2002 ENSAIO – Pesquisa em Educação em Ciências Prezado(a) professor(a), Estamos solicitando a sua colaboração no sentido de responder às perguntas em anexo, o que muito contribuirá para sabermos como nossas escolas têm lidado, no ensino de ciências, com a relação CTS. Desde já agradecemos a sua valiosa colaboração. A equipe da pesquisa 1. Itens gerais de identificação: 1.1. Tipo(s) de disciplina que leciona 1.2. Série(s) em que atua 1.3. Tempo de exercício do magistério 1.4. Tipo de escola em que trabalha: pública / particular 2.1. Que tipos de conteúdo o senhor (a senhora) costuma desenvolver? 2.2. Desses conteúdos quais são, na sua opinião, aqueles em que estão presentes aspectos ligados à relação CTS? Por quê? 3. Solicitação final: se o senhor (a senhora) dispõe de algum material produzido para transmitir ou avaliar conteúdos relativos a CTS (textos de aula, provas ou testes de alunos, trabalhos de aluno etc.), gostaríamos que anexasse um exemplar a este instrumento de pesquisa. Anexo 2 - Ficha de Observação MAST/CNPq Formulário de observação: pesquisa CTS Sala: Data: Hora: Nome do bolsista: Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 28 Anexo 2 - Ficha de Observação MAST/CNPq Formulário de observação: pesquisa CTS Sala: Data: Hora: Nome do bolsista: Anexo 2 - Ficha de Observação MAST/CNPq Formulário de observação: pesquisa CTS Sala: Data: Hora: Nome do bolsista: Anexo 2 - Ficha de Observação MAST/CNPq Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 2 28 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Explicações/ênfases Profs. Prezado(a) professor(a), e monitores Dúvidas, questões e comentários de alunos Anexo 3 – Tabelas com informações sobre os professores Tabela 2 - Séries em que os professores atuam e disciplina que lecionam Nível de Ensino: Fundamental Médio Superio r total Disciplina: CA a 4ª série 5ª a 8ª série 1ª a 3ª série Ciências e Biologia 0 11 10 0 21 Química 0 0 1 0 1 Química e Ciências 1 2 2 0 5 Ciências 2 16 0 0 18 Educação Ambiental e Ciências 0 1 0 0 1 Física 0 0 1 0 1 Ciências, Biologia, Programa de Saúde 0 1 1 0 2 Ciências e Programa de Saúde 0 1 0 0 1 Química, Física e Matemática 0 1 1 0 2 Português, Estudos Sociais, Matemática e Ciências 4 1 2 0 7 Ecologia e Biologia 0 1 1 0 2 Todas - Núcleo Comum 20 0 0 0 20 Biologia, Ciências e Programa de Saúde 0 1 0 0 1 Física e Matemática 0 1 1 1 3 Outras 4 9 4 0 17 TOTAL 31 46 24 1 102 Obs: CA – Ciclo de Alfabetização, que corresponde à 1ª e 2ª séries do Ens Fundamental REFERÊNCIAS BIBLIOGRÁFICAS: ANGOTTI, J. A. P. 1991. Fragmentos e Totalidades do Conhecimento Científico e do Ensino de Ciências. São Paulo: Faculdade de Educação da USP. (Tese, Doutorado). ANGOTTI, J. A. P. 1991. Fragmentos e Totalidades do Conhecimento Científico e do Ensino de Ciências. São Paulo: Faculdade de Educação da USP. (Tese, Doutorado). ARONS, A. B. 1983. Achieving Wider Scientific Literacy. Daedalus, n.112, p. 91-121. AULER, D., Stueder, D. M., CUNHA, Marcio B. O enfoque ciência-tecnologia-sociedade como parâmetro e motivador de alterações curriculares. In: ENCONTRO NACIONAL DE PESQUISA EM ENSINO DE CIÊNCIAS, 1, 1997, Águas de Lindóia – SP. Atas... Porto Alegre: Instituto de Física – UFRGS, 1997. p. 187-192. BARROS, S. S. 1990. O Acidente de Goiânia - subsídio para um módulo de ensino relacionado à ciência-tecnologia-sociedade (CTS). In: GONÇALVES, O. D. (Org.). O ensino de física e a física da atualidade. Rio de Janeiro: Ed. UFRJ. (Trabalhos apresentados durante a 1ª Escola de Verão para Licenciados). BARTHES, R. 1993. Mitologias. Rio de Janeiro: Bertrand Brasil. Anexo 3 – Tabelas com informações sobre os professores Tabela 2 - Séries em que os professores atuam e disciplina que lecionam Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 29 29 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Tabela 3 - Séries em que os professores atuam e tipo de escola em que trabalham Nível de Ensino: Tipo de Escola: Fundamental Médio Superior Educaçã o Especial total CA à 4ª série 5ª à 8ª série 1ª à 3ª série - - - Pública 27 36 13 1 1 78 Particular 3 2 4 0 0 9 Pública/Particul ar 2 8 7 0 0 17 Outras 1 0 0 0 0 1 total 33 46 24 1 1 105 3 - Séries em que os professores atuam e tipo de escola em que trabalham BARTHES, R. 1993. Mitologias. Rio de Janeiro: Bertrand Brasil. BRASIL. Ministério da Educação e do Desporto. Secretaria de Educação Fundamental. Parâmetros Curriculares Nacionais: terceiro e quarto ciclos do ensino fundamental: ciências naturais. Brasília, 1998. 138p. BRUNER, J. 1996. Toward a theory of Instruction. Cambridge: Harvard University Press. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 30 30 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 CAZELLI, S. 1992. Alfabetização Científica e os Museus Interativos de Ciências. Rio de Janeiro: Departamento de Educação da PUC-RJ. (Dissertação, Mestrado). CHRÉTIEN, C. 1994. A Ciência em ação: mitos e limites. Campinas: Papirus. (Coleção Filosofia no Presente). ENGUITA, M. F. 1988. Tecnologia e Sociedade: a ideologia da racionalidade técnica, a origem do trabalho e a educação. Educação e Realidade, Porto Alegre, vol. 13, n. 1, p.39-52, jan./jun. 1988. FINNEGAN, R. 1988. Literacy and Orality: Studies in the Technology of Communication. Oxford: Basil Blackwell. FORQUIN, J.C. 1993. Escola e Cultura. Porto Alegre: Artes Médicas. FORQUIN, J.C. 1993. Escola e Cultura. Porto Alegre: Artes Médicas. FRANÇA, M. S. J. et al. O futuro é agora. Revista Época, São Paulo, n.33, p.36-103, jan. 1999. GRUPO DE REELABORAÇÃO DO ENSINO DE FÍSICA – GREF. 1991. Física. São Paulo: USP. v. 1, 2 e 3. FRANÇA, M. S. J. et al. O futuro é agora. Revista Época, São Paulo, n.33, p.36-103, jan. 1999. FRANÇA, M. S. J. et al. O futuro é agora. Revista Época, São Paulo, n.33, p.36-103, jan. 1999. GRUPO DE REELABORAÇÃO DO ENSINO DE FÍSICA – GREF. 1991. Física. São Paulo: USP. v. 1, 2 e Ç , S J et a O utu o é ago a e sta poca, São au o, 33, p 36 03, ja 999 GRUPO DE REELABORAÇÃO DO ENSINO DE FÍSICA – GREF. 1991. Física. São Paulo: USP. v. 1, 2 e HALLINGEN, H. 1998. Science & Technology Studies. Wollongong: University of Wollongong. LEVINE, D. 1995. Visões da Tradição Sociológica. Rio de Janeiro: Zahar. LIGHTMAN, A. 1966. Sonhos de Einstein. São Paulo: Cia das Letras. MCLUHAN, M., QUENTIN, F. 1967. The Medium is the Message. New York: Bantam. MENEZES, L. 1988. Crise, Cosmos, Vida Humana: Física para uma Educação Humanista. São Paulo: Instituto de Física da USP. (Tese, Livre Docência). MILLER, J. D. 1987. Science Literacy, in the United States. Communicating Science to the Public. In: EVERED, D., O’ CONNOR, M. (Eds.) London: Wiley. MORAES, A. BARTHES, R. 1993. Mitologias. Rio de Janeiro: Bertrand Brasil. M. 1994. A inovação ciência, tecnologia e sociedade no ensino de ciências: uma análise sociológica. Revista de Educação, Lisboa, p.87-99. MORIN, E. 1996. Ciência com Consciência. Rio de Janeiro: Bertrand Brasil. MUSEU DE ASTRONOMIA E CIÊNCIAS AFINS - MAST. 1992. Quatro Cantos de Origem. São Paulo. (Projeto Museológico da Exposição Permanente). Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 31 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 31 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 PIERSON, A. H. C., HOSOUME, Y. O cotidiano, o ensino de física e a formação da cidadania. In: ENCONTRO NACIONAL DE PESQUISA EM ENSINO DE CIÊNCIAS, 1, 1997, Águas de Lindóia – SP. Atas... Porto Alegre: Instituto de Física – UFRGS, 1997. p.86. ROBEENS, K., WEBSTER, F. 1989. The Technical Fix: Education, Computer and Industry. London: MacMillan. RODRIGUES, A. M. 1997. Fundamentos em Filosofia da Tecnologia. Revista Tecnologia e Cultura, Rio de Janeiro, 1, n.1, p.11-8, jul/dez. 1997. RUTHERFORD, F. J., AHLGREEN, A. 1995. Ciência para todos. Lisboa: Publicação Lid. RYE, J. A. 1998. Teaching Beliefs and Practices of Research Scientist Faculty MemberEngaged in Science-Technology-Society (STS). Horgantown: West University. SCHARMANN, L. C. 1998. Preservice Secundary Science Teacher’s Orientations Toward Science- Technology-Society (STS) Education. Manhattan: Kansas State University. SHEN, B. S. P. 1975. Science Literacy. American Scientist, n. 39, p.265-68. SOLOMON, J. 1993. Teaching Science, Technology and Society. Buckingham: Open University Press. (Coleção Developing Science and Technology Education). ZANETIC, J. 1989. Física Também é Cultura. São Paulo: Faculdade de Educação da USP. (Tese, Doutorado). ZIMAN, J. 1985. Enseñanza y Aprendizage sobre la Ciencia y la Sociedad. México: Fondo de Cultura Económica. ------------. 1978. Reliable Knowledge. An Exploration of the Grounds for Belief in Science. Cambridge: Cambridge University Press. ZUCKERMAN, M. J. 1999. Computadores sofrem outras ameaças. Folha de São Paulo, São Paulo, 06 jun. 1999. Informática, 5, p.3. 32 Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 32 ENSAIO – Pesquisa em Educação em Ciências Volume 02 / Número 1 – Març. 2002 Abstract: The article shows that it is possible and necessary to develop scientific literacy by integrating formal with non-formal education. It is argued that the idea of scientific literacy is directly linked to the Science, Technology and Society approach to science education. BARTHES, R. 1993. Mitologias. Rio de Janeiro: Bertrand Brasil. The meanings of scientific literacy and CTS are reviewed and the importance of including narrative, myth, science and technology in science education defended. It is also reported the results of a survey conducted with different members of the public of Museu de Astronomia e Ciências Afins in Rio de Janeiro (108 teachers attending a course, 18 participants a seminar plus groups of visiting students). The survey shows, on the one hand, the possibilities seen by teachers on choosing to teach science through a CTS perspective. On the other hand, it shows the incoherence that emerges when certain academic topics are explored when students visit a science museum. Maria Cristina Leal; Avenida Borges de Medeiros 3371/401 –Rio de Janeiro, RJ – cep 22.470- 001. Correio eletrônico: leal4512@rionet.com.br. Guaracira Gouvêa de Sousa; Rua Belizário Távora 431/401 – Rio de Janeiro, RJ – cep 22.245- 070. Correspondência: Maria Cristina Leal; Avenida Borges de Medeiros 3371/401 –Rio de Janeiro, RJ – cep 22.470- 001. Correio eletrônico: leal4512@rionet.com.br. Guaracira Gouvêa de Sousa; Rua Belizário Távora 431/401 – Rio de Janeiro, RJ – cep 22.245- 070. Submetido em 15/01/1998, aceito para publicação em 23/11/1999. Rev. Ensaio | Belo Horizonte | v.02 | n.01 | p.05-33 | jan-jun | 2000 33 33
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Interpretasi Semiotika Ferdinand De Saussure dalam Hadis Liwa dan Rayah
Mashdar
2,019
cc-by-sa
3,706
Abstrak Artikel ini merupakan penelitian yang mengakaji interpretarsi hadis nabi dalam bedera Rayah dan Liwa atau bendera tauhid. Di Indonesia organisasi yang menggunakan simbol bendera tauhid adalah organisasi Hizbut Tahriri Indonesia. Bendera tersebut ada dua warana yaitu hitam dan putih. Maising-masing dari warna tersebut bertulisan Laa illaaha illaa Allah Muhammad Rasul Allah dan keduanya mempunyai makna yang berbeda. Dalam konteks sejarah bendera Liwa dan Rayah digunakan oleh Nabi Muhammad dan pada konteks budaya bendera Liwa dan Rayah digunakan untuk mendirikan negara Khilafah. Dengan legitimasi bahwa bendera Tauhid adalah bendera kemenenagan sehingga organisasi Hizbit Tahrir Indonesia menggunakan bendera tersebut sebagai wujud akan berdirinya sistem pemerintahan yang beridiologikan Khilafah. Hizbut Tahrir menegaskan bahwa bendera Liwa dan Rayah bukan benderanya melainkan bendera Islam. Analisis semiotika Ferdinand De Saussure. Dengan teori semiotikanya yang terdiri dari empat konsep, namun dalam penelitian ini peneliti hanya menggunakan dua konsep diataranya adalah yang pertama signifiant dan signifie dan kedua kosep langue dan parole. Sebagai bentuk obyek bendera Hizbut Tahrir dan teks hadis tentang liwa dan rayah menjadi objek fokus dalam penelitian ini. Kata kunci : Hadis Liwa dan Rayah; Hizbut Tahrir Indonesia; Semiotika Ferdinand De Saussure M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... Interpretasi Semiotika Ferdinand De Saussure dalam Hadis Liwa dan Rayah Interpretasi Semiotika Ferdinand De Saussure dalam Hadis Liwa dan Rayah M. Dani Habibi UIN Sunan Kalijaga Yogyakarta e-mail : dhany24habibi@gmail.com Keywords : Hadith Liwa and Rayah; Hizbut Tahrir Indonesia; Semiotics Ferdinand de Saussure Ab t k eywords : Hadith Liwa and Rayah; Hizbut Tahrir Indonesia; Semiotics Ferdinand de Saussure Abstract Abstract This article is a study that mengakaji interpretarsi Hadith in the flag Rayah and Liwa or the flag of monotheism. In Indonesia, an organization that uses the banner of Tawheed is the symbol of the organization Hizbut Tahrir Indonesia. There are two warana flag that is black and white. Maising each of the color markedLaa illaaha illaa Allah Muhammad Messenger of God and both have a different meaning. In the context of the history of Liwa and Rayah flag used by the Prophet Muhammad and the cultural context and Rayah Liwa flag is used to establish the Khilafah state. With the legitimacy that the flag of Tawheed is the flag of victory, so the organization Hizbut Tahrir Indonesia using the flag as a form would be the establishment of system of government that has the ideology of Khilafah. Hizb ut-Tahrir insists that the flag Liwa and Rayah not the flag but the flag of Islam. Semiotic analysis of Ferdinand de Saussure, With the theory of semiotics consisting of four concepts, but in this study the researchers only used two concepts among which the first signifiant and signifie both langue and parole. As the shape of the object flag Hizbut Tahrir Indonesia and hadith texts about Liwa and Rayah become the object of focus in this study. 3 Deni Junaedi, “Bendera Hizbut Tahrir Indonesia Daerah Istimewa Yogyakarta"kajian Konteks Sejarah, Budaya dan Estitika Semiotis,” Jurnal Kawistara 2, no. 3 (22 Desember 2012): 265, https://doi.org/10.22146/kawistara.3938. 2 Syamsul Arifin, “Gerakan Hizbut tahrir dan Realitas Politik Islam Kontemporer di Indonesia: Tafsir Sosial Atas Hizbut Tahrir,” Al-Tahrir: Jurnal 1 Siti Fatkhiyatul Jannah, “Diskursus Negara Antara Nahdlatul Ulama dan Hisbut Tahrir Indonesia di Jawa Timur,” Paradigma 1, no. 3 (28 Agustus 2013): hlm 2, http://jurnalmahasiswa.unesa.ac.id/index.php/paradi gma/article/view/4143. Pemikiran Islam 14, no. 1 (1 Mei 2014): 4, https://doi.org/10.21154/al-tahrir.v14i1.80. Agustus 2013): hlm 2, http://jurnalmahasiswa.unesa.ac.id/index.php/paradi gma/article/view/4143. 1 Siti Fatkhiyatul Jannah, “Diskursus Negara Antara Nahdlatul Ulama dan Hisbut Tahrir Indonesia di Jawa Timur,” Paradigma 1, no. 3 (28 Agustus 2013): hlm 2, PENDAHULUAN mengembangkan paham-paham tentang keisalaman sepeti organisasi Hizbut Tahrir Indonesia. Hizabut Tahrir Indonesia merupakan organisasi Islam yang bergerak Indonesia dengan negara yang mempunyai penduduk Muslim terbanyak didunia menajadi sebuah media untuk 115 116 | Mashdar : Jurnal Studi al-Quran dan Hadis, Vol.1, No.2, (2019) pergerakan perubahan dengan penawaran baru berupa idiologi dan sistem pemerintahan Khilafah.2 Secara harfiah HTI atau Hizbut Tahrir mempunyai makna “ parati pembebasan”, didalam bahasa arab kata hizb berati partai dan at-tahrir berati pembebasan. Artinya bahwa Hizbut Tahrir adalah sebuah gerakan partai Islam yang bertujuan menyatukan umat Muslim diseluruh dunia dengan ideologi dan sistem Khilafah3. dibidang dakwah. Padamulamnya organisasi Hizbut Tahrir didikikan oleh Taqiyuddin an- Nabhani pada tahun 1953. Organisasi Hizbut Tahrir mempunyai sebuah tujuan yakni mengembalikan kejayaan Islam melalui penegakan negara Khilafah Islamiyah. Penyatuan pemerintahan berbasis sitem Khilafah dari berbagai penjurudunia salah satu misi besar Hizbut Tahrir. Pada tahun 1992 Hibut tahrir masuk ke Indonesia dan menjadi organisasi Islam konserfatif dan fundamentalis. Karena dalam mempunayi sebuah ideologi kembali ke Al-Qur’an dan Sunah sebagai sumber hukum Islam yang mutkal kebenarannya. Pemahaman tekstual ketika memahami Al-Qur’an dan Sunah menjadikan organisasi ini radikal dan tidak sedikit negara-negara yang menolak organisasi Hizbut Tahrir termasuk Indonesia.1 Pada saat melakukan kegiatan terbuka maupun tertutup, Hizbut Tahrir selalu mengibarkan bendera yang bernama Liwa dan Rayah. Bendera tersebut masing-masing terdapat tulisan lafaz Laa illaaha illaa Allah Muhammad Rasul Allah. Bendera liwa adalah bendera yang berwarna putih dan bendera rayah mempunyai warnah hitam. Kedua bendera tersebut masing-masing mempunyai makna yang berbeda. Dalam konteks budaya ketika menganalisa liwa dan rayah terbagi menjadi tiga unsur diantaranya sistem budaya, aktivitas, dan artafak. Sistem budaya yang terdiri dari kosep, gagasan, ideologi pemikiran, nilai Pasca Orde Baru, proses demokrarsi tidak hanya ditandai dengan munculnya partai-partai politik. Melainkan juga bermunculan kelompok-kelompok gerakan Islam termasuk HTI. Sehingga pada pasca Orde Baru, kelompok Islam HTI mengidentifikasikan sebagai kelompok M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... | 117 | 117 dan norma-norma atau jenisnya yang bersifat abstrak. Sedangkan aktivitas yaitu suatu tindakan dalam prilaku budaya dan artefak adalah berupa benda ciptaan manusia. Idelogi yang tersusun dalam sebuah sistem pemerintahan Khilafah melalui simbol bendera HTI disusun untuk menyerang atau mendukung suatu misi atau maksud tertentu. 4 David Kaplan dan Albart A. Manners “ Teori Budaya”, trj, Landang Simatupang. (Yogyakarta: Pustaka Pelajar .2012).hlm 154 PENDAHULUAN Oleh sebab itu tidak heran bahwa sistem pemerintahan yang di bangun Khilafah di tolak diberbagai negara termasuk Indonesia karena ideologi yang diperjuangkan berbeda atau berbenturan dengan ideologi Pancasila.4 Dengan menggunakan bendera liwa dan rayah sebagai tanda dimana eksistensi keberadaan kelompok HTI bergerak dan melakukan kegiatan dakwah-dakwahnya. rayah adalah bendera yang digunakan oleh rasulullah. Dengan memperhatikan kosep signifier (penanda) dan signifind (Petanda) juga dengan memperhatikan langue dan parole. 5Syafieh Syafieh dan Nurbaiti Nurbaiti, “Potret Karakteristik Kepemimpinan Perempuan" (Analisis Semiotika Surat Al-Naml: 23-44),” Jurnal At-Tibyan: Jurnal Ilmu Alquran Dan Tafsir 3, no. 1 (9 Agustus 2018): 54, ( g ) https://doi.org/10.32505/tibyan.v3i1.477. 7 Ferdinand de Saussure “Cours de Linguistique General” trj. Rahayu S. Hidayat. (Yogyakarta. Gajah Mada Press.1996). hlm.374. 6 Kaelan “ Filsafat Bahasa Semiotika dan Herrmeneutika” ( Yogyakarta : Paradigma. 2009). hlm.181 PERSPEKTIF METODOLOGI Istilah semiotika modern diperkenalkan oleh dua tokoh yaitu Ferdinand de Saussure (1857-1913) dan Charles Sanders Peirce (1839-1914). Dua tokoh inilah yang sangat berpegaruh dalam linguistik dan semiotik. Kedua tokoh tersebut masing-masing mempunyai konsep seperti Saussure dengan konsep tanda dan penanda dan Pierce mempunyai konsep sign, object dan interpretant5. Namun dalam penelitian ini peneliti akan berfokus pada aplikasi teori Ferdinand De Saussure sebagai analisis obyek dalam hal ini adalah bendera Hizbut Tahrir Indonesia HTI. Dengan menggunakan pendekatan semiotika dan meminjam teori Ferdinand De Saussure, peneliti mencoba untuk menganalisa problem tanda berupa bendera liwa dan rayah dalam konteks organisasi HTI. HTI dengan Benderanya tersebut sudah menjadi legitimasi kebenaran mutlak oleh mereka bahwa bendera liwa dan Ferdinand De Saussure dilahirkan di kota Jenewa pada tanggal 26 November pada tahun 1857. Ia dilahirkan dari keluarga yang sangat terkenal di kotanya. Dengan keberhasilanya dalam bidang ilmu bahasa atau linguistik beliau mendapat sebutan 118 | Mashdar : Jurnal Studi al-Quran dan Hadis, Vol.1, No.2, (2019) bapak linguistik. Saussure lahir sezaman dengan Email Durkheim. Sejak kecil ia sudah mempunyai banyak karya berupa Essai dibidang bahasa. Dan pada tahun 1874 ia mulai memulai belajar bahsa Sansekerta. Kiprahnya dibidang linguistik semakin terlihat ketika pada tahun 1880 ia berhasil mempertahankan tesisnya tentang kasus genetatif mutlak dalam bidang bahasa Sansekerta6. berupa (tanda, suara, bentuk, gambar maupun gerak). Kedua aspek penanda (singnifer). Dan yang ketiga aspek petanda (singnified)8 Sehingga hubungan antara tanda dan penanda bersifat arbiter (bebas). Namun didalam sebuah tanda tentu memilki nilai-nilai tertentu (value) sedangkan menurut Saussure tanda-tanda tersebut direlasikan dengan sistem tanda-tanda yang lain (sintagma) yang akan bisa menjadikan perbedaan (difference)9. Namun didalam sebuah tanda tentu memilki nilai-nilai tertentu (value) sedangkan menurut Saussure tanda-tanda tersebut direlasikan dengan sistem tanda-tanda yang lain (sintagma) yang akan bisa menjadikan perbedaan (difference)9. Saussure memang terkenal dengan sistem tanda dan penanda. Namun dalam sejarah ia tidak pernah mencetak sebuah buku melainkan setiap ada kuliah atau kuliah umum catatan-catatan dari uraian diskusinya dicatat oleh murid-muridnya lalu dijadikan sebuah outline. Salah satu karya yang telah terbit adalah sebuah buku yang berjudul Course in General linguistics. Kemudian karya tersebut menjadi sebuah karya yang sangat berpengaruh dibidang kebahasaan atau Linguistik. Dan karya itulah yang dinamakan dengan istilah “strukturalisme”.7 8 Wildan Taufiq, “Ideologi di Balik Simbol- Simbol Surga dan Kenikmatan dalam Ayat-Ayat Al- Qur'an,” Desember 2008, 156, http://publikasiilmiah.ums.ac.id/handle/11617/181. 9Ferdinand de Saussure “Cours de Linguistique General” trj. Rahayu S. Hidayat. (Yogyakarta. Gajah Mada Press.1996). hlm.7. 8 Wildan Taufiq, “Ideologi di Balik Simbol- Simbol Surga dan Kenikmatan dalam Ayat-Ayat Al- Qur'an,” Desember 2008, 156, http://publikasiilmiah.ums.ac.id/handle/11617/181. 9Ferdinand de Saussure “Cours de Linguistique General” trj. Rahayu S. Hidayat. (Yogyakarta. Gajah Mada Press.1996). hlm.7. Sejarah Bendera Liwa dan Rayah Dalam sejarah bendera liwa dan rayah terbentuk di kota madinah pada tahun 622, dan ketika Nabi Muhammad memerintahkan penggunaan liwa (bendera) dan rayah yang berarti panji keislaman. Liwa yang berwana putih dan rayah berwarna hitam. Hal tersebut terdapat dalam hadis nabi yang berbunyi : َحَدَّثَنَا مُحَمَّدُ بْنُ رَافِعٍ حَدَّثَنَا يَحْيَى بْنُ إِسْحَق وَ هُوَ السَّالِحَانِيُّ حَدَّثَنَا يَزِ يدُ بْنُ حَيَّانَ قَال ْسَمِعْتُ أَبَا مِجْلَزٍ َلَ حِ قَ بْنَ حُمَيْدٍ يُحَد ِثُ عَن ابْنِ عَبَّاسٍ قَال كَانَتْ رَايَةُ رَسُولِ َّللاَّ ِ صَلَّى Dalam kajian semiologi misalnya, Saussure menegaskan bahwa sistem tanda memiliki tiga aspek, yaitu itu sendiri yaitu Pertama (sing) atau aspek material baik M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... | 119 | 119 M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... ََّللاَّ ُ عَلَيْهِ وَ سَلَّمَ سَوْ دَاءَ وَ لِوَ اؤُهُ أَبْيَض قَالَ أَبُو ِعِيسَى هَذَا حَدِيثٌ حَسَنٌ غَرِ يبٌ مِنْ هَذَا الْوَ جْه ٍمِنْ حَدِيثِ ابْنِ عَبَّاس ََّللاَّ ُ عَلَيْهِ وَ سَلَّمَ سَوْ دَاءَ وَ لِوَ اؤُهُ أَبْيَض قَالَ أَبُو ِعِيسَى هَذَا حَدِيثٌ حَسَنٌ غَرِ يبٌ مِنْ هَذَا الْوَ جْه ٍمِنْ حَدِيثِ ابْنِ عَبَّاس bertulisan Laa illaaha illaa Allah Muhammad Rasul Allah. Dibawah ini adalah gambar bendera liwa dan rayah yang digunakan oleh ormas Hizbut Tahrir Indonesia. Garmbar 1: Liwa berwarna dasar putih dengan kalimat sahadat berwarna hitam (Foto: Dani Habibi, 2018) Telah menceritakan kepada kami Muhammad bin Rafi' berkata, telah menceritakan kepada kami Yahya bin Ishaq, yaitu As Salihani- berkata, telah menceritakan kepada kami Yazid bin Hayyan ia berkata; Aku mendengar Abu Mijlaz Lahiq bin Humaid menceritakan dari Ibnu Abbas ia berkata, "Bendera Rasulullah shallallahu 'alaihi wasallam berwarna hitam dan umbul-umbulnya berwarna putih." Abu Isa berkata, "Hadits ini derajatnya hasan gharib melalui jalur ini, dari Ibnu Abbas. Telah menceritakan kepada kami Muhammad bin Rafi' berkata, telah menceritakan kepada kami Yahya bin Ishaq, yaitu As Salihani- berkata, telah menceritakan kepada kami Yazid bin Hayyan ia berkata; Aku mendengar Abu Mijlaz Lahiq bin Humaid menceritakan dari Ibnu Abbas ia berkata, "Bendera Rasulullah shallallahu 'alaihi wasallam berwarna hitam dan umbul-umbulnya berwarna putih." Abu Isa berkata, "Hadits ini derajatnya hasan gharib melalui jalur ini, dari Ibnu Abbas. Liwa dan rayah memang dulu digunakan oleh nabi Muhammad saw sebagai tanda pemerintahan Islam waktu itu. Namun, didalam konteks saat ini tanda yang disebut liwa dan rayah digunakan oleh ormas HTI sebagai bendera ideologis10 Khilafah Islamiyah. Menjadi masalah jika dalam hadis liwa dan rayah tidak tertulis kalimat tauhid. 10 Masnun Masnun dan Zusiana Elly Triantini, “Spiritualitas Islam, Khilafah Islamiyah dan Gerakan Politik Hukum Ingkar Nkri (Studi terhadap Gerakan Politik Hizbut Tahrir di Indonesia),” Istinbath: Jurnal Hukum Islam IAIN Mataram 15, no. 2 (2016): 196. Problem Interpretasi Berdera Hizbut Tahrir Indonesia Bendera HTI diklaim bendera yang dikabarkan oleh rasulullah dengan kata lain siapa yang mengibarkan bendera rasulullah maka ia termasuk kedalam golongannya12. Simbol berupa bendera identitas organisasi Hizbut Tahrir Indonesia dinilai tidak layak Sejarah Bendera Liwa dan Rayah Berbeda dengan bendera liwa dan rayah yang digunakan oleh HTI. Bendera tersebut berwarna hitam dan putih yang masing-masing bertulisan kalimat Melalui bendera tersebutlah, Hizbut Tahir menyebarkan panji-panji idiologis politik kepada masyarakat Muslim. Sehingga mereka mempunyai anggapan bahwa bendera yang rasulullah adalah 120 | Mashdar : Jurnal Studi al-Quran dan Hadis, Vol.1, No.2, (2019) bendera yang sama digunakan oleh Hizbut Tahrir. Dengan mengibarkan bendera tersebutlah panji-panji keislaman akan menjadi lebih kuat dan lebih sesuai dengan yang diajarkan oleh nabi Muhammad saw. Namun pada umumnya bendera liwa dan rayah yang digunkana oleh nabi untuk peperangan. Liwa yang berada dekat pada pemimpin tertinggi dan ruyah digunakan untuk komandan perang11. Sebagai konteks budaya, sebuah bendera memang menjadi sebuah identitas yang menunjukan eksistensinya didalam masyarakat. Baik yang berfungsi sebagai tanda didaerah, identitas kelompok, dan simbol pertempuran. Namun dalam konteks ini, peneliti berfokus pada sebuah tanda berupa simbol bendera rasulullah sebagai identitas kenegaraan. dikibarkan di Negara Kesatuan Replublik Indonesia. Sebab sebagaian besar masyarakat memandang bahwa bendera HTI adalah bedera yang menjadikan idiologi bangsa seperti Indonesia menjadi rapuh. Namun, bagi masyarakat penganut Hizbut Tahrir menilai bendera liwa dan rayah adalah bendera rasulullah. Sebenarnya bendera liwa dan rayah menjadi kontofersi ketika didalamnya terdapat idiologi tertentu yang bertujuan merusak idiologi yang sudah ada di tiap-tiap negara seperti Indonesia. Kebangkitan organisasi Hizbut Tahrir di Indonesai memang sangat di waspadai karena dapat merusak sistem dan idiologi bangsa.13 Perbentuaran dua idiologi yang mempunyai visi dan misi berbeda menimbulkan konflik. Sehingga setiap orang jika membawa bendera liwa dan rayah di Indonesia maka dinilai sebagai pengikut Hizbut Tahrir Indonesia. 13 Rosi Selly, “Globalisasi dan Kebangkitan Khilafah Islamiyah Dalam Perspektif Pemikiran Hizbut Tahrir,” 29 Agustus 2008, 28, http://repository.uinjkt.ac.id/dspace/handle/1234567 89/7538. 11 Deni Junaedi, “Bendera Hizbut Tahrir Indonesia Daerah Istimewa Yogyakarta"kajian Konteks Sejarah, Budaya dan Estitika Semiotis,” Jurnal Kawistara 2, no. 3 (22 Desember 2012): 267, https://doi.org/10.22146/kawistara.3938 12 Arifin, “Gerakan Keagamaan Baru dalam Indonesia Kontemporer,” Komunika Jurnal dakwah dan Komukasi hlm 6. 15 Ferdinand de Saussure “Pengantar Linguistik Umum” trj. Rahayu S. Hidayat. (Yogyakarta. Gajah Mada Press.1996). hlm.25. 14Ferdinand de Saussure “Pengantar Linguistik Umum” trj. Rahayu S. Hidayat. (Yogyakarta. Gajah Mada Press.1996). hlm 6 Analisis Interpretasi Berdera Hizbut Tahrir Indonesia Dalam penelitian ini, peneliti menggunakan pendekatan semiotika dalam meninterpetasikan ulang simbol bendera M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... | 12 | 121 tauhid dalam organisasi Hizbut Tahrir Indonesia. Dengan menggunakan pendekatan semiotika yang digagas oleh Ferdinand de Saussure peneliti akan mencoba untuk menafsirkan kembali simbol bendera HTI yang bersumber sari sebuah hadis Nabi tentang bendera. masyarakat tentunya banyak ditemukan parole-parole yang mempunyai relasi kepada realitas. Sehingga gabungan dari parole-parole dalam kaidah bahasa oleh Saussure disebut dengan langue. Langue adalah keseluruhan kebiasaan yang didapatkan dari masyrakat. Terjadinya komunikasi antara satu parole dengan parole yang lain sehingga membentuk suatu pemahaman yang klektif di masyarakat. Kejadian seperti ini sering dialami oleh masyarakat, lebih-lebih didalam masyarakat majemuk yang didalamnya terdapat banyak aliran dan suku. Sehingga mengerucut pada penelitian ini yang berfokus pada interpretasi objek Liwa dan Rayah didalam hadis nabi diatas dengan menggunakan pendekatan semiotika dan teori Fardinand de Saussure. ُحَدَّثَنَا مُحَمَّدُ بْنُ رَافِعٍ حَدَّثَنَا يَحْيَى بْن َإِسْحَقَ وَ هُوَ السَّالِحَانِيُّ حَدَّثَنَا يَزِ يدُ بْنُ حَيَّان َقَال سَمِعْتُ أَبَا مِجْل ُزٍ َلَ حِ قَ بْنَ حُمَيْدٍ ي ُحَد ِث عَنْ ابْنِ عَبَّاسٍ قَال ِ َّكَانَتْ رَايَةُ رَسُولِ َّللا َصَلَّى َّللاَّ ُ عَلَيْهِ وَ سَلَّمَ سَوْ دَاءَ وَ لِوَ اؤُهُ أَبْيَض ْقَالَ أَبُو عِيسَى هَذَا حَدِيثٌ حَسَنٌ غَرِ يبٌ مِن ٍهَذَا الْوَ جْهِ مِنْ حَدِيثِ ابْنِ عَبَّاس Saussure mempunyai kerangka teoritis yang ia bangun yaitu keraka tersebut seperti langue, parole dan langage. Didalam buku yang berjudul Cours de Linguistique Gernerale karya Fardinand de Saussure yang sudah diterjemahkan menjadi Pengantar Linguistik Umum dijelaskan bahwa yang dimaksud dengan parole adalah keseluruhan apa yang diajarkan oleh orang, termasuk kontruksi-kontruksi individu yang muncul dari ucapan penutur14. Jelasnya yang dimaksud dengan istilah parole ialah manifestasi individu dari bahasa. Didalam Didalam buku yang Pengantar Linguistik Umum, Saussure mendefinisiskan beberapa istilah dalam teorinya seperti, Parole, Langue, Sinkronik dan Diakronik. Parole adalah tuturan, tiap-tiap individu yang menjadi sebuah satu kesatuan sistem yang mentuk norma-norma kolektif didalam masyarakat15. Jika merujuk pada teks hadis diatas parole-parol yang muncul didalam masyarakat dahulu menjadikan lagitiammsi individu berupa liwa yang sering diucapkan 122 | Mashdar : Jurnal Studi al-Quran dan Hadis, Vol.1, No.2, ( oleh masyarkat pada zaman nabi sebagai identitas bendera. yan kea 122 | Mashdar : Jurnal Studi al-Quran dan Hadis, Vol.1, No.2, (2019) yang ada dan aturan sinkronis mengatur keadaan tiap-tiap objek. Sedangkan diakroni kebalikan dari sinkronis. Diakroni adalah faktor-faktor dinamis yang bisa menghasilakan dampak, suatu yang dikerjakan. 16 Kaelan “ Filsafat Bahasa Semiotika dan Herrmeneutika” ( Yogyakarta : Paradigma.2009).hlm 191. Lihat, Ferdinand de Saussure “Pengantar Linguistik Umum” trj. Rahayu S. Hidayat.(Yogyakarta.Gajah Mada Press.1996).hlm 191. Lihat, Ferdinand de Saussure “Pengantar Linguistik Umum” trj. Rahayu S. Hidayat.(Yogyakarta.Gajah Mada Press.1996).hlm 17 Syaiful Arif, “Kontradiksi Pandangan HTI Atas Pancasila,” Jurnal Keamanan Nasional 2, no. 1 (1 Mei 2016): 24, https://doaj.org. Analisis Interpretasi Berdera Hizbut Tahrir Indonesia Akan tetapi ciri yang mengharuskan kurang cukup untuk bisa menerapkan istilah aturan atau fakta yang evolutif. Lalu parole-parole tersebut menjadi satu kesatuan dalam sistem yang menjadi legitimasi kolektif Langue seperti liwa sebagai bendera pemerintahan. Langue bersifat konveksi yang dapat diterima oleh masyarakat yang siap untuk dipakai dan dari pendahulu. Artinya jika Liwa dan Rayah menajadi langue atau legitimasi kolektif yang sudah ada sejak zaman nabi. Kesepakatan konveksi berupa liwa sebagai bendera dan Rayah sebagai ajaran memang sudah ada sejak zaman nabi Muhammad saw. Dalam kemunculanyapun tidak begitu saja pasti mempunyai historitas sebab musabab kemunculannya. Dalam penerapanya terdapat beberapa komponen penting dalam membangun interprretasi bendera HTI berupa liwa dan rayah dengan pendekatan semiotika Fardinand de Saussure. Terdapat teks yang tidak bisa berubah maknanya dan teksnya dari dulu hingga sekarang yang disebut parole. Liwa berati bendera “ parole” yang didalam teks hadis tersebut mempunyai cerita historis sebagai identitas didalam pemerintahan nabi Muhammad saw. Lalu liwa yang disebut oleh nabi didalam teks hadis diatas menjadi parole-parore lain. Sehingga dari parole yang banyak diucapkan oleh para sahabat menjadi satu kesatuan utuh dalam interpertasi bendera liwa adalah bendera pemerintahan. Saussure mempunyai pandangan bahwa untuk bisa melihat lebih jauh, bagaimana sebuah simbol terbentuk maka ia mempunyai sebuah istilah Sinkronis dan diakronis. Sinkronis adalah kata atau makna yang tidak bisa dirubah dan diakronis adalah makna yang dapat berubah dikarnakan faktor historis.16 Sinkronis bersifat umum yang tidak mengharuskan. Artinya didalam langue tidak ada satu kesatuan utuh yang dapat menjamin dan memlihara keteraturan dalam tiap-tiap butir dalam parole. Aturan sinkronis hanya mengungkapkan kelompok Dalam perkembangnya parole menjadi satu bangunan interpretasi yang menjadi legitimasi kebenaran mutlak oleh M. Dani Habibi, Interpretasi Semiotika Ferdinand De Saussure dalam... | | 123 organisasi Hizbut Tahrir Indonesia yaitu liwa adalah bendera Nabi Muhammad saw. bendera idiologi politik. Dengan kata lain, simbol bendera tersebut sudah bertrensformasi menjadi bendera yang mempunyai makna idiologis. Sassure mempunyai istilah diakrini sebagai makna yang selalu berkembang mengikuti zaman dan mempunyai faktir historis. Salah satu sejarah kemunculan bendera tersebut karena sebagai penanda kekuasaan atau pemerintahan nabi Muhammad saw. Namun dalam perkembanganya, bendera liwa dan rayah digunakan oleh HTI sebagai identitas idiologis. Transformasi makna dan perubahan simbol liwa dan rayah pada zaman rasul dan yang digunakan oleh HTI disebabkan oleh beberapa faktor. Diantaranya sebagai berikut : 18 Masnun dan Triantini, “Spiritualitas Islam, Khilafah Islamiyah dan Gerakan Politik Hukum Ingkar Nkri (Studi terhadap Gerakan Politik Hizbut Tahrir di Indonesia),” 199. SIMPULAN DAN REKOMENDASI Bendera liwa dan rayah memang bendera yang digunakan oleh rasulullah ketika memimpin pemerintahan kala itu. Namun, bendera yang digunakan merupakan bendera yang tidak bertulisan kalimat tauhid dan tidak mempunyai idiologi Khilafah. Sehingga ketika organisasi Hizbut Tahrir Indonesia menggunakan bendera liwa dan rayah yang bertulisakan kata tahuid tidak sedikit masyarakat Indonesia mengklaim bahwa itu merupakan bendera yang tidak sesuai dengan idiologi bangsa Indonesia yaitu pancasila. 1. Mengembalikan politik Islam yang saat ini telah dilupakan dan diganti oleh sistem kapitalisme dan liberalisme17. Merujuk pada pemikiran Ferddinad de Saussure kdalam interpretasi simbol bendera HTI, menyimpulakan bahwa setiap parole-parole menjadi satu kesatuan sistem utuh dan kolektif. Sehingga menjadi langue yang membangun sistem, norma-norma tertentu sesuai dengan yang diharapakan oleh masyarakat. 2. Menegakakan syari’at Islam. 3. Menumbuhkan semangat juang kembali peradaban Islam pada masa nabi. 4. Menjadikan sistem pemerintahan yang dipimpin oleh satu Khilafah. 18 Dari beberapa faktor diatas sudah mulai tergambarkan bahwa bendera yang menajadi identitas oleh organisasi Hizbut Tahrir Indonesia merupakan identitas Bendera Hizbut Tahrir Indonesia mengandung idiologi yang bertentangan 124 | Mashdar : Jurnal Studi al-Quran dan Hadis, Vol.1, No.2, (2019) Indonesaia meniali bendera tersebut adalah bendera kemunafikan idiologi. dengan idiologi Pancasila. Dikarnakan ketika masyarakat Hizbut Tahrir Indonesia mengibarkan panji-panji keislaman dan bendera liwa dan rayah maka secara tidak langsung visi dan misi menjadi tujuan HTI diorasikan. Tidak heran bahwa masyarakat Sejarah, Konteks Budaya, dan Estetika Semiotis).” Jurnal Kawistara 2, no. 3 (22 Desember 2012). https://doi.org/10.22146/kawistara.3 938 Sejarah, Konteks Budaya, dan Estetika Semiotis).” Jurnal Kawistara 2, no. 3 (22 Desember 2012). https://doi.org/10.22146/kawistara.3 938 DAFTAR PUSTAKA Kaelan “Filsafat Bahasa Semiotika dan Herrmeneutika”, Yogyakarta : Paradigma.2009. Saussure, Ferdinand. De. “Cours de Linguistique General” trj. Rahayu S Hidayat.Yogyakarta: Gajah Mada Press,1996. Masnun, Masnun, dan Zusiana Elly Triantini. “Spiritualitas Islam, Khilafah Islamiyah dan Gerakan Politik Hukum Ingkar NKRI" (Studi terhadap Gerakan Politik Hizbut Tahrir di Indonesia).” Istinbath: Jurnal Hukum Islam IAIN Mataram 15, no. 2 (2016): 193–215. David Kaplan dan Albart A. Manners “ Teori Budaya”, trj, Landang Simatupang. Yogyakarta: Pustaka Pelajar.2012. Arif, Syaiful. “Kontradiksi Pandangan HTI Atas Pancasila.” Jurnal Keamanan Nasional 2, no. 1 (1 Mei 2016). https://doaj.org. Selly, Rosi. “Globalisasi dan Kebangkitan Khilafah Islamiyah Dalam Perspektif Pemikiran Hizbut Tahrir,” 29 Agustus 2008. http://repository.uinjkt.ac.id/dspace/ handle/123456789/7538. Arifin, Syamsul. “Gerakan Keagamaan Baru dalam Indonesia Kontemporer: Tafsir Sosial Atas Hizbut Tahrir.” Al-Tahrir: Jurnal Pemikiran Islam 14, no. 1 (1 Mei 2014): 117–38. https://doi.org/10.21154/al- tahrir.v14i1.80. Syafieh, Syafieh, dan Nurbaiti Nurbaiti. “Potret Karakteristik Kepemimpinan Perempuan" (Analisis Semiotika Surat Al-Naml: 23-44).” Jurnal At- Tibyan: Jurnal Ilmu Alquran Dan Tafsir 3, no. 1 (9 Agustus 2018): 52– 68. https://doi.org/10.32505/tibyan.v3i1 .477. Fatkhiyatul Jannah, Siti. “Diskursus Negara Antara Nahdlatul Ulama dan Hizbut Tahrir Indonesia di Jawa Timur.” Paradigma 1, no. 3 (28 Agustus 2013). Taufiq, Wildan. “Ideologi di Balik Simbol- Simbol Surga dan Kenikmatannya dalam Ayat-Ayat al-Quran,” Desember 2008. http://publikasiilmiah.ums.ac.id/han dle/11617/181. http://jurnalmahasiswa.unesa.ac.id/index.ph p/paradigma/article/view/4143. Junaedi, Deni. “Bendera di Hizbut Tahrir Indonesia Daerah Istimewa Yogyakarta (Kajian Konteks
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RLocator: Reinforcement Learning for Bug Localization
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[2] J. Han, C. Huang, S. Sun, Z. Liu, and J. Liu, “bjXnet: an improved bug localization model based on code property graph and attention mechanism,” Automated Software Engineering, vol. 30, no. 1, Mar. 2023. [1] S. Cheng, X. Yan, and A. A. Khan, “A similarity integration method based information retrieval and word embedding in bug localization,” in 2020 IEEE 20th International Conference on Software Quality, Reliability and Security (QRS). IEEE, Dec. 2020. A.1 Performance comparison of RLocator with prior approaches 1 Table 1: Performance of RLocator in comparison to prior approaches Table 1: Performance of RLocator in comparison to prior approaches Project Model Top 1 Top 5 Top 10 MAP MRR AspectJ RLocator 0.40 0.63 0.70 0.46 0.50 Cheng et al. [1] 0.46 0.76 0.84 0.38 0.60 bjXnet [2] - - - - - Birt RLocator 0.25 0.41 0.48 0.38 0.41 Cheng et al. - - - - - bjXnet - - - - - Eclipse Platform UI RLocator 0.37 0.63 0.73 0.42 0.50 Cheng et al. 0.47 0.74 0.83 0.48 0.59 bjXnet 0.60 0.83 0.90 0.70 0.61 JDT RLocator 0.33 0.61 0.75 0.44 0.45 Cheng et al. 0.48 0.67 0.81 0.49 0.58 bjXnet 0.43 0.80 0.88 0.60 0.52 SWT RLocator 0.30 0.51 0.58 0.42 0.44 Cheng et al. 0.60 0.82 0.89 0.62 0.70 bjXnet 0.52 0.79 0.88 0.65 Tomcat RLocator 0.39 0.55 0.68 0.47 0.51 Cheng et al. - - - - - bjXnet - - - - - References 2
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Geldgeschichten in transepochaler Perspektive
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Die Münze hat viele Funktionen – richtig eingesetzt wird sie zur Glückbringerin. Das Fotomodell Margot Nünke und der Schauspieler Ric Badaglia werfen Münzen in den Trevi-Brunnen in Rom (Aufnahme von 1956). Geldgeschichten in transepochaler Perspektive Money in fact is the most successful story ever invented and told by humans, because it is the only story everybody believes. Olivia Denk Münzen haben viel zu erzählen. Den Lebenslauf einer antiken Münze genau zu verfolgen, von der Herstellung über ihre mannigfache Verwendung bis zu ihrem Nachleben im digitalen Sammlungskatalog, erlaubt uns, die Entwicklung von Wirtschaftsweisen und politischen Interaktionen über Jahrhunderte hinweg besser zu verstehen. Yuval Noah Harari, 21 Lessons for the 21st Century, 2018 Menschen glauben schon seit langer Zeit an die «Geschichte des Geldes». Die ersten Münzen der Menschheitsgeschichte entstanden bereits im 7. Jahrhundert vor Christus in Lydien in Kleinasien – ein Prozess, der als Revolution bezeichnet werden kann. 48 Um ein Optimum an Informationen über antike Münzen, ihren Herstellungsprozess und vor allem über ihre Verwendung zu erzielen, werden in der heutigen Numismatik traditionelle Ansätze und moderne Methoden miteinander verwoben. Stefan Krmnicek, Juniorprofessor für Numismatik in Tübingen, entwickelte für Fundmünzen das Konzept der Objektbiografie. Um die hypothetische Lebensspanne einer Münze zu skizzieren, beginnt man in diesem Modell bei der Herstellungsphase (A). Nach der erfolgten Prägung ist anzunehmen, dass die Münze in den Geldumlauf gerät und somit ihre erste monetäre Funktion als Zahlungsmittel (B1) erfüllt. Es folgt eine aktive Weiterbenutzung (B2), die möglicherweise eine monetäre Funktionserweiterung beinhaltet, indem die Münze einen Gegenstempel bekommt und damit als Zahlungsmittel in einem anderen Währungsraum akzeptiert wird. Die Münze läuft so durch verschiedene Hände, bis ihr aktiver Gebrauch nach einiger Zeit endet (C), etwa indem ein Besitzer sie einbehält. Die Beweggründe für eine solche «Thesaurierung» können vielseitig sein. Gerade in kriegerischen Zeiten ist das Bedürfnis stets gross, gewisse Wertgegenstände sicherzustellen; so können auch Münzen in einen passiven Gebrauch geraten und beispielsweise als Hort vergesellschaftet werden. Nach einiger Zeit kann die Münze erneut in die aktive Benutzung übertreten (B3) und wieder den Besitzer wechseln. Durch neue Eigentümer oder die Entwertung der Münze kann das Stück einen alternativen Gebrauch (D) erfahren: Denkbar ist eine Lochung der Münze, um sie als Schmuckstück zu verwenden oder eine Verwendung als Talisman gegen Dämonen oder als Amulett zum Schutz des Hauses. Andere Nutzungskontexte wie zur Kommunikation mit den Göttern sind ebenfalls vorstellbar. Bekannte Beispiele für einen alternativen Münzgebrauch sind für die griechische Welt der Tempelschatz, der zwar unter göttlicher Schirmherrschaft aufbewahrt wird, aber auch für militärische Zwecke aufgewendet werden kann, sowie der Charonspfennig, der Verstorbenen ins Grab beigegeben wird, um den Fährmann Charon bei der Überquerung des Flusses Styx in das Totenreich des Hades zu bezahlen. Über Jahrhunderte hinweg war das Geld in seiner Münzform direkt an Edelmetall gebunden. 1971 läutete USPräsident Nixon eine neue Ära in der Geschichte des Geldes ein, indem er Geld von Edelmetall enkoppelte. Heute sprechen wir von «Fiatgeld» («Es werde Geld!»). Der Wert des Geldes wird dabei durch die Macht einer Regierung gesichert, aber erst mit der Akzeptanz und dem Vertrauen der Nutzer wird Geld ein Zahlungsmittel. Tag ein Tag aus zahlen und rechnen wir mit Geld. Wir kaufen im Geschäft ein, bezahlen Rechnungen, überweisen die Miete oder kalkulieren das Monatsbudget. Die modernen Formen des Geldes sind dabei heute sehr divers und reichen von Münz- und Papiergeld bis zu digitalem Geld in Form von Kreditkarten oder Kryptoassets wie Bitcoin. Kryptoassets wiederum, die ursprünglich als alternatives Währungssystem gedacht waren, entwickelten sich in eine andere Richtung. Derzeit existieren rund 6 000 bis 10 000 verschiedene Assets dieses «neuen Gelds». Dieser Wandel von einem physischen Geldstück zu elektronischen Zahlungsmitteln ist eine geldgeschichtliche Innovation innerhalb unserer modernen Gesellschaft. Die Vielfältigkeit der Münze Mehr als andere Geldformen werden Münzen auch in nicht monetärer Form verwendet. Beispielsweise wird nach griechischer Tradition im Neujahrskuchen (Vasilopita) eine Münze versteckt und soll dem Finder im neuen Jahr Glück bringen. Im Zürcher Osterbrauchtum «Zwänzgerle» muss ein Erwachsener ein 20-Rappen-Stück so auf das von einem Kind gehaltene Ei werfen, dass die Münze darin stecken bleibt. Ebenso übernehmen Münzen die Rolle als Sammlungsobjekt in einer privaten Kollektion, fungieren als Glücksbringer im Trevi-Brunnen in Rom, dienen als Schmuckstück für den persönlichen Gebrauch oder werden als modisches Accessoire inszeniert. Das Juwelierunternehmen «Tiffany & Co.» lancierte im April 2022 mit dem «TiffCoin» (eine 18-karätige Goldmünze) eine limitierte Neuauflage des berühmten «Tiffany-Geldes» aus den 1970er-Jahren – Gold- und Silbermünzen, die gegen Tiffany-Schmuck eingetauscht werden konnten und sich grosser Beliebtheit als Hochzeitsgeschenk erfreuten. Irgendwann kommt die antike Nutzung der Münze dann an einen Endpunkt (E). Die Münze kann verloren gehen, wird als Opfergabe in einem Votivdepot niedergelegt oder in Krisenzeiten mit weiteren Münzen als Münzschatz gehortet. Die bewegten Biografien antiker Münzen Die Numismatik ist eine eigenständige Disziplin, die durch das Studium von Münzen, die Vergangenheit dieser metallischen Artefakte erschliesst und untersucht. Die Analyse von kleinen Metallstücken mit sogenannten «Typen» auf Vorder- und Rückseite, Symbolen, Zeichen und Inschriften ermöglicht den Numismatikern, die Mechanismen des Wirtschaftswesens sowie religiöse und politische Interaktionen zu entschlüsseln. Die Disziplin der Numismatik hat eine lange Geschichte, die mit dem Interesse am Sammeln von Münzen begann und ab Ende des 18. Jahrhunderts ein erstes «goldenes Zeitalter» erlebte. Aus Schweizer Sicht ist Friedrich Imhoof-Blumer hervorzuheben, der als Gründerfigur des Münzkabinetts Winterthur gilt. 49 Bulletin SAGW 3 | 2022 DOSSIER Résumé En ces temps marqués par l’inflation, le thème de l’argent est d’une grande pertinence. Dans le pa­ norama monétaire des différentes formes d’argent, les pièces ont beaucoup à nous raconter. Suivre de près la vie d’une pièce de monnaie antique, de sa fa­ brication à ses multiples usages, jusqu’à sa postérité dans le catalogue numérique de la collection, nous permet de mieux comprendre l’évolution des modes économiques et des interactions politiques au fil des siècles. Cet article se concentre sur les différentes utilisations des pièces de monnaie, en mettant égale­ ment en lumière leurs aspects non monétaires. Das Nachleben der antiken Münze Wird die Münze in moderner Zeit wiederentdeckt, sei es in einer archäologischen Ausgrabung oder durch einen Zufallsfund, kommen neue biografische Stationen und Benutzungsrealitäten hinzu (F1–F3). Die Münzen werden international gehandelt, landen in privaten Sammlungen oder in staatlichen Einrichtungen wie Museen oder Münzkabinetten. Ein interessanter Aspekt dabei: In Auktionen wird (antikes) Geld mit (modernem) Geld bezahlt, bei besonders seltenen Stücken mit extrem viel modernem Geld sogar.1 In Münzkabinetten oder Museen transformiert sich die antike Münze zum Ausstellungs- und Forschungsobjekt. Bei all diesen neuzeitlichen Anwendungsszenarien entsteht ein transepochaler Dialog zwischen den Besitzern der Münze in der Antike und den verschiedenen Nachnutzern in der Moderne. Obwohl die detaillierte Reise eines Münzstücks in der Regel nicht rekonstruiert werden kann, lässt sich über den Erhaltungszustand ein Echo der verschiedenen Zeitstufen ablesen. Durch physikalische und chemische Prozesse treten über die Jahrhunderte hinweg bestimmte Abnutzungs- und Korrosionserscheinungen auf. Zudem wird durch die Zirkulation der Münze das Relief im Laufe der Zeit abgerieben und einzelne Konturen können unscharf erscheinen. 1 Die Tetradrachmen Alexanders des Grossen (356–323 v. Chr.), aus Silber hergestellt, gelten als erste Weltwährung in der Geschichte. Vorderseite (oben): Kopf des Herakles mit Löwenfellexuvie, Rückseite: Zeus sitzt auf einem Hocker und trägt auf der rechten Hand einen Adler und mit der linken ein Zepter. 2020 wurde für einen EID MAR Aureus des Brutus der höchste Preis erzielt, der je für eine antike Münze bei einer Auktion bezahlt wurde (fast 4,2 Millionen USD). Die Goldmünze wird mit der Ermordung Caesars an den Iden des März im Jahr 44 v. Chr. assoziiert und ist eines von insgesamt nur drei erhaltenen Exemplaren. 50 DOSSIER Literatur Digitale Erweiterung • Hofmann, Kerstin P. et al. (2019): Ding-Editionen. Vom Die geschilderte numismatische Objektbiografie lässt sich durch die digitale Sphäre erweitern. Die Numismatik stellt einen Idealfall für die Verwendung von digitalen Mehtoden dar, wordurch digitalisierte Münzsammlungen pionierhaften Charakter aufweisen. Das digitale Nachleben von Münzen kann beispielsweise im interaktiven Online-Katalog des Münzkabinetts Berlin besichtigt werden. Dort sind die Münzen fotografisch mit Vorder- und Rückseite erfasst und mit allen relevanten Normdaten wie Gewicht, Durchmesser, Material sowie Beschreibung dokumentiert. Im Sinne der Prinzipien von Linked-Open-Data werden bestimmte Informationen miteinander verknüpft und zueinander in Beziehung gesetzt,2 die Münzen werden so zu «Digital Objects», zu «programmierten Dingen mit neuen Handhabungsmöglichkeiten».3 archäologischen (Be-)Fund übers Corpus ins Netz (e-Forschungsberichte des Deutschen Archäologischen Instituts Fasz. 2), S. 1–12. https://doi.org/10.34780/s7a5-71aj • Jung, Matthias (2015): Das Konzept der Objektbiogra- phie im Lichte einer Hermeneutik materieller Kultur, in: Boschung, Dietrich, Kreuz, Patric-Alexander und Kienlin, Tobias (Hg.), Biography of Objects: Aspekte eines kulturhistorischen Konzepts, Paderborn, S. 35–65. • Krmnicek, Stefan (2009): Das Konzept der Objektbio­ graphie in der antiken Numismatik, in: Von Kaenel, Hans-Markus und Kemmers, Fleur (Hg.), Coins in Context I. New perspectives for the interpretation of coin finds, Mainz, S. 47–59. • Schär, Fabian und Aleksander Berentsen (2020): Bitcoin, Die Münze erhält zudem eine einmalige Objekt-ID, wodurch stets genau dieses Stück identifiziert wird und die Münzdokumentation als Kulturgüterschutz bezeichnet werden kann. Der interaktive Münzkatalog von Berlin gehört zum gemeinsamen Portal «ikmk.net» (Interaktiver Katalog der Münzkabinette), welches seit Mai 2021 existiert und bei dem Berlin mit seinem Dokumentationsstandard federführend ist. Insgesamt sind 29 Münzsammlungen beteiligt und weitere wie das Münzkabinett Winterthur sowie die KIPKE Collection des Benaki Museums in Athen folgen mit ihren numismatischen Sammlungen. Besonders im Verlauf der Corona-Pandemie wurde deutlich, wie relevant digitalisierte Bestände sind. Wie Matthias Jung bemerkt, können die verschiedenen Bedeutungsebenen eines numismatischen Objektes «nicht nur in einer diachronen Abfolge sich ablösend, sondern synchron und damit sich überlagernd sein».4 Dies gilt auch für die Münze, da sie beispielsweise aktuell als Ausstellungsobjekt im Rahmen einer Sonderausstellung fungieren kann, aber gleichzeitig online als Digitalisat zu Forschungszwecken für das wissenschaftliche Netzwerk zugänglich ist. Die Funktion changiert zwischen moderner und digitaler Welt. Als Digital Object muss die Münze in ihrer nachhaltigen und fairen Datenlandschaft digital gepflegt werden, um sie für die Zukunft als Kulturgut zu bewahren. Blockchain, and Cryptoassets: a Comprehensive Introduction, Cambridge. • Wigg-Wolf, David und Frédérique Duyrat (2017): The Links Projekt Nomisma.org: http://nomisma.org Interaktive Kataloge der Münzkabinette: https://ikmk.net Inventar der Fundmünzen der Schweiz: www.fundmuenzen.ch DOI https://doi.org/10.5281/zenodo.7328543 Zur Autorin Olivia Denk ist Archäologin und Numismatikerin und schliesst derzeit ihre Promotion an der Universität Basel ab. Sie arbeitet als wissenschaftliche Mitarbeiterin und Spezialistin für Open Science bei den Akademien der Wissenschaften Schweiz. • Numismatisches Kunstprojekt im digitalen Raum von Olivia Denk 2 3 4 Wigg-Wolf und Duyrant 2017. Hofmann 2019, 4. Jung 2015, 52. 51 Bulletin SAGW 3 | 2022 Linked Open Data Revolution in Numismatics. The examples of nomisma.org and Online Greek Coinage (Digital Archaeology 1). https://doi.org/10.21494/ISTE.OP.2017.0171